1
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Huang Y, Zhao Z, Yi G, Zhang M. Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays. J Mater Chem B 2024; 12:4063-4079. [PMID: 38572575 DOI: 10.1039/d3tb02947f] [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: 04/05/2024]
Abstract
DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.
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Affiliation(s)
- Yuqi Huang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
| | - Zixin Zhao
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Gang Yi
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China.
| | - Mingjun Zhang
- Clinical Laboratory, Chongqing Jiulongpo District People's Hospital, Chongqing 400050, China.
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2
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Chen Q, Xia X, Liang Z, Zuo T, Xu G, Wei F, Yang J, Hu Q, Zhao Z, Tang BZ, Cen Y. Self-Assembled DNA Nanospheres Driven by Carbon Dots for MicroRNAs Imaging in Tumor via Logic Circuit. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2310728. [PMID: 38229573 DOI: 10.1002/smll.202310728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/26/2023] [Indexed: 01/18/2024]
Abstract
DNA nanostructures with diverse biological functions have made significant advancements in biomedical applications. However, a universal strategy for the efficient production of DNA nanostructures is still lacking. In this work, a facile and mild method is presented for self-assembling polyethylenimine-modified carbon dots (PEI-CDs) and DNA into nanospheres called CANs at room temperature. This makes CANs universally applicable to multiple biological applications involving various types of DNA. Due to the ultra-small size and strong cationic charge of PEI-CDs, CANs exhibit a dense structure with high loading capacity for encapsulated DNA while providing excellent stability by protecting DNA from enzymatic hydrolysis. Additionally, Mg2+ is incorporated into CANs to form Mg@CANs which enriches the performance of CANs and enables subsequent biological imaging applications by providing exogenous Mg2+ . Especially, a DNAzyme logic gate system that contains AND and OR Mg@CANs is constructed and successfully delivered to tumor cells in vitro and in vivo. They can be specifically activated by endogenic human apurinic/apyrimidinic endonuclease 1 and recognize the expression levels of miRNA-21 and miRNA-155 at tumor sites by logic biocomputing. A versatile pattern for delivery of diverse DNA and flexible logic circuits for multiple miRNAs imaging are developed.
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Affiliation(s)
- Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zhigang Liang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Tongshan Zuo
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zheng Zhao
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, P. R. China
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, P. R. China
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
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3
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Smith DM, Keller A. DNA Nanostructures in the Fight Against Infectious Diseases. ADVANCED NANOBIOMED RESEARCH 2021; 1:2000049. [PMID: 33615315 PMCID: PMC7883073 DOI: 10.1002/anbr.202000049] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.
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Affiliation(s)
- David M. Smith
- DNA Nanodevices UnitDepartment DiagnosticsFraunhofer Institute for Cell Therapy and Immunology IZI04103LeipzigGermany
- Peter Debye Institute for Soft Matter PhysicsFaculty of Physics and Earth SciencesUniversity of Leipzig04103LeipzigGermany
- Institute of Clinical ImmunologyUniversity of Leipzig Medical School04103LeipzigGermany
- Dhirubhai Ambani Institute of Information and Communication TechnologyGandhinagar382 007India
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
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4
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Abstract
DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.
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Affiliation(s)
- Arun Richard Chandrasekaran
- grid.265850.c0000 0001 2151 7947The RNA Institute, University at Albany, State University of New York, Albany, NY USA
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5
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Zeng Y, Nixon RL, Liu W, Wang R. The applications of functionalized DNA nanostructures in bioimaging and cancer therapy. Biomaterials 2020; 268:120560. [PMID: 33285441 DOI: 10.1016/j.biomaterials.2020.120560] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 11/03/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022]
Abstract
Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields. Those DNA nanostructures, synthesized via Watson-Crick base pairing, show a wide range of attributes along with excellent applicability, precise programmability, and extremely low cytotoxicity in vitro and in vivo. In this review, the applications of functionalized DNA nanostructures in bioimaging and tumor therapy are summarized. We focused on approaches involving DNA origami nanostructures due to their widespread use in previous and current reports. Non-DNA origami nanostructures such as DNA tetrahedrons are also covered. Finally, the remaining challenges and perspectives regarding DNA nanostructures in the biomedical arena are discussed.
