1
|
Akmal Shukri AM, Wang SM, Feng C, Chia SL, Mohd Nawi SFA, Citartan M. In silico selection of aptamers against SARS-CoV-2. Analyst 2024. [PMID: 39221970 DOI: 10.1039/d4an00812j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Aptamers are molecular recognition elements that have been extensively deployed in a wide array of applications ranging from diagnostics to therapeutics. Due to their unique properties as compared to antibodies, aptamers were also largely isolated during the COVID-19 pandemic for multiple purposes. Typically generated by conventional SELEX, the inherent drawbacks of the process including the time-consuming, cumbersome and resource-intensive nature catalysed the move to adopt in silico approaches to isolate aptamers. Impressive performances of these in silico-derived aptamers in their respective assays have been documented thus far, bearing testimony to the huge potential of the in silico approaches, akin to the traditional SELEX in isolating aptamers. In this study, we provide an overview of the in silico selection of aptamers against SARS-CoV-2 by providing insights into the basic steps involved, which comprise the selection of the initial single-stranded nucleic acids, determination of the secondary and tertiary structures and in silico approaches that include both rigid docking and molecular dynamics simulations. The different approaches involving aptamers against SARS-CoV-2 were illuminated and the need to verify these aptamers by experimental validation was also emphasized. Cognizant of the need to continuously improve aptamers, the strategies embraced thus far for post-in silico selection modifications were enumerated. Shedding light on the steps involved in the in silico selection can set the stage for further improvisation to augment the functionalities of the aptamers in the future.
Collapse
Affiliation(s)
- Amir Muhaimin Akmal Shukri
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Seok Mui Wang
- Institute of Medical Molecular Biotechnology (IMMB), Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
- Non-Destructive Biomedical and Pharmaceutical Research Center, Smart Manufacturing Research Institute (SMRI), Universiti Teknologi MARA, Puncak Alam Campus, Selangor, Malaysia
| | - Chaoli Feng
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
| | - Suet Lin Chia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang, Selangor, Malaysia
| | - Siti Farah Alwani Mohd Nawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang, Malaysia.
| |
Collapse
|
2
|
Wang B, Rocca JR, Hoshika S, Chen C, Yang Z, Esmaeeli R, Wang J, Pan X, Lu J, Wang KK, Cao YC, Tan W, Benner SA. A folding motif formed with an expanded genetic alphabet. Nat Chem 2024:10.1038/s41557-024-01552-7. [PMID: 38858518 DOI: 10.1038/s41557-024-01552-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 05/07/2024] [Indexed: 06/12/2024]
Abstract
Adding synthetic nucleotides to DNA increases the linear information density of DNA molecules. Here we report that it also can increase the diversity of their three-dimensional folds. Specifically, an additional nucleotide (dZ, with a 5-nitro-6-aminopyridone nucleobase), placed at twelve sites in a 23-nucleotides-long DNA strand, creates a fairly stable unimolecular structure (that is, the folded Z-motif, or fZ-motif) that melts at 66.5 °C at pH 8.5. Spectroscopic, gel and two-dimensional NMR analyses show that the folded Z-motif is held together by six reverse skinny dZ-:dZ base pairs, analogous to the crystal structure of the free heterocycle. Fluorescence tagging shows that the dZ-:dZ pairs join parallel strands in a four-stranded compact down-up-down-up fold. These have two possible structures: one with intercalated dZ-:dZ base pairs, the second without intercalation. The intercalated structure would resemble the i-motif formed by dC:dC+-reversed pairing at pH ≤ 6.5. This fZ-motif may therefore help DNA form compact structures needed for binding and catalysis.
Collapse
Affiliation(s)
- Bang Wang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China
- Center for Research at Bio/Nano Interface, Department of Chemistry, Department of Physiology and Functional Genomics, Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - James R Rocca
- AMRIS, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
- Firebird Biomolecular Sciences LLC, Alachua, FL, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences LLC, Alachua, FL, USA.
| | - Reza Esmaeeli
- Center for Research at Bio/Nano Interface, Department of Chemistry, Department of Physiology and Functional Genomics, Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Jianguo Wang
- College of Chemistry and Chemical Engineering, Inner Mongolia Key Laboratory of Fine Organic Synthesis, Inner Mongolia University, Hohhot, China
| | - Xiaoshu Pan
- Center for Research at Bio/Nano Interface, Department of Chemistry, Department of Physiology and Functional Genomics, Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Kevin K Wang
- Department of Emergency Medicine, University of Florida, Gainesville, FL, USA
| | - Y Charles Cao
- Center for Research at Bio/Nano Interface, Department of Chemistry, Department of Physiology and Functional Genomics, Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Weihong Tan
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, China.
- Center for Research at Bio/Nano Interface, Department of Chemistry, Department of Physiology and Functional Genomics, Health Cancer Center, University of Florida, Gainesville, FL, USA.
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences LLC, Alachua, FL, USA.
| |
Collapse
|
3
|
Cao XM, Cheng YQ, Chen MM, Yao SY, Ying AK, Wang XZ, Guo DS, Li Y. Sulfonated Azocalix[4]arene-Modified Metal-Organic Framework Nanosheets for Doxorubicin Removal from Serum. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:864. [PMID: 38786820 PMCID: PMC11124067 DOI: 10.3390/nano14100864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
Chemotherapy is one of the most commonly used methods for treating cancer, but its side effects severely limit its application and impair treatment effectiveness. Removing off-target chemotherapy drugs from the serum promptly through adsorption is the most direct approach to minimize their side effects. In this study, we synthesized a series of adsorption materials to remove the chemotherapy drug doxorubicin by modifying MOF nanosheets with sulfonated azocalix[4]arenes. The strong affinity of sulfonated azocalix[4]arenes for doxorubicin results in high adsorption strength (Langmuir adsorption constant = 2.45-5.73 L mg-1) and more complete removal of the drug. The extensive external surface area of the 2D nanosheets facilitates the exposure of a large number of accessible adsorption sites, which capture DOX molecules without internal diffusion, leading to a high adsorption rate (pseudo-second-order rate constant = 0.0058-0.0065 g mg-1 min-1). These adsorbents perform effectively in physiological environments and exhibit low cytotoxicity and good hemocompatibility. These features make them suitable for removing doxorubicin from serum during "drug capture" procedures. The optimal adsorbent can remove 91% of the clinical concentration of doxorubicin within 5 min.
