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KURUL F, İSTANBULLU H, KAYA HO, ÇETİN AE, TOPKAYA SN. Electrochemical Properties of Fused Pyrimidine-Triazole Heterocyclic Molecules as Novel Drug Candidates. Turk J Pharm Sci 2024; 21:113-124. [PMID: 38742813 PMCID: PMC11096787 DOI: 10.4274/tjps.galenos.2023.46095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/13/2023] [Indexed: 05/16/2024]
Abstract
Objectives Triazolopyrimidinones are compounds used in medicinal chemistry. In this study, three novel triazolopyrimidinone derivatives were synthesized as drug candidates: (5-(chloromethyl)-2-(4-methoxyphenyl)-[1,2,4]triazolo[1,5-a]pyrimidin-7(3H)-one) (S1-TP), 2-(4-methoxyphenyl)-5-(piperidinomethyl)-[1,2,4]triazolo[1,5-a]pyrimidin-7(3H)-one) (S2-TP), and 2-(4-methoxyphenyl)-5-(morpholinomethyl)-[1,2,4]triazolo[1,5-a] pyrimidin-7(3H)-one) (S3-TP). Their electrochemical properties were investigated for the first time using voltammetric techniques on carbon graphite electrodes. Moreover, stability tests for each drug candidate were performed on different days. After revealing the electrochemical properties of the drug candidates, their effect on double-stranded (ds) DNA was examined by measuring the oxidation currents of the guanine of dsDNA before and after the interaction. Materials and Methods An electrochemical setup that included a pencil graphite electrode as the working electrode, an Ag/AgCl reference electrode, and a platinum wire as the auxiliary electrode was used in this study. Experiments for optimum pH, scan rate, and concentration of drug candidates were conducted. The interaction between Ss-TP and dsDNA was evaluated using differential pulse voltammetry. The stability of each drug candidate was tested on various days. Results A comprehensive characterization of the S1-TP, S2-TP, and S3-TP compounds was performed for the first time. This study showed that the electrochemical oxidation of S1-TP and S2-TP was irreversible and diffusion-controlled. In addition, the transfer of electrons in S3-TP was controlled by adsorption. The interaction between Ss-TP and dsDNA resulted in notable changes in the peak potentialof dsDNA. The dsDNA peak potential shifted negatively after interaction with S1-TP, S2-TP, and S3-TP. Under optimum conditions, the detection limits for S1-TP, S2-TP, and S3-TP were 1.5 µg/mL, 1.0 µg/mL, and 2.0 µg/mL, respectively. Conclusion From our experimental data, we concluded that these molecules can be used as drug molecules because of their remarkable effects on DNA.
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Affiliation(s)
- Fatma KURUL
- Dokuz Eylül University, İzmir International Biomedicine and Genome Institute, İzmir, Türkiye
| | - Hüseyin İSTANBULLU
- İzmir Katip Çelebi University Faculty of Pharmacy, Department of Pharmaceutical Chemistry, İzmir, Türkiye
| | - Hüseyin Oğuzhan KAYA
- İzmir Katip Çelebi University Faculty of Pharmacy, Department of Analytical Chemistry İzmir, Türkiye
| | | | - Seda Nur TOPKAYA
- İzmir Katip Çelebi University Faculty of Pharmacy, Department of Analytical Chemistry İzmir, Türkiye
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2
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Kashani GK, Naghib SM, Soleymani S, Mozafari MR. A review of DNA nanoparticles-encapsulated drug/gene/protein for advanced controlled drug release: Current status and future perspective over emerging therapy approaches. Int J Biol Macromol 2024; 268:131694. [PMID: 38642693 DOI: 10.1016/j.ijbiomac.2024.131694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
In the last ten years, the field of nanomedicine has experienced significant progress in creating novel drug delivery systems (DDSs). An effective strategy involves employing DNA nanoparticles (NPs) as carriers to encapsulate drugs, genes, or proteins, facilitating regulated drug release. This abstract examines the utilization of DNA NPs and their potential applications in strategies for controlled drug release. Researchers have utilized the distinctive characteristics of DNA molecules, including their ability to self-assemble and their compatibility with living organisms, to create NPs specifically for the purpose of delivering drugs. The DNA NPs possess numerous benefits compared to conventional drug carriers, such as exceptional stability, adjustable dimensions and structure, and convenient customization. Researchers have successfully achieved a highly efficient encapsulation of different therapeutic agents by carefully designing their structure and composition. This advancement enables precise and targeted delivery of drugs. The incorporation of drugs, genes, or proteins into DNA NPs provides notable advantages in terms of augmenting therapeutic effectiveness while reducing adverse effects. DNA NPs serve as a protective barrier for the enclosed payloads, preventing their degradation and extending their duration in the body. The protective effect is especially vital for delicate biologics, such as proteins or gene-based therapies that could otherwise be vulnerable to enzymatic degradation or quick elimination. Moreover, the surface of DNA NPs can be altered to facilitate specific targeting towards particular tissues or cells, thereby augmenting the accuracy of delivery. A significant benefit of DNA NPs is their capacity to regulate the kinetics of drug release. Through the manipulation of the DNA NPs structure, scientists can regulate the rate at which the enclosed cargo is released, enabling a prolonged and regulated dispensation of medication. This control is crucial for medications with limited therapeutic ranges or those necessitating uninterrupted administration to attain optimal therapeutic results. In addition, DNA NPs have the ability to react to external factors, including alterations in temperature, pH, or light, which can initiate the release of the payload at precise locations or moments. This feature enhances the precision of drug release control. The potential uses of DNA NPs in the controlled release of medicines are extensive. The NPs have the ability to transport various therapeutic substances, for example, drugs, peptides, NAs (NAs), and proteins. They exhibit potential for the therapeutic management of diverse ailments, including cancer, genetic disorders, and infectious diseases. In addition, DNA NPs can be employed for targeted drug delivery, traversing biological barriers, and surpassing the constraints of conventional drug administration methods.
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Affiliation(s)
- Ghazal Kadkhodaie Kashani
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran
| | - Seyed Morteza Naghib
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran.
| | - Sina Soleymani
- Nanotechnology Department, School of Advanced Technologies, Iran University of Science and Technology (IUST), Tehran 1684613114, Iran; Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia; Biomaterials and Tissue Engineering Research Group, Interdisciplinary Technologies Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Iran University of Science and Technology (IUST), Tehran, Iran
| | - M R Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia
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3
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Jiang Q, Shang Y, Xie Y, Ding B. DNA Origami: From Molecular Folding Art to Drug Delivery Technology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2301035. [PMID: 37715333 DOI: 10.1002/adma.202301035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/08/2023] [Indexed: 09/17/2023]
Abstract
DNA molecules that store genetic information in living creatures can be repurposed as building blocks to construct artificial architectures, ranging from the nanoscale to the microscale. The precise fabrication of self-assembled DNA nanomaterials and their various applications have greatly impacted nanoscience and nanotechnology. More specifically, the DNA origami technique has realized the assembly of various nanostructures featuring rationally predesigned geometries, precise addressability, and versatile programmability, as well as remarkable biocompatibility. These features have elevated DNA origami from academic interest to an emerging class of drug delivery platform for a wide range of diseases. In this minireview, the latest advances in the burgeoning field of DNA-origami-based innovative platforms for regulating biological functions and delivering versatile drugs are presented. Challenges regarding the novel drug vehicle's safety, stability, targeting strategy, and future clinical translation are also discussed.
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Affiliation(s)
- Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
| | - Yiming Xie
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
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4
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Garcia-Diosa JA, Grundmeier G, Keller A. Effect of DNA Origami Nanostructures on Bacterial Growth. Chembiochem 2024; 25:e202400091. [PMID: 38299762 DOI: 10.1002/cbic.202400091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/02/2024]
Abstract
DNA origami nanostructures are a powerful tool in biomedicine and can be used to combat drug-resistant bacterial infections. However, the effect of unmodified DNA origami nanostructures on bacteria is yet to be elucidated. With the aim to obtain a better understanding of this phenomenon, the effect of three DNA origami shapes, i.e., DNA origami triangles, six-helix bundles (6HBs), and 24-helix bundles (24HBs), on the growth of Gram-negative Escherichia coli and Gram-positive Bacillus subtilis is investigated. The results reveal that while triangles and 24HBs can be used as a source of nutrients by E. coli and thereby promote population growth, their effect is much smaller than that of genomic single- and double-stranded DNA. However, no effect on E. coli population growth is observed for the 6HBs. On the other hand, B. subtilis does not show any significant changes in population growth when cultured with the different DNA origami shapes or genomic DNA. The detailed effect of DNA origami nanostructures on bacterial growth thus depends on the competence signals and uptake mechanism of each bacterial species, as well as the DNA origami shape. This should be considered in the development of antimicrobial DNA origami nanostructures.