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Affiliation(s)
- Yun Zeng
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA; Engineering Research Center of Molecular and Neuroimaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi, 710126, PR China.
| | - Rachel L Nixon
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA
| | - Wenyan Liu
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA; Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, MO, 65409, USA
| | - Risheng Wang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, 65409, USA.
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6
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Reddy KK, Bandal H, Satyanarayana M, Goud KY, Gobi KV, Jayaramudu T, Amalraj J, Kim H. Recent Trends in Electrochemical Sensors for Vital Biomedical Markers Using Hybrid Nanostructured Materials. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902980. [PMID: 32670744 PMCID: PMC7341105 DOI: 10.1002/advs.201902980] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/12/2020] [Indexed: 05/09/2023]
Abstract
This work provides a succinct insight into the recent developments in electrochemical quantification of vital biomedical markers using hybrid metallic composite nanostructures. After a brief introduction to the biomarkers, five types of crucial biomarkers, which require timely and periodical monitoring, are shortlisted, namely, cancer, cardiac, inflammatory, diabetic and renal biomarkers. This review emphasizes the usage and advantages of hybrid nanostructured materials as the recognition matrices toward the detection of vital biomarkers. Different transduction methods (fluorescence, electrophoresis, chemiluminescence, electrochemiluminescence, surface plasmon resonance, surface-enhanced Raman spectroscopy) reported for the biomarkers are discussed comprehensively to present an overview of the current research works. Recent advancements in the electrochemical (amperometric, voltammetric, and impedimetric) sensor systems constructed with metal nanoparticle-derived hybrid composite nanostructures toward the selective detection of chosen vital biomarkers are specifically analyzed. It describes the challenges involved and the strategies reported for the development of selective, sensitive, and disposable electrochemical biosensors with the details of fabrication, functionalization, and applications of hybrid metallic composite nanostructures.
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Affiliation(s)
- K. Koteshwara Reddy
- Smart Living Innovation Technology CentreDepartment of Energy Science and TechnologyMyongji UniversityYonginGyeonggi‐do17058Republic of Korea
- Laboratory of Materials ScienceInstituto de Química de Recursos NaturalesUniversidad de TalcaP.O. Box 747Talca3460000Chile
| | - Harshad Bandal
- Smart Living Innovation Technology CentreDepartment of Energy Science and TechnologyMyongji UniversityYonginGyeonggi‐do17058Republic of Korea
| | - Moru Satyanarayana
- Department of ChemistryNational Institute of Technology WarangalWarangalTelangana506004India
| | - Kotagiri Yugender Goud
- Department of ChemistryNational Institute of Technology WarangalWarangalTelangana506004India
| | | | - Tippabattini Jayaramudu
- Laboratory of Materials ScienceInstituto de Química de Recursos NaturalesUniversidad de TalcaP.O. Box 747Talca3460000Chile
| | - John Amalraj
- Laboratory of Materials ScienceInstituto de Química de Recursos NaturalesUniversidad de TalcaP.O. Box 747Talca3460000Chile
| | - Hern Kim
- Smart Living Innovation Technology CentreDepartment of Energy Science and TechnologyMyongji UniversityYonginGyeonggi‐do17058Republic of Korea
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7
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Chandrasekaran AR, Punnoose JA, Zhou L, Dey P, Dey BK, Halvorsen K. DNA nanotechnology approaches for microRNA detection and diagnosis. Nucleic Acids Res 2019; 47:10489-10505. [PMID: 31287874 PMCID: PMC6847506 DOI: 10.1093/nar/gkz580] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.