Collapse
Affiliation(s)
- Xiao-Min Cao
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
| | - Yuan-Qiu Cheng
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
- State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Meng-Meng Chen
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
- State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Shun-Yu Yao
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
- State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - An-Kang Ying
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
- State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
| | - Xiu-Zhen Wang
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
| | - Dong-Sheng Guo
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
- State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), Frontiers Science Center for New Organic Matter, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China
- Xinjiang Key Laboratory of Novel Functional Materials Chemistry, College of Chemistry, and Environmental Sciences, Kashi University, Kashi 844000, China
| | - Yue Li
- College of Chemistry, Nankai University, Tianjin 300071, China; (X.-M.C.); (Y.-Q.C.); (M.-M.C.); (S.-Y.Y.); (A.-K.Y.); (X.-Z.W.)
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Nankai University, Tianjin 300071, China
| |
Collapse
|
4
|
Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution. Nat Commun 2024; 15:4057. [PMID: 38744910 PMCID: PMC11094070 DOI: 10.1038/s41467-024-48408-9] [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: 12/11/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
With just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve receptors, ligands, and catalysts. Accordingly, synthetic biology has created "artificially expanded genetic information systems" (AEGIS) to add nucleotides, functionality, and information density. With the expected improvements seen in AegisBodies and AegisZymes, the task for synthetic biologists shifts to developing for expanded DNA the same analytical tools available to natural DNA. Here we report one of these, an enzyme-assisted sequencing of expanded genetic alphabet (ESEGA) method to sequence six-letter AEGIS DNA. We show how ESEGA analyses this DNA at single base resolution, and applies it to optimized conditions for six-nucleotide PCR, assessing the fidelity of various DNA polymerases, and extending this to AEGIS components with functional groups. This supports the renewed exploitation of expanded DNA alphabets in biotechnology.
Collapse
Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | | | - Roberto Laos
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Cen Chen
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | | | - Luran Manfio
- Foundation for Applied Molecular Evolution, Alachua, FL, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL, USA.
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA.
| |
Collapse
|
5
|
Xu C, Tan Y, Zhang LY, Luo XJ, Wu JF, Ma L, Deng F. The Application of Aptamer and Research Progress in Liver Disease. Mol Biotechnol 2024; 66:1000-1018. [PMID: 38305844 PMCID: PMC11087326 DOI: 10.1007/s12033-023-01030-4] [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: 09/26/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024]
Abstract
Aptamers, as a kind of small-molecule nucleic acid, have attracted much attention since their discovery. Compared with biological reagents such as antibodies, aptamers have the advantages of small molecular weight, low immunogenicity, low cost, and easy modification. At present, aptamers are mainly used in disease biomarker discovery, disease diagnosis, treatment, and targeted drug delivery vectors. In the process of screening and optimizing aptamers, it is found that there are still many problems need to be solved such as the design of the library, optimization of screening conditions, the truncation of screened aptamer, and the stability and toxicity of the aptamer. In recent years, the incidence of liver-related diseases is increasing year by year and the treatment measures are relatively lacking, which has attracted the people's attention in the application of aptamers in liver diseases. This article mainly summarizes the research status of aptamers in disease diagnosis and treatment, especially focusing on the application of aptamers in liver diseases, showing the crucial significance of aptamers in the diagnosis and treatment of liver diseases, and the use of Discovery Studio software to find the binding target and sequence of aptamers, and explore their possible interaction sites.
Collapse
Affiliation(s)
- Cheng Xu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Yong Tan
- Hubei Selenium and Human Health Institute, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Li-Ye Zhang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Xiao-Jie Luo
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Jiang-Feng Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Lan Ma
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
| | - Fei Deng
- Department of Oncology, The Second People's Hospital of China Three Gorges University, Yichang, 443000, China.
| |
Collapse
|
6
|
Liu Y, Lin Y, Xiao H, Fu Z, Zhu X, Chen X, Li C, Ding C, Lu C. mRNA-responsive two-in-one nanodrug for enhanced anti-tumor chemo-gene therapy. J Control Release 2024; 369:765-774. [PMID: 38593976 DOI: 10.1016/j.jconrel.2024.04.007] [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: 01/22/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
The combination of chemotherapy and gene therapy holds great promise for the treatment and eradication of tumors. However, due to significant differences in physicochemical properties between chemotherapeutic agents and functional nucleic acid drugs, direct integration into a single nano-agent is hindered, impeding the design and construction of an effective co-delivery nano-platform for synergistic anti-tumor treatments. In this study, we have developed an mRNA-responsive two-in-one nano-drug for effective anti-tumor therapy by the direct self-assembly of 2'-fluoro-substituted antisense DNA against P-glycoprotein (2'F-DNA) and chemo drug paclitaxel (PTX). The 2'-fluoro modification of DNA could significantly increase the interaction between the therapeutic nucleic acid and the chemotherapeutic drug, promoting the successful formation of 2'F-DNA/PTX nanospheres (2'F-DNA/PTX NSs). Due to the one-step self-assembly process without additional carrier materials, the prepared 2'F-DNA/PTX NSs exhibited considerable loading efficiency and bioavailability of PTX. In the presence of endogenous P-glycoprotein mRNA, the 2'F-DNA/PTX NSs were disassembled. The released 2'F-DNA could down-regulate the expression of P-glycoprotein, which decreased the multidrug resistance of tumor cells and enhanced the chemotherapy effect caused by PTX. In this way, the 2'F-DNA/PTX NSs could synergistically induce the apoptosis of tumor cells and realize the combined anti-tumor therapy. This strategy might provide a new tool to explore functional intracellular co-delivery nano-systems with high bioavailability and exhibit potential promising in the applications of accurate diagnosis and treatment of tumors.