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Affiliation(s)
- Jaime Andres Garcia-Diosa
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098, Paderborn, Germany
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5
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Seo HS, Han JH, Lim J, Bae GH, Byun MJ, Wang CPJ, Han J, Park J, Park HH, Shin M, Park TE, Kim TH, Kim SN, Park W, Park CG. Enhanced Postsurgical Cancer Treatment Using Methacrylated Glycol Chitosan Hydrogel for Sustained DNA/Doxorubicin Delivery and Immunotherapy. Biomater Res 2024; 28:0008. [PMID: 38532906 PMCID: PMC10964224 DOI: 10.34133/bmr.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 03/28/2024] Open
Abstract
Background: Cancer recurrence and metastasis are major contributors to treatment failure following tumor resection surgery. We developed a novel implantable drug delivery system utilizing glycol chitosan to address these issues. Glycol chitosan is a natural adjuvant, inducing dendritic cell activation to promote T helper 1 cell immune responses, macrophage activation, and cytokine production. Effective antigen production by dendritic cells initiates T-cell-mediated immune responses, aiding tumor growth control. Methods: In this study, we fabricated multifunctional methacrylated glycol chitosan (MGC) hydrogels with extended release of DNA/doxorubicin (DOX) complex for cancer immunotherapy. We constructed the resection model of breast cancer to verify the anticancer effects of MGC hydrogel with DNA/DOX complex. Results: This study demonstrated the potential of MGC hydrogel with extended release of DNA/DOX complex for local and efficient cancer therapy. The MGC hydrogel was implanted directly into the surgical site after tumor resection, activating tumor-related immune cells both locally and over a prolonged period of time through immune-reactive molecules. Conclusions: The MGC hydrogel effectively suppressed tumor recurrence and metastasis while enhancing immunotherapeutic efficacy and minimizing side effects. This biomaterial-based drug delivery system, combined with cancer immunotherapy, can substantial improve treatment outcomes and patient prognosis.
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Affiliation(s)
- Hee Seung Seo
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Jun-Hyeok Han
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Jaesung Lim
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Ga-Hyun Bae
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of MetaBioHealth,
SKKU Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Min Ji Byun
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Chi-Pin James Wang
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Jieun Han
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Institute of Biotechnology and Bioengineering, College of Biotechnology and Bioengineering, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Juwon Park
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School Medicine,
University of Hawai'i at Manoa, Honolulu, HI 96813, USA
| | - Hee Ho Park
- Department of Bioengineering,
Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, Republic of Korea
| | - Mikyung Shin
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
| | - Tae-Eun Park
- Department of Biomedical Engineering,
Ulsan National Institute of Science and Technology, 50, UNIST-gil, Ulsan 44919, Republic of Korea
| | - Tae-Hyung Kim
- School of Integrative Engineering,
Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Se-Na Kim
- Research and Development Center,
MediArk Inc., 1, Chungdae-ro, Seowon-gu, Cheongju, Chungcheongbuk 28644, Republic of Korea
| | - Wooram Park
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering,
SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of MetaBioHealth,
SKKU Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Institute of Biotechnology and Bioengineering, College of Biotechnology and Bioengineering, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Biomaterials Research Center,
Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Chun Gwon Park
- Department of Biomedical Engineering,
SKKU Institute for Convergence, Sungkyunkwan University (SKKU), 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence,
Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
- Biomedical Institute for Convergence, SKKU, 2066, Seobu-ro, Jangan-gu, Suwon, Gyeonggi 16419, Republic of Korea
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6
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Postigo A, Martínez-Vicente P, Baumann KN, Del Barrio J, Hernández-Ainsa S. Assessing the influence of small structural modifications in simple DNA-based nanostructures on their role as drug nanocarriers. Biomater Sci 2024; 12:1549-1557. [PMID: 38305143 DOI: 10.1039/d3bm01987j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
DNA nanotechnology leverages Watson-Crick-Franklin base-pairing interactions to build complex DNA-based nanostructures (DNS). Due to DNA specific self-assembly properties, DNS can be designed with a total control of their architecture, which has been demonstrated to have an impact on the overall DNS features. Indeed, structural properties such as the shape, size and flexibility of DNS can influence their biostability as well as their ability to internalise into cells. We present here two series of simple DNS with small and precise variations related to their length or flexibility and study the influence that these structural changes have on their overall properties as drug nanocarriers. Results indicate that shorter and more flexible DNS present higher stability towards nuclease degradation. These structural changes also have a certain effect on their cell internalisation ability and drug release rate. Consequently, drug-loaded DNS cytotoxicity varies according to the design, with lower cell viability values obtained in the DNS exhibiting faster drug release and larger cell interaction rates. In summary, small changes in the structure of simple DNS can have an influence on their overall capabilities as drug nanocarriers. The effects reported here could guide the design of simple DNS for future therapeutic uses.
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Affiliation(s)
- Alejandro Postigo
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
| | - Pablo Martínez-Vicente
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
| | | | - Jesús Del Barrio
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
| | - Silvia Hernández-Ainsa
- Instituto de Nanociencia y Materiales de Aragón, CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain.
- ARAID Foundation, Government of Aragon, Zaragoza 50018, Spain
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7
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Neyra K, Everson HR, Mathur D. Dominant Analytical Techniques in DNA Nanotechnology for Various Applications. Anal Chem 2024; 96:3687-3697. [PMID: 38353660 DOI: 10.1021/acs.analchem.3c04176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
DNA nanotechnology is rapidly gaining traction in numerous applications, each bearing varying degrees of tolerance to the quality and quantity necessary for viable nanostructure function. Despite the distinct objectives of each application, they are united in their reliance on essential analytical techniques, such as purification and characterization. This tutorial aims to guide the reader through the current state of DNA nanotechnology analytical chemistry, outlining important factors to consider when designing, assembling, purifying, and characterizing a DNA nanostructure for downstream applications.
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Affiliation(s)
- Kayla Neyra
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Heather R Everson
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland Ohio 44106, United States
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8
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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Navarro N, Aviñó A, Domènech Ò, Borrell JH, Eritja R, Fàbrega C. Defined covalent attachment of three cancer drugs to DNA origami increases cytotoxicity at nanomolar concentration. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 55:102722. [PMID: 38007069 DOI: 10.1016/j.nano.2023.102722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/27/2023]
Abstract
DNA nanostructures have captured great interest as drug delivery vehicles for cancer therapy. Despite rapid progress in the field, some hurdles, such as low cellular uptake, low tissue specificity or ambiguous drug loading, remain unsolved. Herein, well-known antitumor drugs (doxorubicin, auristatin, and floxuridine) were site-specifically incorporated into DNA nanostructures, demonstrating the potential advantages of covalently linking drug molecules via structural staples instead of incorporating the drugs by noncovalent binding interactions. The covalent strategy avoids critical issues such as an unknown number of drug-DNA binding events and premature drug release. Moreover, covalently modified origami offers the possibility of precisely incorporating several synergetic antitumor drugs into the DNA nanostructure at a predefined molar ratio and to control the exact spatial orientation of drugs into DNA origami. Additionally, DNA-based nanoscaffolds have been reported to have a low intracellular uptake. Thus, two cellular uptake enhancing mechanisms were studied: the introduction of folate units covalently linked to DNA origami and the transfection of DNA origami with Lipofectamine. Importantly, both methods increased the internalization of DNA origami into HTB38 and HCC2998 colorectal cancer cells and produced greater cytotoxic activity when the DNA origami incorporated antiproliferative drugs. The results here present a successful and conceptually distinct approach for the development of DNA-based nanostructures as drug delivery vehicles, which can be considered an important step towards the development of highly precise nanomedicines.
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Affiliation(s)
- Natalia Navarro
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain
| | - Anna Aviñó
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain
| | - Òscar Domènech
- Physical Chemistry Section, Faculty of Pharmacy and Food Sciences, University of Barcelona (UB), Barcelona 08028, Spain; Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB), Barcelona 08028, Spain
| | - Jordi H Borrell
- Physical Chemistry Section, Faculty of Pharmacy and Food Sciences, University of Barcelona (UB), Barcelona 08028, Spain; Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona (UB), Barcelona 08028, Spain
| | - Ramon Eritja
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain.
| | - Carme Fàbrega
- Nucleic Acids Chemistry Group, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona 08034, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona 08034, Spain.
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De Luca E, Wang Y, Baars I, De Castro F, Lolaico M, Migoni D, Ducani C, Benedetti M, Högberg B, Fanizzi FP. Wireframe DNA Origami for the Cellular Delivery of Platinum(II)-Based Drugs. Int J Mol Sci 2023; 24:16715. [PMID: 38069036 PMCID: PMC10706596 DOI: 10.3390/ijms242316715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
The DNA origami method has revolutionized the field of DNA nanotechnology since its introduction. These nanostructures, with their customizable shape and size, addressability, nontoxicity, and capacity to carry bioactive molecules, are promising vehicles for therapeutic delivery. Different approaches have been developed for manipulating and folding DNA origami, resulting in compact lattice-based and wireframe designs. Platinum-based complexes, such as cisplatin and phenanthriplatin, have gained attention for their potential in cancer and antiviral treatments. Phenanthriplatin, in particular, has shown significant antitumor properties by binding to DNA at a single site and inhibiting transcription. The present work aims to study wireframe DNA origami nanostructures as possible carriers for platinum compounds in cancer therapy, employing both cisplatin and phenanthriplatin as model compounds. This research explores the assembly, platinum loading capacity, stability, and modulation of cytotoxicity in cancer cell lines. The findings indicate that nanomolar quantities of the ball-like origami nanostructure, obtained in the presence of phenanthriplatin and therefore loaded with that specific drug, reduced cell viability in MCF-7 (cisplatin-resistant breast adenocarcinoma cell line) to 33%, while being ineffective on the other tested cancer cell lines. The overall results provide valuable insights into using wireframe DNA origami as a highly stable possible carrier of Pt species for very long time-release purposes.