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Affiliation(s)
| | | | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Bijan K Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
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8
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DNA Nanotechnology for Building Sensors, Nanopores and Ion-Channels. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:331-370. [PMID: 31713205 DOI: 10.1007/978-981-13-9791-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has revolutionised the capabilities to shape and control three-dimensional structures at the nanometre scale. Designer sensors, nanopores and ion-channels built from DNA have great potential for both cross-disciplinary research and applications. Here, we introduce the concept of structural DNA nanotechnology, including DNA origami, and give an overview of the work flow from design to assembly, characterisation and application of DNA-based functional systems. Chemical functionalisation of DNA has opened up pathways to transform static DNA structures into dynamic nanomechanical sensors. We further introduce nanopore sensing as a powerful label-free single-molecule technique and discuss how it can benefit from DNA nanotechnology. Especially exciting is the possibility to create membrane-inserted DNA nanochannels that mimic their protein-based natural counterparts in form and function. In this chapter we review the status quo of DNA sensors, nanopores and ion channels, highlighting opportunities and challenges for their future development.
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9
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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10
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Ishikawa D, Suzuki Y, Kurokawa C, Ohara M, Tsuchiya M, Morita M, Yanagisawa M, Endo M, Kawano R, Takinoue M. DNA Origami Nanoplate‐Based Emulsion with Nanopore Function. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Daisuke Ishikawa
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences Tohoku University 6-3 Aramaki aza Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Chikako Kurokawa
- Department of Applied Physics Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Masayuki Ohara
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Misato Tsuchiya
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Masamune Morita
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
| | - Miho Yanagisawa
- Department of Applied Physics Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
- Komaba Institute for Science Graduate School of Arts and Sciences The University of Tokyo 3-8-1 Komaba, Meguro Tokyo 153-8902 Japan
| | - Masayuki Endo
- Department of Chemistry Graduate School of Science Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science Tokyo University of Agriculture and Technology 2-24-6 Naka-cho, Koganei Tokyo 184-8588 Japan
| | - Masahiro Takinoue
- Department of Computer Science Tokyo Institute of Technology 4259 Nagatsuta-cho Midori-ku, Yokohama Kanagawa 226-8502 Japan
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11
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Ishikawa D, Suzuki Y, Kurokawa C, Ohara M, Tsuchiya M, Morita M, Yanagisawa M, Endo M, Kawano R, Takinoue M. DNA Origami Nanoplate-Based Emulsion with Nanopore Function. Angew Chem Int Ed Engl 2019; 58:15299-15303. [PMID: 31411794 DOI: 10.1002/anie.201908392] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Indexed: 11/10/2022]
Abstract
Bio-inspired functional microcapsules have attracted increasing attention in many fields from physical/chemical science to artificial-cell engineering. Although particle-stabilised microcapsules are advantageous for their stability and functionalisation potential, versatile methods for their functionalisation are desired to expand their possibilities. This study reports a water-in-oil microdroplet stabilised with amphiphilic DNA origami nanoplates. By utilising DNA nanotechnology, DNA nanoplates were designed as a nanopore device for ion transportation and to stabilise the oil-water interface. Microscopic examination revealed the microcapsule formed by the accumulation of amphiphilic DNA nanoplates at the oil-water interface. Ion current measurements revealed the nanoplate pores functioned as channel to transport ions. These findings provide a general strategy for the programmable design of microcapsules to engineer artificial cells and molecular robots.
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Affiliation(s)
- Daisuke Ishikawa
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Chikako Kurokawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Masayuki Ohara
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Misato Tsuchiya
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Masamune Morita
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Miho Yanagisawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan.,Komaba Institute for Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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12
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Ottaviani A, Iacovelli F, Idili A, Falconi M, Ricci F, Desideri A. Engineering a responsive DNA triple helix into an octahedral DNA nanostructure for a reversible opening/closing switching mechanism: a computational and experimental integrated study. Nucleic Acids Res 2019; 46:9951-9959. [PMID: 30247614 PMCID: PMC6212788 DOI: 10.1093/nar/gky857] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/19/2018] [Indexed: 11/12/2022] Open
Abstract
We propose an experimental and simulative approach to study the effect of integrating a DNA functional device into a large-sized DNA nanostructure. We selected, as a test bed, a well-known and characterized pH-dependent clamp-switch, based on a parallel DNA triple helix, to be integrated into a truncated octahedral scaffold. We designed, simulated and experimentally characterized two different functionalized DNA nanostructures, with and without the presence of a spacer between the scaffold and the functional elements. The experimental and simulative data agree in validating the need of a spacer for the occurrence of the pH dependent switching mechanism. The system is fully reversible and the switching can be monitored several times without any perturbation, maintaining the same properties of the isolated clamp switch in solution.