Collapse
Affiliation(s)
- Yongfei Liu
- Department of Neurosurgery, Fujian Institute of Brain Disorders and Brain Science, Fujian Clinical Research Center for Neurological Diseases, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China; Department of Neurosurgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China; MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, PR China
| | - Yuhong Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, PR China; Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou Key Laboratory of Biomedicine and Advanced Dosage Forms, School of Life Sciences, Taizhou University, Taizhou, Zhejiang 318000, PR China
| | - Han Xiao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China
| | - Zhangcheng Fu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, PR China
| | - Xiaohui Zhu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, PR China
| | - Xiaoyong Chen
- Department of Neurosurgery, Fujian Institute of Brain Disorders and Brain Science, Fujian Clinical Research Center for Neurological Diseases, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China; Department of Neurosurgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, PR China.
| | - Chenyu Ding
- Department of Neurosurgery, Fujian Institute of Brain Disorders and Brain Science, Fujian Clinical Research Center for Neurological Diseases, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China; Department of Neurosurgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China.
| | - Chunhua Lu
- Department of Neurosurgery, Fujian Institute of Brain Disorders and Brain Science, Fujian Clinical Research Center for Neurological Diseases, First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China; Department of Neurosurgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, PR China; MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, PR China.
| |
Collapse
|
7
|
Zhu C, Feng Z, Qin H, Chen L, Yan M, Li L, Qu F. Recent progress of SELEX methods for screening nucleic acid aptamers. Talanta 2024; 266:124998. [PMID: 37527564 DOI: 10.1016/j.talanta.2023.124998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.
Collapse
Affiliation(s)
- Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Ziru Feng
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Hongwei Qin
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Mengmeng Yan
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| |
Collapse
|
8
|
Wang B, Bradley KM, Kim MJ, Laos R, Chen C, Gerloff DL, Manfio L, Yang Z, Benner SA. Enzyme-Assisted High Throughput Sequencing of an Expanded Genetic Alphabet at Single Base Resolution. RESEARCH SQUARE 2023:rs.3.rs-3678081. [PMID: 38196584 PMCID: PMC10775363 DOI: 10.21203/rs.3.rs-3678081/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Many efforts have sought to apply laboratory in vitro evolution (LIVE) to natural nucleic acid (NA) scaffolds to directly evolve functional molecules. However, synthetic biology can move beyond natural NA scaffolds to create molecular systems whose libraries are far richer reservoirs of functionality than natural NAs. For example, "artificially expanded genetic information systems" (AEGIS) add up to eight nucleotides to the four found in standard NA. Even in its simplest 6-letter versions, AEGIS adds functional groups, information density, and folding motifs that natural NA libraries lack. To complete this vision, however, tools are needed to sequence molecules that are created by AEGIS LIVE. Previous sequencing approaches, including approaches from our laboratories, exhibited limited performance and lost many sequences in diverse library mixtures. Here, we present a new approach that enzymatically transforms the target AEGIS DNA. With higher transliteration efficiency and fidelity, this Enzyme-Assisted Sequencing of Expanded Genetic Alphabet (ESEGA) approach produces substantially better sequences of 6-letter (AGCTZP) DNA than previous transliteration approaches. Therefore, ESEGA facilitates precise analysis of libraries, allowing 'next-generation deep sequencing' to accurately quantify the sequences of 6-letter DNA molecules at single base resolution. We then applied ESEGA to three tasks: (a) defining optimal conditions to perform 6-nucleotide PCR (b) evaluating the fidelity of 6-nucleotide PCR with various DNA polymerases, and (c) extending that evaluation to AEGIS components functionalized with alkynyl and aromatic groups. No other approach at present has this scope, allowing this work to be the next step towards exploiting the potential of expanded DNA alphabets in biotechnology.
Collapse
Affiliation(s)
- Bang Wang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Department of Chemistry, University of Florida, Gainesville, FL, USA, 32611
| | | | - Myong-Jung Kim
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| | - Roberto Laos
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Cen Chen
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Dietlind L. Gerloff
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Luran Manfio
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd, Alachua, FL, USA, 32615
- Firebird Biomolecular Sciences, LLC, Alachua, FL, USA, 32615
| |
Collapse
|
9
|
Jabbari A, Sameiyan E, Yaghoobi E, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Aptamer-based targeted delivery systems for cancer treatment using DNA origami and DNA nanostructures. Int J Pharm 2023; 646:123448. [PMID: 37757957 DOI: 10.1016/j.ijpharm.2023.123448] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/14/2023] [Accepted: 09/24/2023] [Indexed: 09/29/2023]
Abstract
Due to the limitations of conventional cancer treatment methods, nanomedicine has appeared as a promising alternative, allowing improved drug targeting and decreased drug toxicity. In the development of cancer nanomedicines, among various nanoparticles (NPs), DNA nanostructures are more attractive because of their precisely controllable size, shape, excellent biocompatibility, programmability, biodegradability, and facile functionalization. Aptamers are introduced as single-stranded RNA or DNA molecules with recognize their corresponding targets. So, incorporating aptamers into DNA nanostructures led to influential vehicles for bioimaging and biosensing as well as targeted cancer therapy. In this review, the recent developments in the application of aptamer-based DNA origami and DNA nanostructures in advanced cancer treatment have been highlighted. Some of the main methods of cancer treatment are classified as chemo-, gene-, photodynamic- and combined therapy. Finally, the opportunities and problems for targeted DNA aptamer-based nanocarriers for medicinal applications have also been discussed.