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Affiliation(s)
- Erik De Luca
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Centro Ecotekne, I-73100 Lecce, Italy; (E.D.L.); (F.D.C.); (D.M.); (M.B.)
| | - Yang Wang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden; (Y.W.); (I.B.); (M.L.); (C.D.); (B.H.)
| | - Igor Baars
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden; (Y.W.); (I.B.); (M.L.); (C.D.); (B.H.)
| | - Federica De Castro
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Centro Ecotekne, I-73100 Lecce, Italy; (E.D.L.); (F.D.C.); (D.M.); (M.B.)
| | - Marco Lolaico
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden; (Y.W.); (I.B.); (M.L.); (C.D.); (B.H.)
| | - Danilo Migoni
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Centro Ecotekne, I-73100 Lecce, Italy; (E.D.L.); (F.D.C.); (D.M.); (M.B.)
| | - Cosimo Ducani
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden; (Y.W.); (I.B.); (M.L.); (C.D.); (B.H.)
| | - Michele Benedetti
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Centro Ecotekne, I-73100 Lecce, Italy; (E.D.L.); (F.D.C.); (D.M.); (M.B.)
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden; (Y.W.); (I.B.); (M.L.); (C.D.); (B.H.)
| | - Francesco Paolo Fanizzi
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, Centro Ecotekne, I-73100 Lecce, Italy; (E.D.L.); (F.D.C.); (D.M.); (M.B.)
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11
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Hanke M, Dornbusch D, Tomm E, Grundmeier G, Fahmy K, Keller A. Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants. NANOSCALE 2023; 15:16590-16600. [PMID: 37747200 DOI: 10.1039/d3nr02045b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The structural stability of DNA origami nanostructures in various chemical environments is an important factor in numerous applications, ranging from biomedicine and biophysics to analytical chemistry and materials synthesis. In this work, the stability of six different 2D and 3D DNA origami nanostructures is assessed in the presence of three different chaotropic salts, i.e., guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl), which are widely employed denaturants. Using atomic force microscopy (AFM) to quantify nanostructural integrity, Gdm2SO4 is found to be the weakest and TPACl the strongest DNA origami denaturant, respectively. Despite different mechanisms of actions of the selected salts, DNA origami stability in each environment is observed to depend on DNA origami superstructure. This is especially pronounced for 3D DNA origami nanostructures, where mechanically more flexible designs show higher stability in both GdmCl and TPACl than more rigid ones. This is particularly remarkable as this general dependence has previously been observed under Mg2+-free conditions and may provide the possibility to optimize DNA origami design toward maximum stability in diverse chemical environments. Finally, it is demonstrated that melting temperature measurements may overestimate the stability of certain DNA origami nanostructures in certain chemical environments, so that such investigations should always be complemented by microscopic assessments of nanostructure integrity.
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Affiliation(s)
- Marcel Hanke
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Daniel Dornbusch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Emilia Tomm
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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12
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Zhang X, Zhang P, Xiao C, Chen X. ROS-Responsive Self-Degradable DNA Nanogels for Targeted Anticancer Drug Delivery. ACS Macro Lett 2023; 12:1317-1323. [PMID: 37713132 DOI: 10.1021/acsmacrolett.3c00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Here, a reactive oxygen species (ROS)-responsive targeted anticancer drug delivery system was developed by embedding a nitrophenyl tetramethyl-dioxaborolanyl benzyl carbamate (NBC)-modified deoxyribonuclease I (DNase I) in a DNase-degradable aptamer-based DNA nanogel. The DNA nanogel was formed by hybridization of three types of building blocks, namely, Y-shaped monomer 1 with three sticky ends, Y-shaped monomer 2 with two sticky ends and an aptamer end, and a DNA linker with two sticky ends. Single doxorubicin (DOX) or ribonuclease A (RNase A) as well as the combination of DOX and RNase A were effectively loaded into the nanogels, wherein DOX was embedded into DNA skeleton, while RNase A was encapsulated into nanogel matrix. The blocked enzymatic activity of DNase I due to NBC modification could be restored upon intracellular ROS-triggered NBC deprotection, resulting in self-degradation of the nanogels to release both DOX and RNase A. Consequently, the DOX and RNase A coloaded nanogels significantly inhibited the proliferation of MCF-7 cells through a synergistic effect. To sum up, this DNA-based drug delivery system with ROS-responsive self-degradation properties should be promising for application in targeted and synergistic cancer therapy.
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Affiliation(s)
- Xiaonong Zhang
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Peng Zhang
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, P. R. China
| | - Chunsheng Xiao
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Xuesi Chen
- Key Laboratory of Polymer Ecomaterials, Jilin Biomedical Polymers Engineering Laboratory, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
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13
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Wang J, Zhang T, Li X, Wu W, Xu H, Xu XM, Zhang T. DNA Nanobarrel-Based Drug Delivery for Paclitaxel and Doxorubicin. Chembiochem 2023; 24:e202300424. [PMID: 37470220 DOI: 10.1002/cbic.202300424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/16/2023] [Accepted: 07/18/2023] [Indexed: 07/21/2023]
Abstract
Co-delivery of anticancer drugs and target agents by endogenous materials is an inevitable approach towards targeted and synergistic therapy. Employing DNA base pair complementarities, DNA nanotechnology exploits a unique nanostructuring method and has demonstrated its capacity for nanoscale positioning and templated assembly. Moreover, the water solubility, biocompatibility, and modifiability render DNA structure suitable candidate for drug delivery applications. We here report single-stranded DNA tail conjugated antitumor drug paclitaxel (PTX), and the co-delivery of PTX, doxorubicin and targeting agent mucin 1 (MUC-1) aptamer on a DNA nanobarrel carrier. We investigated the effect of tail lengths on drug release efficiencies and dual drug codelivery-enabled cytotoxicity. Owing to the rapidly developing field of structural DNA nanotechnology, functional DNA-based drug delivery is promising to achieve clinical therapeutic applications.
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Affiliation(s)
- Jiaoyang Wang
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, School of Pharmacy, Yantai University, Yantai, 264005, China
| | - Tianyu Zhang
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, School of Pharmacy, Yantai University, Yantai, 264005, China
| | - Xueqiao Li
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Wenna Wu
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Hui Xu
- Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Key Laboratory of Molecular Pharmacology and Drug Evaluation, Ministry of Education, School of Pharmacy, Yantai University, Yantai, 264005, China
| | - Xin-Ming Xu
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Tao Zhang
- Department of Applied Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
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14
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Zhang S, Lou XY, Liu L, Yang YW. The Creation of DNA Origami-Based Supramolecular Nanostructures for Cancer Therapy. Adv Healthc Mater 2023; 12:e2301066. [PMID: 37252899 DOI: 10.1002/adhm.202301066] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/23/2023] [Indexed: 06/01/2023]
Abstract
DNA origami technology, a unique type of DNA nanotechnology, has attracted much attention from researchers and is applied in various fields. Through exquisite design and precise self-assembly of four kinds of deoxyribonucleotides, DNA origami nanostructures are endowed with excellent programmability and addressability and show outstanding biocompatibility in bio-related applications, especially in cancer treatment. In this review, nanomaterials based on DNA origami for cancer therapy are concluded, whereby chemotherapy and photo-assisted therapy are the main focus. Furthermore, the working mechanisms of the functional materials attached to the rigid DNA structures to enable targeted delivery and circumvent drug resistance are also discussed. DNA origami nanostructures are valuable carriers for delivering multifunctional therapeutic agents and demonstrate great potential in cancer treatment both in vitro and in vivo. It is undoubted that DNA origami technology is a promising strategy for constructing versatile nanodevices in biological fields and will excel in human healthcare.
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Affiliation(s)
- Siyuan Zhang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Xin-Yue Lou
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
| | - Linlin Liu
- China-Japan Union Hospital of Jilin University, Jilin University, Changchun, 130012, P. R. China
| | - Ying-Wei Yang
- College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun, 130012, P. R. China
- China-Japan Union Hospital of Jilin University, Jilin University, Changchun, 130012, P. R. China
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15
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Rodriguez A, Gandavadi D, Mathivanan J, Song T, Madhanagopal BR, Talbot H, Sheng J, Wang X, Chandrasekaran AR. Self-Assembly of DNA Nanostructures in Different Cations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300040. [PMID: 37264756 PMCID: PMC10538431 DOI: 10.1002/smll.202300040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/10/2023] [Indexed: 06/03/2023]
Abstract
The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions that restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions are used so far (typically Mg2+ and Na+ ). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (~134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca2+ , Ba2+ , Na+ , K+ and Li+ and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na+ , K+ and Li+ ) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg2+ , Ca2+ and Ba2+ ). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.
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Affiliation(s)
- Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Dhanush Gandavadi
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Holonyak Micro and Nanotechnology Lab (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Johnsi Mathivanan
- Department of Chemistry, University of Albany, State University of New York, Albany, NY 12222, USA
| | - Tingjie Song
- Holonyak Micro and Nanotechnology Lab (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University of Albany, State University of New York, Albany, NY 12222, USA
| | - Xing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Holonyak Micro and Nanotechnology Lab (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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16
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Talbot H, Madhanagopal BR, Hayden A, Halvorsen K, Chandrasekaran AR. Fluorometric Determination of DNA Nanostructure Biostability. ACS APPLIED BIO MATERIALS 2023; 6:3074-3078. [PMID: 37262927 PMCID: PMC10999248 DOI: 10.1021/acsabm.3c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The analysis and improvement of DNA nanostructure biostability is one of the keys areas of progress needed in DNA nanotechnology applications. Here, we present a plate-compatible fluorometric assay for measuring DNA nanostructure biostability using the common intercalator ethidium bromide. We demonstrate the assay by testing the biostability of duplex DNA, a double crossover DNA motif, and a DNA origami nanostructure against different nucleases and in fetal bovine serum. This method scales well to measure a large number of samples using a plate reader and can complement existing methods for assessing and developing robust DNA nanostructures.