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Affiliation(s)
- Alessio Ottaviani
- Biology Department, University of Rome Tor Vergata, Rome 00133, Italy
| | | | - Andrea Idili
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Mattia Falconi
- Biology Department, University of Rome Tor Vergata, Rome 00133, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy
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13
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Chen C, Chen S, Shiddiky MJA, Chen C, Wu KC. DNA‐Templated Copper Nanoprobes: Overview, Feature, Application, and Current Development in Detection Technologies. CHEM REC 2019; 20:174-186. [DOI: 10.1002/tcr.201900022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/22/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Chung‐An Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Shih‐Chia Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Muhammad J. A. Shiddiky
- School of Environment and Science & Queensland Micro- and Nanotechnology CentreNathan campus, Griffith University 170 Kessels Road QLD 4111 Australia
| | - Chien‐Fu Chen
- Institute of Applied MechanicsNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
| | - Kevin C.‐W. Wu
- Department of Chemical EngineeringNational Taiwan University, No. 1, Sec. 4 Roosevelt Road Taipei 10617 Taiwan
- Division of Medical Engineering Research, National Health
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14
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Kizer ME, Linhardt RJ, Chandrasekaran AR, Wang X. A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805386. [PMID: 30985074 DOI: 10.1002/smll.201805386] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Precise control of DNA base pairing has rapidly developed into a field full of diverse nanoscale structures and devices that are capable of automation, performing molecular analyses, mimicking enzymatic cascades, biosensing, and delivering drugs. This DNA-based platform has shown the potential of offering novel therapeutics and biomolecular analysis but will ultimately require clever modification to enrich or achieve the needed "properties" and make it whole. These modifications total what are categorized as the molecular hero suit of DNA nanotechnology. Like a hero, DNA nanostructures have the ability to put on a suit equipped with honing mechanisms, molecular flares, encapsulated cargoes, a protective body armor, and an evasive stealth mode.
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Affiliation(s)
- Megan E Kizer
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | | | - Xing Wang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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15
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Ji W, Li D, Lai W, Yao X, Alam MF, Zhang W, Pei H, Li L, Chandrasekaran AR. pH-Operated Triplex DNA Device on MoS 2 Nanosheets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5050-5053. [PMID: 30879305 DOI: 10.1021/acs.langmuir.8b04272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a triplex-based DNA device coupled with molybdenum disulfide (MoS2) nanosheets for use as a pH-sensing platform. The device transitions from a duplex state at pH 8 to a triplex state at pH 5. The interaction of the device with MoS2 nanosheets in the two states is read out as a fluorescence signal from a pH-insensitive dye attached to the device. We characterized the operation of the DNA device on MoS2 nanosheets, analyzed the pH response, and tested the reversibility of the system. Our strategy can lead to the creation of a suite of biosensors where the sensing element is a triplex DNA device and the signal response is modulated by inorganic nanomaterials.