Collapse
Affiliation(s)
- Atena Jabbari
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elham Sameiyan
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Yaghoobi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
10
|
Huo B, Wang C, Hu X, Wang H, Zhu G, Zhu A, Li L. Peripheral substitution effects on unnatural base pairs: A case of brominated TPT3 to enhance replication fidelity. Bioorg Chem 2023; 140:106827. [PMID: 37683537 DOI: 10.1016/j.bioorg.2023.106827] [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: 10/09/2022] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
The high fidelity poses a central role in developing unnatural base pairs (UBPs), which means the high pairing capacity of unnatural bases with their partners, and low mispairing with all the natural bases. Different strategies have been used to develop higher-fidelity UBPs, including optimizing hydrophobic interaction forces between UBPs. Variant substituent groups are allowed to fine tune the hydrophobic forces of different UBPs' candidates. However, the modifications on the skeleton of TPT3 base are rare and the replication fidelity of TPT3-NaM remains hardly to improve so far. In this paper, we reasoned that modifying and/or expanding the aromatic surface by Bromo-substituents to slightly increase hydrophobicity of TPT3 might offer a way to increase the fidelity of this pair. Based on the hypothesis, we synthesized the bromine substituted TPT3, 2-bromo-TPT3 and 2, 4-dibromo-TPT3 as the new TPT3 analogs. While the enzyme reaction kinetic experiments showed that d2-bromo-TPT3-dNaM pair and d2, 4-dibromo-TPT3TP-dNaM pair had slightly less efficient incorporation and extension rates than that of dTPT3-dNaM pair, the assays did reveal that the mispairing of 2-bromo-TPT3 and 2, 4-dibromo-TPT3 with all the natural bases could dramatically decrease in contrast to TPT3. Their lower mispairing capacity promoted us to run polymerase chain amplification reactions, and a higher fidelity of d2-bromo-TPT3-dNaM pair could be obtained with 99.72 ± 0.01% of the in vitro replication fidelity than that of dTPT3-dNaM pair, 99.52 ± 0.09%. In addition, d2-bromo-TPT3-dNaM can also be effectively copied in E. coli cells, which showed the same replication fidelity as that of dTPT3-dNaM in the specific sequence, but a higher fidelity in the random sequence context.
Collapse
Affiliation(s)
- Bianbian Huo
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chao Wang
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xiaoqi Hu
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Honglei Wang
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Gongming Zhu
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Anlian Zhu
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Lingjun Li
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China; Pingyuan Laboratory, Henan Normal University, Xinxiang 453007, China.
| |
Collapse
|
11
|
Chang R, Li T, Fu Y, Chen Z, He Y, Sun X, Deng Y, Zhong Y, Xie Z, Yang Y, Liu J, Chen X, Liu H, Zhao Y. A PD-L1 targeting nanotheranostic for effective photoacoustic imaging guided photothermal-immunotherapy of tumor. J Mater Chem B 2023; 11:8492-8505. [PMID: 37594411 DOI: 10.1039/d3tb00221g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Tumor immunotherapy has been partly effective for specific cancers. However, problems such as low immune response, limited antitumor effectiveness, and high antibody costs still persist. Synergistic therapeutic approaches, such as immune checkpoint inhibition in conjunction with photothermal therapy and photoacoustic imaging, are expected to provide approaches for more precise and efficient immunotherapy of tumors. Furthermore, developing alternatives for antibodies, such as PD-L1 aptamers and nanocarriers, would reduce the cost of tumor immunotherapy. Herein, we develop a PD-L1-targeting nanotheranostic to block immune checkpoints for synergistic photothermal-immunotherapy against tumors, along with effective photoacoustic (PA) imaging. The nanotheranostic is synthesized by the modification of gold nanorods (GNRs) with the PD-L1 aptamer (APDL1), which can sensitively and specifically recognize PD-L1 on the tumor cell surface, and mediate nanoparticle accumulation and strong PA signals in tumors. The aptamer is released from GNR through a competition of glutathione (GSH) and is then functionalized as a PD-L1 blockade. In collaboration with the concurrent photothermal therapy, antitumor immunity is significantly augmented by enhancing the filtration of matured dendritic cells and suppressing regulatory T cells, followed by the activation of cytotoxic T cells and inhibition of T cell exhaustion. Such a nanotheranostic modality effectively suppresses tumor growth in mice, representing an appealing platform for both biological imaging and photoimmunotherapy of tumors.