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Affiliation(s)
- Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Bharath Raj Madhanagopal
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Andrew Hayden
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12203, United States
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17
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Zhang Y, Tian X, Wang Z, Wang H, Liu F, Long Q, Jiang S. Advanced applications of DNA nanostructures dominated by DNA origami in antitumor drug delivery. Front Mol Biosci 2023; 10:1239952. [PMID: 37609372 PMCID: PMC10440542 DOI: 10.3389/fmolb.2023.1239952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/27/2023] [Indexed: 08/24/2023] Open
Abstract
DNA origami is a cutting-edge DNA self-assembly technique that neatly folds DNA strands and creates specific structures based on the complementary base pairing principle. These innovative DNA origami nanostructures provide numerous benefits, including lower biotoxicity, increased stability, and superior adaptability, making them an excellent choice for transporting anti-tumor agents. Furthermore, they can considerably reduce side effects and improve therapy success by offering precise, targeted, and multifunctional drug delivery system. This comprehensive review looks into the principles and design strategies of DNA origami, providing valuable insights into this technology's latest research achievements and development trends in the field of anti-tumor drug delivery. Additionally, we review the key function and major benefits of DNA origami in cancer treatment, some of these approaches also involve aspects related to DNA tetrahedra, aiming to provide novel ideas and effective solutions to address drug delivery challenges in cancer therapy.
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Affiliation(s)
- Yiming Zhang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Zijian Wang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Haochen Wang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Qipeng Long
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People’s Hospital, Shandong First Medical University, Jining, Shandong, China
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18
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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19
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Linko V, Keller A. Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301935. [PMID: 37093216 DOI: 10.1002/smll.202301935] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Programmable, custom-shaped, and nanometer-precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnology and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiological conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct molecular-level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Additionally, specific issues demanding further investigation are identified. This review - through its specific viewpoint - may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiological media.
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Affiliation(s)
- Veikko Linko
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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20
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Hong S, Jiang W, Ding Q, Lin K, Zhao C, Wang X. The Current Progress of Tetrahedral DNA Nanostructure for Antibacterial Application and Bone Tissue Regeneration. Int J Nanomedicine 2023; 18:3761-3780. [PMID: 37457798 PMCID: PMC10348378 DOI: 10.2147/ijn.s403882] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Recently, programmable assembly technologies have enabled the application of DNA in the creation of new nanomaterials with unprecedented functionality. One of the most common DNA nanostructures is the tetrahedral DNA nanostructure (TDN), which has attracted great interest worldwide due to its high stability, simple assembly procedure, high predictability, perfect programmability, and excellent biocompatibility. The unique spatial structure of TDN allows it to penetrate cell membranes in abundance and regulate cellular biological properties as a natural genetic material. Previous studies have demonstrated that TDNs can regulate various cellular biological properties, including promoting cells proliferation, migration and differentiation, inhibiting cells apoptosis, as well as possessing anti-inflammation and immunomodulatory capabilities. Furthermore, functional molecules can be easily modified at the vertices of DNA tetrahedron, DNA double helix structure, DNA tetrahedral arms or DNA tetrahedral cage structure, enabling TDN to be used as a nanocarrier for a variety of biological applications, including targeted therapies, molecular diagnosis, biosensing, antibacterial treatment, antitumor strategies, and tissue regeneration. In this review, we mainly focus on the current progress of TDN-based nanomaterials for antimicrobial applications, bone and cartilage tissue repair and regeneration. The synthesis and characterization of TDN, as well as the biological merits are introduced. In addition, the challenges and prospects of TDN-based nanomaterials are also discussed.
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Affiliation(s)
- Shebin Hong
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, People’s Republic of China
| | - Weidong Jiang
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, People’s Republic of China
| | - Qinfeng Ding
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, People’s Republic of China
| | - Kaili Lin
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, People’s Republic of China
| | - Cancan Zhao
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, People’s Republic of China
| | - Xudong Wang
- Department of Oral & Cranio-Maxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai, People’s Republic of China
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21
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Wang D, Zhang X, Zhu X. Drug-Grafted DNA for Cancer Therapy. J Phys Chem B 2023. [PMID: 37294640 DOI: 10.1021/acs.jpcb.3c01321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
With the development of solid-phase synthesis and DNA nanotechnology, DNA-based drug delivery systems have seen large advancements over the past decades. By combining various drugs (small-molecular drugs, oligonucleotides, peptides, and proteins) with DNA technology, drug-grafted DNA has demonstrated great potential as a promising platform in recent years, in which complementary properties of both components have been discovered; for instance, the synthesis of amphiphilic drug-grafted DNA has enabled the production of DNA nanomedicines for gene therapy and chemotherapy. Through the design of linkages between drug and DNA parts, stimuli-responsiveness can be instilled, which has boosted the application of drug-grafted DNA in various biomedical applications such as cancer therapy. This review discusses the progress of various drug-grafted DNA therapeutic agents, exploring the synthetic techniques and anticancer applications afforded through the combination of drug and nucleic acids.
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Affiliation(s)
- Dali Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240 Shanghai, P. R. China
| | - Xinyue Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240 Shanghai, P. R. China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240 Shanghai, P. R. China
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22
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Wassermann LM, Scheckenbach M, Baptist AV, Glembockyte V, Heuer-Jungemann A. Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2212024. [PMID: 36932052 DOI: 10.1002/adma.202212024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.
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Affiliation(s)
- Lea M Wassermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Anna V Baptist
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
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23
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Baptist AV, Heuer-Jungemann A. Lyophilization Reduces Aggregation of Three-Dimensional DNA Origami at High Concentrations. ACS OMEGA 2023; 8:18225-18233. [PMID: 37251192 PMCID: PMC10210204 DOI: 10.1021/acsomega.3c01680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/28/2023] [Indexed: 05/31/2023]
Abstract
Although for many purposes, low concentrations of DNA origami are sufficient, certain applications such as cryo electron microscopy, measurements involving small-angle X-ray scattering, or in vivo applications require high DNA origami concentrations of >200 nM. This is achievable by ultrafiltration or polyethylene glycol precipitation but often at the expense of increasing structural aggregation due to prolonged centrifugation and final redispersion in low buffer volumes. Here, we show that lyophilization and subsequent redispersion in low buffer volumes can achieve high concentrations of DNA origami while drastically reducing aggregation due to initially very low DNA origami concentrations in low salt buffers. We demonstrate this for four structurally different types of three-dimensional DNA origami. All of these structures exhibit different aggregation behaviors at high concentrations (tip-to-tip stacking, side-to-side binding, or structural interlocking), which can be drastically reduced by dispersion in larger volumes of a low salt buffer and subsequent lyophilization. Finally, we show that this procedure can also be applied to silicified DNA origami to achieve high concentrations with low aggregation. We thus find that lyophilization is not only a tool for long-term storage of biomolecules but also an excellent way for up-concentrating while maintaining well-dispersed solutions of DNA origami.
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Affiliation(s)
- Anna V. Baptist
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Bavaria, Germany
- Center
for NanoScience, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Amelie Heuer-Jungemann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Bavaria, Germany
- Center
for NanoScience, Ludwig-Maximilians University, 80539 Munich, Germany
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24
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Freitag JS, Möser C, Belay R, Altattan B, Grasse N, Pothineni BK, Schnauß J, Smith DM. Integration of functional peptides into nucleic acid-based nanostructures. NANOSCALE 2023; 15:7608-7624. [PMID: 37042085 DOI: 10.1039/d2nr05429a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In many applications such as diagnostics and therapy development, small peptide fragments consisting of only a few amino acids are often attractive alternatives to bulky proteins. This is due to factors such as the ease of scalable chemical synthesis and numerous methods for their discovery. One drawback of using peptides is that their activity can often be negatively impacted by the lack of a rigid, 3D stabilizing structure provided by the rest of the protein. In many cases, this can be alleviated by different methods of rational templating onto nanomaterials, which provides additional possibilities to use concepts of multivalence or rational nano-engineering to enhance or even create new types of function or structure. In recent years, nanostructures made from the self-assembly of DNA strands have been used as scaffolds to create functional arrangements of peptides, often leading to greatly enhanced biological activity or new material properties. This review will give an overview of nano-templating approaches based on the combination of DNA nanotechnology and peptides. This will include both bioengineering strategies to control interactions with cells or other biological systems, as well as examples where the combination of DNA and peptides has been leveraged for the rational design of new functional materials.
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Affiliation(s)
- Jessica S Freitag
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Christin Möser
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Robel Belay
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Basma Altattan
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Nico Grasse
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | | | - Jörg Schnauß
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Unconventional Computing Lab, UWE, Bristol, BS16 1QY, UK
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
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25
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Rodriguez A, Gandavadi D, Mathivanan J, Song T, Madhanagopal BR, Talbot H, Sheng J, Wang X, Chandrasekaran AR. Self-assembly of DNA nanostructures in different cations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539416. [PMID: 37205441 PMCID: PMC10187274 DOI: 10.1101/2023.05.04.539416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures, and assembly conditions typically require high concentrations of magnesium ions which restricts their applications. In other solution conditions tested for DNA nanostructure assembly, only a limited set of divalent and monovalent ions have been used so far (typically Mg 2+ and Na + ). Here, we investigate the assembly of DNA nanostructures in a wide variety of ions using nanostructures of different sizes: a double-crossover motif (76 bp), a three-point-star motif (∼134 bp), a DNA tetrahedron (534 bp) and a DNA origami triangle (7221 bp). We show successful assembly of a majority of these structures in Ca 2+ , Ba 2+ , Na + , K + and Li + and provide quantified assembly yields using gel electrophoresis and visual confirmation of a DNA origami triangle using atomic force microscopy. We further show that structures assembled in monovalent ions (Na + , K + and Li + ) exhibit up to a 10-fold higher nuclease resistance compared to those assembled in divalent ions (Mg 2+ , Ca 2+ and Ba 2+ ). Our work presents new assembly conditions for a wide range of DNA nanostructures with enhanced biostability.