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Affiliation(s)
- Wei Ji
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Dan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Xiaowei Yao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Md Fazle Alam
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Weijia Zhang
- Institutes of Biomedical Sciences and Zhongshan Hospital , Fudan University , Shanghai 200032 , P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany , State University of New York , Albany , New York 12222 , United States
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16
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Chandrasekaran AR, MacIsaac M, Dey P, Levchenko O, Zhou L, Andres M, Dey BK, Halvorsen K. Cellular microRNA detection with miRacles: microRNA- activated conditional looping of engineered switches. SCIENCE ADVANCES 2019; 5:eaau9443. [PMID: 30891499 PMCID: PMC6415953 DOI: 10.1126/sciadv.aau9443] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/29/2019] [Indexed: 05/03/2023]
Abstract
MicroRNAs are short noncoding regulatory RNAs that are increasingly used as disease biomarkers. Detection of microRNAs can be arduous and expensive and often requires amplification, labeling, or radioactive probes. Here, we report a single-step, nonenzymatic microRNA detection assay using conformationally responsive DNA nanoswitches. Termed miRacles (microRNA-activated conditional looping of engineered switches), our assay has subattomole sensitivity and single-nucleotide specificity using an agarose gel electrophoresis readout. We detect cellular microRNAs from nanogram-scale RNA extracts of differentiating muscle cells and multiplex our detection for several microRNAs from one biological sample. We demonstrate 1-hour detection without expensive equipment or reagents, making this assay a compelling alternative to quantitative polymerase chain reaction and Northern blotting.
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Affiliation(s)
| | - Molly MacIsaac
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Oksana Levchenko
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Madeline Andres
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Bijan K. Dey
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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17
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Shang Y, Shi J, Liu H, Liu X, Wang ZG, Ding B. A bumpy gold nanostructure exhibiting DNA-engineered stimuli-responsive SERS signals. NANOSCALE 2018; 10:9455-9459. [PMID: 29749418 DOI: 10.1039/c8nr00986d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a SERS-active gold nanostructure with built-in electromagnetic hotspots formed by densely packed gold nanoparticles on a gold nanorod. Cy3 labeled stimuli-responsive DNA motifs were introduced to the SERS-active nanostructure. The SERS signals can be switched ON and OFF reversibly in response to external stimuli (pH, metal ions or organic molecules).
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Affiliation(s)
- Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, P.R.China.
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18
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Structural polymorphism of a cytosine-rich DNA sequence forming i-motif structure: Exploring pH based biosensors. Int J Biol Macromol 2018; 111:455-461. [DOI: 10.1016/j.ijbiomac.2018.01.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 11/15/2022]
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19
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20
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Peng P, Du Y, Li T. DNA nanodevices monitored with fluorogenic looped-out 2-aminopurine. Analyst 2018; 143:1268-1273. [PMID: 29445799 DOI: 10.1039/c7an01953j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report several DNA nanodevices monitored with fluorogenic looped-out 2-aminopurine. It is found that looped-out 2-AP, an analogue of adenine, in split parallel G-quadruplexes, triplexes and duplexes always shows much higher fluorescence intensity than that in single- or double-stranded DNAs, due to the weaker quenching effects derived from the reduced base stacking environments. Taking advantage of these traits, we introduce a new strategy to monitor the behaviours of DNA nanodevices via the fluorescence signal output by utilizing changes in the base stacking environment of 2-AP. As proof-of-principle experiments, two nanoplatforms for detecting disease genes, as well as a triplex nanoswitch, are constructed and monitored by fluorogenic looped-out 2-AP, illustrating that fluorogenic looped-out 2-AP holds great promise for reading the behaviours of diverse DNA nanodevices. Compared with conventional fluorescence labelling, looped-out 2-AP as a reporter shows good photostability and can be quenched by base-pairing, thereby providing an efficient quencher-free methodology for monitoring DNA nanodevices.
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Affiliation(s)
- Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, P.R. China.