Collapse
Affiliation(s)
- Ruimin Chang
- Department of Dermatology, Xiangya Clinical Research Center for Cancer Immunotherapy, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tan Li
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Yao Fu
- Department of Dermatology, Xiangya Clinical Research Center for Cancer Immunotherapy, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zeyu Chen
- State Key Laboratory of High Performance Complex Manufacturing, College of Mechanical and Electrical Engineering, Central South University, Changsha, 410083, China
| | - Yilang He
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Xin Sun
- State Key Laboratory of High Performance Complex Manufacturing, College of Mechanical and Electrical Engineering, Central South University, Changsha, 410083, China
| | - Yiyi Deng
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Yanqing Zhong
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Zuozhong Xie
- Department of Dermatology, Xiangya Clinical Research Center for Cancer Immunotherapy, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Yang Yang
- College of Biotechnology, Tianjin University of Science & Technology, No. 29, 13th Avenue, TEDA, Tianjin, 300457, China
| | - Jing Liu
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Xiang Chen
- Department of Dermatology, Xiangya Clinical Research Center for Cancer Immunotherapy, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Hong Liu
- Department of Dermatology, Xiangya Clinical Research Center for Cancer Immunotherapy, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Yuetao Zhao
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, 410078, China.
| |
Collapse
|
12
|
Fang L, Shi C, Wang Y, Xiong Z, Wang Y. Exploring the diverse biomedical applications of programmable and multifunctional DNA nanomaterials. J Nanobiotechnology 2023; 21:290. [PMID: 37612757 PMCID: PMC10464147 DOI: 10.1186/s12951-023-02071-2] [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: 04/10/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
DNA nanoparticles hold great promise for a range of biological applications, including the development of cutting-edge treatments and diagnostic tests. Their subnanometer-level addressability enables precise, specific modifications with a variety of chemical and biological entities, making them ideal as diagnostic instruments and carriers for targeted delivery. This paper focuses on the potential of DNA nanomaterials, which offer scalability, programmability, and functionality. For example, they can be engineered to provide highly specific biosensing and bioimaging capabilities and show promise as a platform for disease diagnosis and treatment. Successful operation of various biomedical nanomaterials has been demonstrated both in vitro and in vivo. However, there are still significant challenges to overcome, including the need to improve the scalability and reliability of the technology, and to ensure safety in clinical applications. We discuss these challenges and opportunities in detail and highlight the progress and prospects of DNA nanotechnology for biomedical applications.
Collapse
Affiliation(s)
- Liuru Fang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Chen Shi
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Yuhua Wang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China.
| | - Zuzhao Xiong
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Yumei Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| |
Collapse
|
13
|
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 2023; 25:783-795. [PMID: 37056277 PMCID: PMC10086681 DOI: 10.1016/j.bioactmat.2022.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
Collapse
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
| | - 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
| | - 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
| |
Collapse
|
14
|
Ai L, Jiang X, Zhang K, Cui C, Liu B, Tan W. Tools and techniques for the discovery of therapeutic aptamers: recent advances. Expert Opin Drug Discov 2023; 18:1393-1411. [PMID: 37840268 DOI: 10.1080/17460441.2023.2264187] [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: 03/15/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers. AREAS COVERED The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility. EXPERT OPINION The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.
Collapse
Affiliation(s)
- Lili Ai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Xinyi Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Kejing Zhang
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Bo Liu
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, The People's Republic of China
| |
Collapse
|
15
|
Li Y, Abraham C, Suslov O, Yaren O, Shaw RW, Kim MJ, Wan S, Marliere P, Benner SA. Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets. ACS Synth Biol 2023; 12:1772-1781. [PMID: 37227319 PMCID: PMC10911313 DOI: 10.1021/acssynbio.3c00060] [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: 05/26/2023]
Abstract
One horizon in synthetic biology seeks alternative forms of DNA that store, transcribe, and support the evolution of biological information. Here, hydrogen bond donor and acceptor groups are rearranged within a Watson-Crick geometry to get 12 nucleotides that form 6 independently replicating pairs. Such artificially expanded genetic information systems (AEGIS) support Darwinian evolution in vitro. To move AEGIS into living cells, metabolic pathways are next required to make AEGIS triphosphates economically from their nucleosides, eliminating the need to feed these expensive compounds in growth media. We report that "polyphosphate kinases" can be recruited for such pathways, working with natural diphosphate kinases and engineered nucleoside kinases. This pathway in vitro makes AEGIS triphosphates, including third-generation triphosphates having improved ability to survive in living bacterial cells. In α-32P-labeled forms, produced here for the first time, they were used to study DNA polymerases, finding cases where third-generation AEGIS triphosphates perform better with natural enzymes than second-generation AEGIS triphosphates.
Collapse
Affiliation(s)
- Yubing Li
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd., Alachua, Florida 32615 United States
| | - Clay Abraham
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd., Alachua, Florida 32615 United States
| | - Oleg Suslov
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd., Alachua, Florida 32615 United States
| | - Ozlem Yaren
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd., Alachua, Florida 32615 United States
| | - Ryan W. Shaw
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd., Alachua, Florida 32615 United States
| | - Myong-Jung Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd., Alachua, Florida 32615 United States
| | - Shuo Wan
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd., Alachua, Florida 32615 United States
| | - Philippe Marliere
- Institute of Systems & Synthetic Biology, Génopole, 5 rue Desbruères, 91030 Evry Cedex France
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd., Alachua, Florida 32615 United States
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd., Alachua, Florida 32615 United States
| |
Collapse
|
16
|
Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH. Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. J Am Chem Soc 2023; 145:8560-8568. [PMID: 37036666 DOI: 10.1021/jacs.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today used in molecular diagnostics; to support directed evolution to create medically useful receptors, ligands, and catalysts; and to explore issues related to the early evolution of life. Further applications are limited by the inability to directly sequence DNA containing nonstandard nucleotides. Nanopore sequencing is well-suited for this purpose, as it does not require enzymatic synthesis, amplification, or nucleotide modification. Here, we take the first steps to realize nanopore sequencing of an 8-letter "hachimoji" expanded DNA alphabet by assessing its nanopore signal range using the MspA (Mycobacterium smegmatis porin A) nanopore. We find that hachimoji DNA exhibits a broader signal range in nanopore sequencing than standard DNA alone and that hachimoji single-base substitutions are distinguishable with high confidence. Because nanopore sequencing relies on a molecular motor to control the motion of DNA, we then assessed the compatibility of the Hel308 motor enzyme with nonstandard nucleotides by tracking the translocation of single Hel308 molecules along hachimoji DNA, monitoring the enzyme kinetics and premature enzyme dissociation from the DNA. We find that Hel308 is compatible with hachimoji DNA but dissociates more frequently when walking over C-glycoside nucleosides, compared to N-glycosides. C-glycocide nucleosides passing a particular site within Hel308 induce a higher likelihood of dissociation. This highlights the need to optimize nanopore sequencing motors to handle different glycosidic bonds. It may also inform designs of future alternative DNA systems that can be sequenced with existing motors and pores.