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Affiliation(s)
- Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Dhanush Gandavadi
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Johnsi Mathivanan
- Department of Chemistry, University of Albany, State University of New York, Albany, NY 12222, USA
| | - Tingjie Song
- Holonyak Micro and Nanotechnology Lab (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University of Albany, State University of New York, Albany, NY 12222, USA
| | - Xing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Holonyak Micro and Nanotechnology Lab (HMNTL), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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26
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Ghosal S, Bag S, Bhowmik S. Unravelling the Drug Encapsulation Ability of Functional DNA Origami Nanostructures: Current Understanding and Future Prospects on Targeted Drug Delivery. Polymers (Basel) 2023; 15:1850. [PMID: 37111997 PMCID: PMC10144338 DOI: 10.3390/polym15081850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023] Open
Abstract
Rapid breakthroughs in nucleic acid nanotechnology have always driven the creation of nano-assemblies with programmable design, potent functionality, good biocompatibility, and remarkable biosafety during the last few decades. Researchers are constantly looking for more powerful techniques that provide enhanced accuracy with greater resolution. The self-assembly of rationally designed nanostructures is now possible because of bottom-up structural nucleic acid (DNA and RNA) nanotechnology, notably DNA origami. Because DNA origami nanostructures can be organized precisely with nanoscale accuracy, they serve as a solid foundation for the exact arrangement of other functional materials for use in a number of applications in structural biology, biophysics, renewable energy, photonics, electronics, medicine, etc. DNA origami facilitates the creation of next-generation drug vectors to help in the solving of the rising demand on disease detection and therapy, as well as other biomedicine-related strategies in the real world. These DNA nanostructures, generated using Watson-Crick base pairing, exhibit a wide variety of properties, including great adaptability, precise programmability, and exceptionally low cytotoxicity in vitro and in vivo. This paper summarizes the synthesis of DNA origami and the drug encapsulation ability of functionalized DNA origami nanostructures. Finally, the remaining obstacles and prospects for DNA origami nanostructures in biomedical sciences are also highlighted.
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Affiliation(s)
- Souvik Ghosal
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to Be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry 607402, India
| | - Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Sudipta Bhowmik
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to Be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry 607402, India
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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27
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Fitzgerald G, Low D, Morgan L, Hilt C, Benford M, Akers C, Hornback S, Hilt JZ, Scott D. Controlled Release of DNA Binding Anticancer Drugs from Gold Nanoparticles with Near-Infrared Radiation. J Pharm Sci 2023; 112:1064-1071. [PMID: 36493881 PMCID: PMC10033344 DOI: 10.1016/j.xphs.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Traditional chemotherapies target rapidly developing cells in the human body resulting in harsh side effects including fatigue, immune system suppression, and nausea, among others. Delivery systems to focus the active pharmaceutical ingredients (APIs) to the diseased tissue can diminish the negative side effects while improving treatment outcomes. Gold nanoparticles (AuNP) offer many unique advantages as drug delivery vehicles, including being biologically inert, easily adaptable to various shapes and sizes, able to create a strong Au-thiol bond, and able to generate heat upon the absorption of near-infrared light. To this end, a AuNP delivery vehicle was engineered to load and release two DNA binding anti-cancer drugs, mithramycin and doxorubicin, in a controlled fashion. The drugs were loaded onto the surface of the AuNP with temperature sensitive linkages. The amount of heat generated, and subsequent release of the drugs was controlled by the irradiation time with a near-infrared laser. By modulating the linkage used to load the drugs three different release profiles were able to be achieved, indicating the feasibility of such a system for combinational therapy requiring sequential release of APIs.
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Affiliation(s)
- Gracie Fitzgerald
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Daniel Low
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Luc Morgan
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Cole Hilt
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Micai Benford
- Department of Chemistry, Centre College, Danville, KY 40422, United States
| | - Caleb Akers
- Department of Chemistry and Biochemistry, DePauw University, Greencastle, IN 46135, United States
| | - Skyler Hornback
- Department of Chemical Engineering, University of Kentucky, Lexington, KY 40506, United States
| | - J Zach Hilt
- Department of Chemical Engineering, University of Kentucky, Lexington, KY 40506, United States
| | - Daniel Scott
- Department of Chemistry, Centre College, Danville, KY 40422, United States.
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28
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Wang W, Chen Y, Yin H, Lv J, Lin M, Wu ZS. Center backbone-rigidified DNA polygonal nanostructures and bottom face-templated polyhedral pyramids with structural stability in a complex biological medium. Acta Biomater 2023; 161:100-111. [PMID: 36905953 DOI: 10.1016/j.actbio.2023.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/15/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Due to the sequence programmability, good biocompatibility, versatile functionalities and vast sequence space, DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures in one, two and three dimensions that are capable of engineering of multiple functional nucleic acids into a useful tool to implement intended tasks in biological and medical field. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging mainly because of the molecular flexibility-based uncontrollability of size and shape. In this contribution, utilizing gel electrophoretic analysis and atomic force microscopy, we demonstrate the modeling assembly technique for the construction of wireframe DNA nanostructures that can be divided into two categories: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the construction of DNA polygons and polyhedral pyramids, respectively. The highest assembly efficiency (AE) is about 100%, while the lowest AE is not less than 50%. Moreover, when adding one edge for polygons or one side face for pyramids, we only need to add one oligonucleotide strand. Especially, the advanced polygons (e.g., pentagon and hexagon) of definite shape are for the first time constructed. Along this line, introduction of cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours even if the vulnerable nicks are not sealed. The proposed modeling assembly technique represents important progress toward the development of DNA nanotechnology and is expected to promote the application of DNA nanostructures in biological and biomedical fields. STATEMENT OF SIGNIFICANCE: DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging. In this contribution, we demonstrate the modeling technique for the construction of different wireframe DNA nanostructures: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the assembly of DNA polygons and polyhedral pyramids, respectively. Moreover, cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours, promoting the application of DNA nanostructures in biological and biomedical fields.
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Affiliation(s)
- Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Yaxin Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Hongwei Yin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Jingrui Lv
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Mengling Lin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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29
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A 3D-printed PCL/PEI/DNA bioactive scaffold for chemotherapy drug capture in vivo. Int J Biol Macromol 2023; 236:123942. [PMID: 36889620 DOI: 10.1016/j.ijbiomac.2023.123942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Abstract
Systemic chemotherapy after surgery is necessary to control tumor recurrence, but the severe side effects caused by chemotherapeutic drugs pose a great threat to patients' health. In this study, we originally develop a porous scaffold used for chemotherapy drug capture by using 3D printing technology. The scaffold is mainly composed of poly (ε-caprolactone) (PCL) and polyetherimide (PEI) with a mass ratio of 5/1. Subsequently, the printed scaffold is modified with DNA through the strong electrostatic integration between DNA and PEI to endow the scaffold with the specific absorption to doxorubicin (DOX, a widely used chemotherapy drug). The results show that pore diameter has an important influence on DOX adsorption, and smaller pores will ensure a higher DOX absorption. In vitro, the printed scaffold can absorb about 45 % DOX. While in vivo, it remains a higher absorption ability to DOX when the scaffold is successfully implanted into the common jugular vein of rabbits. What's more, the scaffold has good hemocompatibility and biocompatibility, indicating its safety for in vivo application. Taken together, the 3D-printed scaffold with excellent capture of chemotherapy drugs will play an important role in reducing the toxic side effects of chemotherapy drugs and improving the life quality of patients.
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30
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Mohammad SN, Choi YS, Chung JY, Cedrone E, Neun BW, Dobrovolskaia MA, Yang X, Guo W, Chew YC, Kim J, Baek S, Kim IS, Fruman DA, Kwon YJ. Nanocomplexes of doxorubicin and DNA fragments for efficient and safe cancer chemotherapy. J Control Release 2023; 354:91-108. [PMID: 36572154 DOI: 10.1016/j.jconrel.2022.12.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023]
Abstract
Cancer-targeted therapy by a chemotherapeutic agent formulated in a nanoscale platform has been challenged by complex and inefficient manufacturing, low drug loading, difficult characterization, and marginally improved therapeutic efficacy. This study investigated facile-to-produce nanocomplexes of doxorubicin (DOX), a widely used cancer drug, and clinically approved DNA fragments that are extracted from a natural source. DOX was found to self-assemble DNA fragments into relatively monodispersed nanocomplexes with a diameter of ∼70 nm at 14.3% (w/w) drug loading by simple and scalable mixing. The resulting DOX/DNA nanocomplexes showed sustained DOX release, unlike overly stable Doxil®, cellular uptake via multiple endocytosis pathways, and high hematological and immunological compatibility. DOX/DNA nanocomplexes eradicated EL4 T lymphoma cells in a time-dependent manner, eventually surpassing free DOX. Extended circulation of DOX/DNA nanocomplexes, while avoiding off-target accumulation in the lung and being cleared from the liver, resulted in rapid accumulation in tumor and lowered cardio toxicity. Finally, tumor growth of EL4-challenged C57BL/6 mice (syngeneic model) and OPM2-challenged NSG mice (human xenograft model) were efficiently inhibited by DOX/DNA nanocomplexes with enhanced overall survival, in comparison with free DOX and Doxil®, especially upon repeated administrations. DOX/DNA nanocomplexes are a promising chemotherapeutics delivery platform for their ease of manufacturing, high biocompatibility, desired drug release and accumulation, efficient tumor eradication with improved safety, and further engineering versatility for extended therapeutic applications.