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21
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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22
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Torelli E, Manzano M, Srivastava SK, Marks RS. DNA origami nanorobot fiber optic genosensor to TMV. Biosens Bioelectron 2017; 99:209-215. [PMID: 28759871 DOI: 10.1016/j.bios.2017.07.051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 07/04/2017] [Accepted: 07/20/2017] [Indexed: 01/17/2023]
Abstract
In the quest of greater sensitivity and specificity of diagnostic systems, one continually searches for alternative DNA hybridization methods, enabling greater versatility and where possible field-enabled detection of target analytes. We present, herein, a hybrid molecular self-assembled scaffolded DNA origami entity, intimately immobilized via capture probes linked to aminopropyltriethoxysilane, onto a glass optical fiber end-face transducer, thus producing a novel biosensor. Immobilized DNA nanorobots with a switchable flap can then be actuated by a specific target DNA present in a sample, by exposing a hemin/G-quadruplex DNAzyme, which then catalyzes the generation of chemiluminescence, once the specific fiber probes are immersed in a luminol-based solution. Integrating organic nanorobots to inorganic fiber optics creates a hybrid system that we demonstrate as a proof-of-principle can be utilized in specific DNA sequence detection. This system has potential applications in a wide range of fields, including point-of-care diagnostics or cellular in vivo biosensing when using ultrathin fiber optic probes for research purposes.
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Affiliation(s)
- Emanuela Torelli
- Nanyang Technological University-Hebrew University of Jerusalem-Ben Gurion University (NEW-CREATE) Programme, 1 CREATE Way, Research Wing, #02-06/08, Singapore 138602, Singapore; Dipartimento di Scienze Agroalimentari, Ambientali e Animali University of Udine, via delle Scienze 206, 33100 Udine, Italy.
| | - Marisa Manzano
- Nanyang Technological University-Hebrew University of Jerusalem-Ben Gurion University (NEW-CREATE) Programme, 1 CREATE Way, Research Wing, #02-06/08, Singapore 138602, Singapore; Dipartimento di Scienze Agroalimentari, Ambientali e Animali University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Sachin K Srivastava
- Nanyang Technological University-Hebrew University of Jerusalem-Ben Gurion University (NEW-CREATE) Programme, 1 CREATE Way, Research Wing, #02-06/08, Singapore 138602, Singapore
| | - Robert S Marks
- Nanyang Technological University-Hebrew University of Jerusalem-Ben Gurion University (NEW-CREATE) Programme, 1 CREATE Way, Research Wing, #02-06/08, Singapore 138602, Singapore; Ben-Gurion University of the Negev, Department of Biotechnology Engineering, P.O. Box 653, 84-105 Beer-Sheva, Israel.
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23
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Halvorsen K, Kizer ME, Wang X, Chandrasekaran AR, Basanta-Sanchez M. Shear Dependent LC Purification of an Engineered DNA Nanoswitch and Implications for DNA Origami. Anal Chem 2017; 89:5673-5677. [DOI: 10.1021/acs.analchem.7b00791] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ken Halvorsen
- The
RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Megan E. Kizer
- Department
of Chemistry and Chemical Biology and the Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Xing Wang
- Department
of Chemistry and Chemical Biology and the Center for Biotechnology
and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, United States
| | - Arun Richard Chandrasekaran
- The
RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
- Confer Health, Inc., Suite 208, 56 Roland Street, Charlestown, Massachusetts 02129, United States
| | - Maria Basanta-Sanchez
- The
RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
- Waters Corporation, 34 Maple
Street, Milford, Massachusetts 01757, United States
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24
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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25
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Chandrasekaran AR. Programmable DNA scaffolds for spatially-ordered protein assembly. NANOSCALE 2016; 8:4436-4446. [PMID: 26852879 DOI: 10.1039/c5nr08685j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.
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26
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Chandrasekaran AR. Designer DNA Architectures: Applications in Nanomedicine. Nanobiomedicine (Rij) 2016; 3:6. [PMID: 29942381 PMCID: PMC5998270 DOI: 10.5772/63228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
DNA has been used as a material for the construction of nanoscale objects. These nanostructures are programmable and allow the conjugation of biomolecular guests to improve their functionality. DNA nanostructures display a wide variety of characteristics, such as cellular permeability, biocompatibility and stability, and responsiveness to external stimuli, making them excellent candidates for applications in nanomedicine.
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