Collapse
Affiliation(s)
- Christopher A Thomas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jessica D Carrasco
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Drew C Smith
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
17
|
He J, Duan Q, Ran C, Fu T, Liu Y, Tan W. Recent progress of aptamer‒drug conjugates in cancer therapy. Acta Pharm Sin B 2023; 13:1358-1370. [PMID: 37139427 PMCID: PMC10150127 DOI: 10.1016/j.apsb.2023.01.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/18/2022] [Accepted: 12/15/2022] [Indexed: 01/28/2023] Open
Abstract
Aptamers are single-stranded DNA or RNA sequences that can specifically bind with the target protein or molecule via specific secondary structures. Compared to antibody-drug conjugates (ADC), aptamer‒drug conjugate (ApDC) is also an efficient, targeted drug for cancer therapy with a smaller size, higher chemical stability, lower immunogenicity, faster tissue penetration, and facile engineering. Despite all these advantages, several key factors have delayed the clinical translation of ApDC, such as in vivo off-target effects and potential safety issues. In this review, we highlight the most recent progress in the development of ApDC and discuss solutions to the problems noted above.
Collapse
Affiliation(s)
- Jiaxuan He
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Qiao Duan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunyan Ran
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Ting Fu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Yuan Liu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Weihong Tan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
18
|
Mosley RJ, Rucci B, Byrne ME. Recent advancements in design of nucleic acid nanocarriers for controlled drug delivery. J Mater Chem B 2023; 11:2078-2094. [PMID: 36806872 DOI: 10.1039/d2tb02325c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Research of nanoscale nucleic acid carriers has garnered attention in recent years due to their distinctive and controllable properties. However, current knowledge is limited in how we can efficiently utilize these systems for clinical applications. Several researchers have pioneered new and innovative nanocarrier drug delivery systems, but understanding physiochemical properties and behavior in vivo is vital to implementing them as clinical drug delivery platforms. In this review, we outline the most significant innovations in the synthesis, physical properties, and utilization of nucleic acid nanocarriers in the past 5 years, addressing the crucial properties which improve nanocarrier characteristics, delivery, and drug release. The challenges of controlling the transport of nucleic acid nanocarriers and therapeutic release for biological applications are outlined. Barriers which inhibit effective transport into tissue are discussed with emphasis on the modifications needed to overcome such obstacles. The novel strategies discussed in this work summarize the pivotal features of modern nucleic nanocarriers and postulate where future developments could revolutionize the translation of these tools into a clinical setting.
Collapse
Affiliation(s)
- Robert J Mosley
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA.
| | - Brendan Rucci
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA.
| | - Mark E Byrne
- Biomimetic and Biohybrid Materials, Biomedical Devices, and Drug Delivery Laboratories, Department of Biomedical Engineering, 201 Mullica Hill Rd, Rowan University, Glassboro, NJ, 08028, USA. .,Department of Chemical Engineering, Rowan University, Glassboro, NJ, 08028, USA
| |
Collapse
|
19
|
Hu X, Zhang J, Xiang Q, Huang G, Yuan Q, Wang Y, Shen Z. Study on Sgc8 Aptamer-mediated Nucleic Acid Nanomaterial-doxorubicin Complex for Tumor Targeted Therapy. Eur J Pharm Biopharm 2023; 186:7-17. [PMID: 36858245 DOI: 10.1016/j.ejpb.2023.02.009] [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: 06/17/2022] [Revised: 02/10/2023] [Accepted: 02/18/2023] [Indexed: 03/03/2023]
Abstract
Chemotherapy is one of the most important treatments for malignant cancers, but most chemotherapeutic drugs are poorly targeted, highly toxic and expensive, resulting in unsatisfactory treatment results for cancer patients. Therefore, intelligent drug delivery platforms are needed to be explored urgently to enhance drug treatment and reduce toxicity on normal cells. Nucleic acid nanomaterials are a class of nanomaterials developed on the basis of the "base complementary pairing principle", which have the advantages of good programmability, high stability, good biocompatibility, and strong targeting. Herein, we present a simple Sgc8 aptamer-modified nucleic acid nanomaterial (Sgc8NM) for the targeted delivery of Doxorubicin (Dox), a widely used chemotherapy drug in clinic. Studies have shown the Sgc8NM-Dox performed a precise treatment effect on target cells and low toxicity on non-target cells, providing a new strategy for the potential application of nanocomposite drugs in targeted cancer delivery.