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Affiliation(s)
- Saad N Mohammad
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States
| | - Yeon Su Choi
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States
| | - Jee Young Chung
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States
| | - Edward Cedrone
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
| | - Barry W Neun
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States
| | - Xiaojing Yang
- Zymo Research Corporation, Irvine, CA 92604, United States
| | - Wei Guo
- Zymo Research Corporation, Irvine, CA 92604, United States
| | - Yap Ching Chew
- Zymo Research Corporation, Irvine, CA 92604, United States
| | - Juwan Kim
- Pharma Research, Co, Ltd., Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Seunggul Baek
- Pharma Research, Co, Ltd., Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Ik Soo Kim
- Pharma Research, Co, Ltd., Seongnam-si, Gyeonggi-do, Republic of Korea
| | - David A Fruman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States
| | - Young Jik Kwon
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, United States; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, United States; Department of Biomedical Engineering, University of California, Irvine, CA 92697, United States; Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, United States.
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31
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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Torres-Martinez Z, Pérez D, Torres G, Estrada S, Correa C, Mederos N, Velazquez K, Castillo B, Griebenow K, Delgado Y. A Synergistic pH-Responsive Serum Albumin-Based Drug Delivery System Loaded with Doxorubicin and Pentacyclic Triterpene Betulinic Acid for Potential Treatment of NSCLC. BIOTECH 2023; 12:13. [PMID: 36810440 PMCID: PMC9944877 DOI: 10.3390/biotech12010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Nanosized drug delivery systems (DDS) have been studied as a novel strategy against cancer due to their potential to simultaneously decrease drug inactivation and systemic toxicity and increase passive and/or active drug accumulation within the tumor(s). Triterpenes are plant-derived compounds with interesting therapeutic properties. Betulinic acid (BeA) is a pentacyclic triterpene that has great cytotoxic activity against different cancer types. Herein, we developed a nanosized protein-based DDS of bovine serum albumin (BSA) as the drug carrier combining two compounds, doxorubicin (Dox) and the triterpene BeA, using an oil-water-like micro-emulsion method. We used spectrophotometric assays to determine protein and drug concentrations in the DDS. The biophysical properties of these DDS were characterized using dynamic light scattering (DLS) and circular dichroism (CD) spectroscopy, confirming nanoparticle (NP) formation and drug loading into the protein structure, respectively. The encapsulation efficiency was 77% for Dox and 18% for BeA. More than 50% of both drugs were released within 24 h at pH 6.8, while less drug was released at pH 7.4 in this period. Co-incubation viability assays of Dox and BeA alone for 24 h demonstrated synergistic cytotoxic activity in the low μM range against non-small-cell lung carcinoma (NSCLC) A549 cells. Viability assays of the BSA-(Dox+BeA) DDS demonstrated a higher synergistic cytotoxic activity than the two drugs with no carrier. Moreover, confocal microscopy analysis confirmed the cellular internalization of the DDS and the accumulation of the Dox in the nucleus. We determined the mechanism of action of the BSA-(Dox+BeA) DDS, confirming S-phase cell cycle arrest, DNA damage, caspase cascade activation, and downregulation of epidermal growth factor receptor (EGFR) expression. This DDS has the potential to synergistically maximize the therapeutic effect of Dox and diminish chemoresistance induced by EGFR expression using a natural triterpene against NSCLC.
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Affiliation(s)
- Zally Torres-Martinez
- Chemistry Department, University of Puerto Rico, Rio Piedras Campus, San Juan 00925, Puerto Rico
| | - Daraishka Pérez
- Neuroscience Department, Universidad Central del Caribe, Bayamon 00960, Puerto Rico
| | - Grace Torres
- Biochemistry & Pharmacology Department, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico
| | - Sthephanie Estrada
- Biology Department, University of Puerto Rico—Cayey, Cayey 00736, Puerto Rico
| | - Clarissa Correa
- Biochemistry & Pharmacology Department, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico
| | - Natasha Mederos
- Biochemistry & Pharmacology Department, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico
| | - Kimberly Velazquez
- Biochemistry & Pharmacology Department, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico
| | - Betzaida Castillo
- Chemistry Department, University of Puerto Rico—Humacao, Humacao 00727, Puerto Rico
| | - Kai Griebenow
- Chemistry Department, University of Puerto Rico, Rio Piedras Campus, San Juan 00925, Puerto Rico
| | - Yamixa Delgado
- Biochemistry & Pharmacology Department, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico
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33
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Zhao Y, Guo L, Cao S, Xie M, Peng H, Li J, Luo S, Ma L, Wang L. DNA framework carriers with asymmetric hydrophobic drug patterns for enhanced cellular cytotoxicity. Chem Commun (Camb) 2023; 59:306-309. [PMID: 36507912 DOI: 10.1039/d2cc05763h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We devise a class of amphiphilic drug complexes by programming hydrophobic drug patterns (HDPs) on DNA frameworks. We investigate the effect of HDPs on cellular uptake efficiency and drug potency. We achieve enhanced cytotoxicity against tumor cells by using an asymmetric HDP.
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Affiliation(s)
- Yan Zhao
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Linjie Guo
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Shuting Cao
- Division of Physical Biology Department, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Mo Xie
- Key Laboratory for Organic Electronics and Information Displays (KLOEID) & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, Jiangsu 210023, China
| | - Hongzhen Peng
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Lan Ma
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Zhangjiang Laboratory, Shanghai 201210, China
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Ijäs H, Liedl T, Linko V, Posnjak G. A label-free light-scattering method to resolve assembly and disassembly of DNA nanostructures. Biophys J 2022; 121:4800-4809. [PMID: 36811525 PMCID: PMC9811603 DOI: 10.1016/j.bpj.2022.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 11/02/2022] Open
Abstract
DNA self-assembly, and in particular DNA origami, has evolved into a reliable workhorse for organizing organic and inorganic materials with nanometer precision and with exactly controlled stoichiometry. To ensure the intended performance of a given DNA structure, it is beneficial to determine its folding temperature, which in turn yields the best possible assembly of all DNA strands. Here, we show that temperature-controlled sample holders and standard fluorescence spectrometers or dynamic light-scattering setups in a static light-scattering configuration allow for monitoring the assembly progress in real time. With this robust label-free technique, we determine the folding and melting temperatures of a set of different DNA origami structures without the need for more tedious protocols. In addition, we use the method to follow digestion of DNA structures in the presence of DNase I and find strikingly different resistances toward enzymatic degradation depending on the structural design of the DNA object.
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Affiliation(s)
- Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland; Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland; LIBER Center of Excellence, Aalto University, Aalto, Finland.
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany.
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Scherf M, Scheffler F, Maffeo C, Kemper U, Ye J, Aksimentiev A, Seidel R, Reibetanz U. Trapping of protein cargo molecules inside DNA origami nanocages. NANOSCALE 2022; 14:18041-18050. [PMID: 36445741 DOI: 10.1039/d2nr05356j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The development of the DNA origami technique has directly inspired the idea of using three-dimensional DNA cages for the encapsulation and targeted delivery of drug or cargo molecules. The cages would be filled with molecules that would be released at a site of interest upon cage opening triggered by an external stimulus. Though different cage variants have been developed, efficient loading of DNA cages with freely-diffusing cargo molecules that are not attached to the DNA nanostructure and their efficient retention within the cages has not been presented. Here we address these challenges using DNA origami nanotubes formed by a double-layer of DNA helices that can be sealed with tight DNA lids at their ends. In a first step we attach DNA-conjugated cargo proteins to complementary target strands inside the DNA tubes. After tube sealing, the cargo molecules are released inside the cavity using toehold-mediated strand displacement by externally added invader strands. We show that DNA invaders are rapidly entering the cages through their DNA walls. Retention of ∼70 kDa protein cargo molecules inside the cages was, however, poor. Guided by coarse-grained simulations of the DNA cage dynamics, a tighter sealing of the DNA tubes was developed which greatly reduced the undesired escape of cargo proteins. These improved DNA nanocages allow for efficient encapsulation of medium-sized cargo molecules while remaining accessible to small molecules that can be used to trigger reactions, including a controlled release of the cargo via nanocage opening.
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Affiliation(s)
- Merle Scherf
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Science, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany
| | - Florian Scheffler
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Science, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA
| | - Ulrich Kemper
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Science, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany
| | - Jingjing Ye
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Science, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany
- Cluster for Advancing Electronic Devices Dresden, University of Dresden, Helmholtzstraße 18, 01069 Dresden, Germany
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, IL 61801, USA
| | - Ralf Seidel
- Peter Debye Institute for Soft Matter Physics, Faculty of Physics and Earth Science, University of Leipzig, Linnéstraße 5, 04103 Leipzig, Germany
- Cluster for Advancing Electronic Devices Dresden, University of Dresden, Helmholtzstraße 18, 01069 Dresden, Germany
| | - Uta Reibetanz
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.