Collapse
Affiliation(s)
- Xuemei Hu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China; Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325088, P.R. China
| | - Jing Zhang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China
| | - Qi Xiang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China
| | - Guoqiao Huang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China
| | - Quan Yuan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China
| | - Yuzhe Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, Department of Cell Biology and Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, PR China.
| |
Collapse
|
20
|
Benner SA. Rethinking nucleic acids from their origins to their applications. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220027. [PMID: 36633284 PMCID: PMC9835595 DOI: 10.1098/rstb.2022.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/17/2022] [Indexed: 01/13/2023] Open
Abstract
Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand their natural history, on Earth and throughout the cosmos. From this, we have learned that: • the core structure of nucleic acids appears to be a natural outcome of non-biological chemical processes probably in constrained, intermittently irrigated, sub-aerial aquifers on the surfaces of rocky planets like Earth and/or Mars approximately 4.36 ± 0.05 billion years ago; • however, this core is not unique. Synthetic biology has generated many different molecular systems able to support the evolution of molecular information; • these alternatives to standard DNA and RNA support biotechnology, including DNA synthesis, human diagnostics, biomedical research and medicine; • in particular, they support laboratory in vitro evolution (LIVE) with performance to generate catalysts at least 104-105 fold better than standard DNA libraries, enhancing access to receptors and catalysts on demand. Coupling nanostructures to the products of LIVE with expanded DNA offers new approaches for disease therapy; and • nevertheless, a polyelectrolyte structure and size regular building blocks are required for any informational polymer to support Darwinian evolution. These features serve as universal and agnostic biosignatures, useful for seeking life throughout the Solar System. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
Collapse
Affiliation(s)
- Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard no. 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard no. 17, Alachua, FL 32615, USA
| |
Collapse
|
21
|
Cao M, Vial A, Minder L, Guédin A, Fribourg S, Azéma L, Feuillie C, Molinari M, Di Primo C, Barthélémy P, Jeanne LC. Aptamer-based nanotrains and nanoflowers as quinine delivery systems. Int J Pharm X 2023; 5:100172. [PMID: 36861067 PMCID: PMC9969250 DOI: 10.1016/j.ijpx.2023.100172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
In this study, we designed aptamer-based self-assemblies for the delivery of quinine. Two different architectures were designed by hybridizing quinine binding aptamers and aptamers targeting Plasmodium falciparum lactate dehydrogenase (PfLDH): nanotrains and nanoflowers. Nanotrains consisted in controlled assembly of quinine binding aptamers through base-pairing linkers. Nanoflowers were larger assemblies obtained by Rolling Cycle Amplification of a quinine binding aptamer template. Self-assembly was confirmed by PAGE, AFM and cryoSEM. The nanotrains preserved their affinity for quinine and exhibited a higher drug selectivity than nanoflowers. Both demonstrated serum stability, hemocompatibility, low cytotoxicity or caspase activity but nanotrains were better tolerated than nanoflowers in the presence of quinine. Flanked with locomotive aptamers, the nanotrains maintained their targeting ability to the protein PfLDH as analyzed by EMSA and SPR experiments. To summarize, nanoflowers were large assemblies with high drug loading ability, but their gelating and aggregating properties prevent from precise characterization and impaired the cell viability in the presence of quinine. On the other hand, nanotrains were assembled in a selective way. They retain their affinity and specificity for the drug quinine, and their safety profile as well as their targeting ability hold promise for their use as drug delivery systems.
Collapse
Affiliation(s)
- Mengyuan Cao
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France,Corresponding authors.
| | - Anthony Vial
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Laetitia Minder
- Univ. Bordeaux, INSERM, CNRS, IECB, US001, UAR 3033, Pessac, France
| | - Aurore Guédin
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Laurent Azéma
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Cécile Feuillie
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Michael Molinari
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Carmelo Di Primo
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
| | - Leblond Chain Jeanne
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France,Corresponding authors.
| |
Collapse
|
22
|
Okamura H, Trinh GH, Dong Z, Fan W, Nagatsugi F. Synthesis of 6-Alkynylated Purine-Containing DNA via On-Column Sonogashira Coupling and Investigation of Their Base-Pairing Properties. Molecules 2023; 28:molecules28041766. [PMID: 36838761 PMCID: PMC9965804 DOI: 10.3390/molecules28041766] [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: 01/23/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Synthetic unnatural base pairs have been proven to be attractive tools for the development of DNA-based biotechnology. Our group has very recently reported on alkynylated purine-pyridazine pairs, which exhibit selective and stable base-pairing via hydrogen bond formation between pseudo-nucleobases in the major groove of duplex DNA. In this study, we attempted to develop an on-column synthesis methodology of oligodeoxynucleotides (ODNs) containing alkynylated purine derivatives to systematically explore the relationship between the structure and the corresponding base-pairing ability. Through Sonogashira coupling of the ethynyl pseudo-nucleobases and CPG-bound ODNs containing 6-iodopurine, we have demonstrated the synthesis of the ODNs containing three NPu derivatives (NPu1, NPu2, NPu3) as well as three OPu derivatives (OPu1, OPu2, OPu3). The base-pairing properties of each alkynylated purine derivative revealed that the structures of pseudo-nucleobases influence the base pair stability and selectivity. Notably, we found that OPu1 bearing 2-pyrimidinone exhibits higher stability to the complementary NPz than the original OPu, thereby demonstrating the potential of the on-column strategy for convenient screening of the alkynylated purine derivatives with superior pairing ability.
Collapse
Affiliation(s)
- Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Correspondence: (H.O.); (F.N.)
| | - Giang Hoang Trinh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Zhuoxin Dong
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Wenjue Fan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8577, Miyagi, Japan
- Correspondence: (H.O.); (F.N.)
| |
Collapse
|
23
|
Cao M, Vial A, Minder L, Guédin A, Fribourg S, Azéma L, Feuillie C, Molinari M, Di Primo C, Barthélémy P, Leblond Chain J. WITHDRAWN: Aptamer-based nanotrains and nanoflowers as quinine delivery systems. Int J Pharm 2023; 632:122552. [PMID: 36587777 DOI: 10.1016/j.ijpharm.2022.122552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/30/2022]
Abstract
This article has been withdrawn: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been withdrawn at the request of the author, editor and publisher. The publisher regrets that an error occurred during the publication of this paper, which was intended to be published in International Journal of Pharmaceutics: X (not International Journal of Pharmaceutics). This error bears no reflection on the scientific content of this article or its authors. The publisher apologizes to the readers for this unfortunate error.