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Cytotoxic Potential of Bioactive Compounds from Aspergillus flavus, an Endophytic Fungus Isolated from Cynodon dactylon, against Breast Cancer: Experimental and Computational Approach. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248814. [PMID: 36557944 PMCID: PMC9784115 DOI: 10.3390/molecules27248814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
Endophytic fungi are a diverse group of microorganisms that colonize the inter- or intracellular spaces of plants and exhibit mutual benefits. Their interactions with the host plant and other microbiomes are multidimensional and play a crucial role in the production of secondary metabolites. We screened bioactive compounds present in the extracts of Aspergillus flavus, an endophytic fungus isolated from the roots of the medicinal grass Cynodon dactylon, for its anticancer potential. An in vitro analysis of the Ethyl acetate extract from A. flavus showed significant cytostatic effects (IC50: 16.25 μg/mL) against breast cancer cells (MCF-7). A morphological analysis of the cells and a flow cytometry of the cells with annexin V/Propidium Iodide suggested that the extract induced apoptosis in the MCF-7 cells. The extract of A. flavus increased reactive oxygen species (ROS) generation and caused a loss of mitochondrial membrane potential in MCF-7 cells. To identify the metabolites that might be responsible for the anticancer effect, the extract was subjected to a gas chromatography-mass spectrometry (GC-MS) analysis. Interestingly, nine phytochemicals that induced cytotoxicity in the breast cancer cell line were found in the extract. The in silico molecular docking and molecular dynamics simulation studies revealed that two compounds, 2,4,7-trinitrofluorenone and 3α, 5 α-cyclo-ergosta-7,9(11), 22t-triene-6beta-ol exhibited significant binding affinities (-9.20, and -9.50 Kcal/mol, respectively) against Bcl-2, along with binding stability and intermolecular interactions of its ligand-Bcl-2 complexes. Overall, the study found that the endophytic A. flavus from C. dactylon contains plant-like bioactive compounds that have a promising effect in breast cancer.
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Singh M, Sharma D, Garg M, Kumar A, Baliyan A, Rani R, Kumar V. Current understanding of biological interactions and processing of DNA origami nanostructures: Role of machine learning and implications in drug delivery. Biotechnol Adv 2022; 61:108052. [DOI: 10.1016/j.biotechadv.2022.108052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/02/2022]
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38
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Theoretical modelling of electrostatic interactions in pH-dependent drug loading and releasing by functionalized mesoporous silica nanoparticles. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02562-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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39
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Liu J, Li M, Zuo X. DNA Nanotechnology-Empowered Live Cell Measurements. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204711. [PMID: 36124715 DOI: 10.1002/smll.202204711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The systematic analysis and precise manipulation of a variety of biomolecules should lead to unprecedented findings in fundamental biology. However, conventional technology cannot meet the current requirements. Despite this, there has been progress as DNA nanotechnology has evolved to generate DNA nanostructures and circuits over the past four decades. Many potential applications of DNA nanotechnology for live cell measurements have begun to emerge owing to the biocompatibility, nanometer addressability, and stimulus responsiveness of DNA. In this review, the DNA nanotechnology-empowered live cell measurements which are currently available are summarized. The stability of the DNA nanostructures, in a cellular microenvironment, which is crucial for accomplishing precise live cell measurements, is first summarized. Thereafter, measurements in the extracellular and intracellular microenvironment, in live cells, are introduced. Finally, the challenges that are innate to, and the further developments that are possible in this nascent field are discussed.
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Affiliation(s)
- Jiangbo Liu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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Mukhija A. Influence of Oxidative Stress on Drug-DNA Binding: Microcalorimetric and Mechanistic Insights with Anticancer Drugs. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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He PP, Du X, Cheng Y, Gao Q, Liu C, Wang X, Wei Y, Yu Q, Guo W. Thermal-Responsive MXene-DNA Hydrogel for Near-Infrared Light Triggered Localized Photothermal-Chemo Synergistic Cancer Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200263. [PMID: 36056901 DOI: 10.1002/smll.202200263] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Stimuli-responsive DNA hydrogels are promising candidates for cancer treatment, as they not only possess biocompatible and biodegradable 3D network structures as highly efficient carriers for therapeutic agents but also are capable of undergoing programmable gel-to-solution transition upon external stimuli to achieve controlled delivery. Herein, a promising platform for highly efficient photothermal-chemo synergistic cancer therapy is established by integrating DNA hydrogels with Ti3 C2 TX -based MXene as a photothermal agent and doxorubicin (DOX) as a loaded chemotherapeutic agent. Upon the irradiation of near-infrared light (NIR), temperature rise caused by photothermal MXene nanosheets triggers the reversible gel-to-solution transition of the DOX-loaded MXene-DNA hydrogel, during which the DNA duplex crosslinking structures unwind to release therapeutic agents for efficient localized cancer therapy. Removal of the NIR irradiation results in the re-formation of DNA duplex structures and the hydrogel matrix, and the recombination of free DOX and adaptive hydrogel transformations can also be achieved. As demonstrated by both in vitro and in vivo models, the MXene-DNA hydrogel system, with excellent biocompatibility and injectability, dynamically NIR-triggered drug delivery, and enhanced drug uptake under mild hyperthermia conditions, exhibits efficient localized cancer treatment with fewer side effects to the organisms.
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Affiliation(s)
- Ping-Ping He
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Xiaoxue Du
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yuan Cheng
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Qi Gao
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Chang Liu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Xiaowen Wang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yonghua Wei
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, P. R. China
| | - Weiwei Guo
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
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Ober MF, Baptist A, Wassermann L, Heuer-Jungemann A, Nickel B. In situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification. Nat Commun 2022; 13:5668. [PMID: 36167861 PMCID: PMC9515200 DOI: 10.1038/s41467-022-33083-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Silicification of DNA origami structures increases their stability and provides chemical protection. Yet, it is unclear whether the whole DNA framework is embedded or if silica just forms an outer shell and how silicification affects the origami's internal structure. Employing in situ small-angle X-ray scattering (SAXS), we show that addition of silica precursors induces substantial condensation of the DNA origami at early reaction times by almost 10 %. Subsequently, the overall size of the silicified DNA origami increases again due to increasing silica deposition. We further identify the SAXS Porod invariant as a reliable, model-free parameter for the evaluation of the amount of silica formation at a given time. Contrast matching of the DNA double helix Lorentzian peak reveals silica growth also inside the origami. The less polar silica forming within the origami structure, replacing more than 40 % of the internal hydration water, causes a hydrophobic effect: condensation. DNA origami objects with flat surfaces show a strong tendency towards aggregation during silicification, presumably driven by the same entropic forces causing condensation. Maximally condensed origami displayed thermal stability up to 60 °C. Our studies provide insights into the silicification reaction allowing for the formulation of optimized reaction protocols.
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Affiliation(s)
- Martina F Ober
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Anna Baptist
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Lea Wassermann
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bert Nickel
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
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Kumar A, Ahmad A, Ansari MM, Gowd V, Rashid S, Chaudhary AA, Rudayni HA, Alsalamah SA, Khan R. Functionalized-DNA nanostructures as potential targeted drug delivery systems for cancer therapy. Semin Cancer Biol 2022; 86:54-68. [PMID: 36087856 DOI: 10.1016/j.semcancer.2022.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 01/14/2023]
Abstract
Seeman's pioneer idea has led to the foundation of DNA nanostructures, resulting in a remarkable advancement in DNA nanotechnology. Over the last few decades, remarkable advances in drug delivery techniques have resulted in the self-assembly of DNA for encapsulating candidate drug molecules. The nuclear targeting capability of DNA nanostructures is lies within their high spatial addressability and tremendous potential for active targeting. However, effective programming and assembling those DNA molecules remains a challenge, making the path to DNA nanostructures for real-world applications difficult. Because of their small size, most nanostructures are self-capable of infiltrating into the tumor cellular environment. Furthermore, to enable controlled and site-specific delivery of encapsulated drug molecules, DNA nanostructures are functionalized with special moieties that allow them to bind specific targets and release cargo only at targeted sites rather than non-specific sites, resulting in the prevention/limitation of cellular toxicity. In light of this, the current review seeks to shed light on the versatility of the DNA molecule as a targeting and encapsulating moiety for active drugs in order to achieve controlled and specific drug release with spatial and temporal precision. Furthermore, this review focused on the challenges associated with the construction of DNA nanostructures as well as the most recent advances in the functionalization of DNA nanostructures using various materials for controlled and targeted delivery of medications for cancer therapy.
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Affiliation(s)
- Ajay Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Anas Ahmad
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Md Meraj Ansari
- Centre for Pharmaceutical Nanotechnology, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Sector 67, Mohali, Punjab 160062, India
| | - Vemana Gowd
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh, 11623, Saudi Arabia
| | - Hassan Ahmed Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh, 11623, Saudi Arabia
| | - Sulaiman A Alsalamah
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh, 11623, Saudi Arabia
| | - Rehan Khan
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India.
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Seitz I, Ijäs H, Linko V, Kostiainen MA. Optically Responsive Protein Coating of DNA Origami for Triggered Antigen Targeting. ACS APPLIED MATERIALS & INTERFACES 2022; 14:38515-38524. [PMID: 35984232 PMCID: PMC9437894 DOI: 10.1021/acsami.2c10058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA nanostructures have emerged as modular building blocks in several research fields including biomedicine and nanofabrication. Their proneness to degradation in various environments has led to the development of a variety of nature-inspired protection strategies. Coating of DNA origami nanostructures with proteins can circumvent degradation and alter their properties. Here, we have used a single-chain variable antibody fragment and serum albumin to construct positively charged and stimuli-responsive protein-dendron conjugates, which were complexed with DNA origami through electrostatic interactions. Using a stepwise assembly approach, the coated nanostructures were studied for their interaction with the corresponding antigen in fluorescence-based immunoassays. The results suggest that the antibody-antigen interaction can be disturbed by the addition of the bulky serum albumin. However, this effect is fully reversible upon irradiation of the structures with an optical stimulus. This leads to a selective dissociation of the serum albumin from the nanostructure due to cleavage of a photolabile group integrated in the dendron structure, exposing the antibody fragment and enabling triggered binding to the antigen, demonstrating that serum albumin can be considered as an externally controlled "camouflaging" agent. The presented stimuli-responsive complexation approach is highly versatile regarding the choice of protein components and could, therefore, find use in DNA origami protection, targeting, and delivery as well as their spatiotemporal control.
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Affiliation(s)
- Iris Seitz
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Heini Ijäs
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Veikko Linko
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER
Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER
Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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45
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Hanke M, Grundmeier G, Keller A. Direct visualization of the drug loading of single DNA origami nanostructures by AFM-IR nanospectroscopy. NANOSCALE 2022; 14:11552-11560. [PMID: 35861612 DOI: 10.1039/d2nr02701a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The efficient loading of DNA nanostructures with intercalating or groove-binding drugs is an important prerequisite for various applications in drug delivery. However, unambiguous verification and quantification of successful drug loading is often rather challenging. In this work, AFM-IR nanospectroscopy is thus employed to directly visualize the loading of DNA origami nanostructures with the photosensitizer methylene blue (MB). Single MB-loaded DNA origami nanostructures can be clearly resolved in high-resolution infrared (IR) maps and the occurrence of MB-specific IR absorption correlates well with the topographic signals of the DNA origami nanostructures. The intensity of the recorded MB absorption bands furthermore scales with the MB concentration used for MB loading. By comparing single- and multilayer DNA origami nanostructures, it is also shown that the IR signal intensity of the loaded MB increases with the thickness of the DNA origami nanostructures. This indicates that also DNA double helices located in the core of bulky 3D DNA origami nanostructures are accessible for MB loading. AFM-IR nanospectroscopy thus has the potential to become an invaluable tool for quantifying drug loading of DNA origami nanostructures and optimizing drug loading protocols.
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Affiliation(s)
- Marcel Hanke
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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46
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Deng Y, Tan Y, Zhang Y, Zhang L, Zhang C, Ke Y, Su X. Design of Uracil-Modified DNA Nanotubes for Targeted Drug Release via DNA-Modifying Enzyme Reactions. ACS APPLIED MATERIALS & INTERFACES 2022; 14:34470-34479. [PMID: 35867518 DOI: 10.1021/acsami.2c09488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA nanostructure-based responsive drug delivery has become an increasingly potent method in cancer therapy. However, a variety of important cancer biomarkers have not been explored in searching of new and efficient targeted delivery systems. Uracil degradation glycosylase and human apurinic/apyrimidinic endonuclease are significantly more active in cancer cells. Here, we developed uracil-modified DNA nanotubes that can deliver drugs to tumor cells through an enzyme-induced disassembly process. Although the reaction of these enzymes on their natural DNA substrates has been established, their reactivity on self-assembled nanostructures of nucleic acids is not well understood. We leveraged molecular dynamic simulation based on coarse-grained model to forecast the enzyme reactivity on different DNA designs. The experimental data are highly consistent with the simulation results. It is the first example of molecule simulation being used to guide the design of enzyme-responsive DNA nano-delivery systems. Importantly, we found that the efficiency of drug release from the nanotubes can be regulated by tuning the positions of uracil modification. The DNA nanotubes equipped with cancer-specific aptamer AS1411 are used to deliver doxorubicin to tumor-bearing mice not only effectively inhibiting tumor growth but also protecting major organs from drug-caused damage. We believe that this work provides new knowledge on and insights into future design of enzyme-responsive DNA-based nanocarriers for drug delivery.
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Affiliation(s)
- Yingnan Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanhang Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - YingWei Zhang
- College of Material Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - ChunYi Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yonggang Ke
- Wallance H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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47
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Hanke M, Hansen N, Tomm E, Grundmeier G, Keller A. Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate. Int J Mol Sci 2022; 23:ijms23158547. [PMID: 35955680 PMCID: PMC9368935 DOI: 10.3390/ijms23158547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Guanidinium (Gdm) undergoes interactions with both hydrophilic and hydrophobic groups and, thus, is a highly potent denaturant of biomolecular structure. However, our molecular understanding of the interaction of Gdm with proteins and DNA is still rather limited. Here, we investigated the denaturation of DNA origami nanostructures by three Gdm salts, i.e., guanidinium chloride (GdmCl), guanidinium sulfate (Gdm2SO4), and guanidinium thiocyanate (GdmSCN), at different temperatures and in dependence of incubation time. Using DNA origami nanostructures as sensors that translate small molecular transitions into nanostructural changes, the denaturing effects of the Gdm salts were directly visualized by atomic force microscopy. GdmSCN was the most potent DNA denaturant, which caused complete DNA origami denaturation at 50 °C already at a concentration of 2 M. Under such harsh conditions, denaturation occurred within the first 15 min of Gdm exposure, whereas much slower kinetics were observed for the more weakly denaturing salt Gdm2SO4 at 25 °C. Lastly, we observed a novel non-monotonous temperature dependence of DNA origami denaturation in Gdm2SO4 with the fraction of intact nanostructures having an intermediate minimum at about 40 °C. Our results, thus, provide further insights into the highly complex Gdm–DNA interaction and underscore the importance of the counteranion species.
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48
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Li R, Wu X, Li J, Lu X, Zhao RC, Liu J, Ding B. A covalently conjugated branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery. NANOSCALE 2022; 14:9369-9378. [PMID: 35726974 DOI: 10.1039/d2nr01252a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Targeted delivery of therapeutic drugs is essential for precise treatment of various diseases to reduce possible serious side-effects. A screened DNA aptamer has been widely developed for active targeting delivery. Herein, we report a facile strategy for the construction of a branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery. In our design, the terminal-modified DNA aptamer can be covalently conjugated to form a branched aptamer cluster by click reaction easily. The branched aptamer cluster-modified DNA tetrahedron (TET) demonstrates highly targeted cellular uptake with the modification of only one site. After loading the chemotherapeutic drug (doxorubicin, DOX), the DNA aptamer cluster-based nanoplatform elicits a remarkable and selective inhibition of tumor cell proliferation by much-enhanced targeted delivery. This covalently conjugated branched DNA aptamer cluster-based nanoplatform provides a new strategy for the development of targeted drug delivery.
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Affiliation(s)
- Runze Li
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Dongdan Santiao No. 5, Beijing 100005, China.
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Dongdan Santiao No. 5, Beijing 100005, China.
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
| | - Robert Chunhua Zhao
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Dongdan Santiao No. 5, Beijing 100005, China.
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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49
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Li S, Li F, Wan D, Chen Z, Pan J, Liang XJ. A micelle-based stage-by-stage impelled system for efficient doxorubicin delivery. Bioact Mater 2022; 25:783-795. [PMID: 37056277 PMCID: PMC10086681 DOI: 10.1016/j.bioactmat.2022.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
Chemotherapy remains the mainstay of cancer treatment, benefiting millions of patients each year, but the side effects of chemotherapy drugs severely limit their clinical use. Doxorubicin (DOX) can cause various side effects such as heart damage and treatment-related tumors. The effective use of active and passive targeting will improve the clinical application of DOX. Here, TPGS3350 and bioactive peptides were utilized to construct a micelle-based stage-by-stage impelled efficient system (missiles) for DOX delivery (DOX missiles). By taking advantage of the EPR effect, DOX missiles are efficiently enriched at the tumor site. After being cleaved by matrix metalloproteinase2 (MMP2), the peptide (VRGD) targets tumor cells to facilitate uptake of the missiles by the tumor cells via receptor-mediated endocytosis. The intracellular activated caspase-3-catalyzed explosion of DOX missiles further enables efficient tumor killing. This study provides an efficient approach for DOX delivery and toxicity reduction.
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Affiliation(s)
- Sunfan Li
- School of Chemical Engineering and Technology, Tiangong University, Tianjin, 300387, PR China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, No. 11, First North Road, Zhongguancun, Beijing, 100190, PR China
| | - Fangzhou Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, No. 11, First North Road, Zhongguancun, Beijing, 100190, PR China
| | - Dong Wan
- School of Chemical Engineering and Technology, Tiangong University, Tianjin, 300387, PR China
- Corresponding author.
| | - Zuqin Chen
- Medical School of Chinese PLA, No.28 Fuxing Road, Beijing, 100853, PR China
- Department of Radiology, The First Medical Centre, Chinese PLA General Hospital, Beijing, PR China
- Department of Radiology, Chinese PAP Guangxi Corps Hospital, Nanning, Guangxi, PR China
| | - Jie Pan
- School of Chemical Engineering and Technology, Tiangong University, Tianjin, 300387, PR China
- Corresponding author.
| | - Xing-Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, No. 11, First North Road, Zhongguancun, Beijing, 100190, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
- Corresponding author. University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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50
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Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. ACS NANO 2022; 16:8954-8966. [PMID: 35640255 PMCID: PMC9649841 DOI: 10.1021/acsnano.1c11575] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyun Min Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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