Collapse
Affiliation(s)
- Mengyuan Cao
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Anthony Vial
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Laetitia Minder
- Univ. Bordeaux, INSERM, CNRS, IECB, US001, UAR 3033, Pessac, France
| | - Aurore Guédin
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Sébastien Fribourg
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Laurent Azéma
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Cécile Feuillie
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Michael Molinari
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, IPB, Université de Bordeaux, Pessac, France
| | - Carmelo Di Primo
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | - Philippe Barthélémy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000, Bordeaux, France
| | | |
Collapse
|
24
|
Liu H, Chen Y, Ju H. Functional DNA structures for cytosensing. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
25
|
Zhao Y, Xie Z, Deng Y, Huang A, He Y, Wen B, Liao X, Chang R, Zhang G, Zhu L, Wang Y, Li T, Zhong Y, Zuo J, Zhang H, Chen M, Liu J, Chen X, Liu H. Photothermal nanobomb blocking metabolic adenosine-A2AR potentiates infiltration and activity of T cells for robust antitumor immunotherapy. CHEMICAL ENGINEERING JOURNAL 2022; 450:138139. [DOI: 10.1016/j.cej.2022.138139] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/03/2024]
|
26
|
Zhang S, Deng J, Li J, Tian F, Liu C, Fang L, Sun J. Advanced microfluidic technologies for isolating extracellular vesicles. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
27
|
Cui M, Zhao Y, Gao W, Cui X, Zhang C, Zhang C, Meng Q. Theoretical Simulation on Regulating the Magnetic Coupling Properties of Diradical Artificial Bases. J Phys Chem A 2022; 126:7820-7828. [DOI: 10.1021/acs.jpca.2c04354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Menglu Cui
- School of Physics and Electronics, Shandong Normal University, Jinan250358, P. R. China
| | - Yu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan250358, P. R. China
| | - Wen Gao
- School of Physics and Electronics, Shandong Normal University, Jinan250358, P. R. China
| | - Xixi Cui
- School of Physics and Electronics, Shandong Normal University, Jinan250358, P. R. China
| | - Chenyang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan250358, P. R. China
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan250358, P. R. China
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan250358, P. R. China
| |
Collapse
|
28
|
Sun L, Ma X, Zhang B, Qin Y, Ma J, Du Y, Chen T. From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma. RSC Chem Biol 2022; 3:1173-1197. [PMID: 36320892 PMCID: PMC9533422 DOI: 10.1039/d2cb00116k] [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: 05/06/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Nucleic acids have been extensively modified in different moieties to expand the scope of genetic materials in the past few decades. While the development of unnatural base pairs (UBPs) has expanded the genetic information capacity of nucleic acids, the production of synthetic alternatives of DNA and RNA has increased the types of genetic information carriers and introduced novel properties and functionalities into nucleic acids. Moreover, the efforts of tailoring DNA polymerases (DNAPs) and RNA polymerases (RNAPs) to be efficient unnatural nucleic acid polymerases have enabled broad application of these unnatural nucleic acids, ranging from production of stable aptamers to evolution of novel catalysts. The introduction of unnatural nucleic acids into living organisms has also started expanding the central dogma in vivo. In this article, we first summarize the development of unnatural nucleic acids with modifications or alterations in different moieties. The strategies for engineering DNAPs and RNAPs are then extensively reviewed, followed by summarization of predominant polymerase mutants with good activities for synthesizing, reverse transcribing, or even amplifying unnatural nucleic acids. Some recent application examples of unnatural nucleic acids with their polymerases are then introduced. At the end, the approaches of introducing UBPs and synthetic genetic polymers into living organisms for the creation of semi-synthetic organisms are reviewed and discussed.
Collapse
Affiliation(s)
- Leping Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Binliang Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Jiezhao Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| |
Collapse
|
29
|
Huo B, Zhang X, Wang C, Wang H, Zhu G, Zhu W, Zhu A, Mei H, Li L. Mechanistic Insight into the Photoinduced Damage of an Unnatural Base Pair. Chemistry 2022; 28:e202201730. [DOI: 10.1002/chem.202201730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Bianbian Huo
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
- State Key Laboratory of Cell Differentiation Regulation and Target Drug Henan Normal University Xinxiang Henan 453007 P. R. China
| | - Xiguang Zhang
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
| | - Chao Wang
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
| | - Honglei Wang
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
- State Key Laboratory of Cell Differentiation Regulation and Target Drug Henan Normal University Xinxiang Henan 453007 P. R. China
| | - Gongming Zhu
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
| | - Wuyuan Zhu
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
| | - Anlian Zhu
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
| | - Hui Mei
- Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic Genomics CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 P. R. China
| | - Lingjun Li
- Department Henan Key Laboratory of Organic Functional Molecule and Drug Innovation Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals School of Chemistry and Chemical Engineering Key Laboratory of Green Chemical Media and Reactions Ministry of Education Henan Normal University Xinxiang Henan 453007 P. R. China
- State Key Laboratory of Cell Differentiation Regulation and Target Drug Henan Normal University Xinxiang Henan 453007 P. R. China
| |
Collapse
|
30
|
Zhang J, Fan Y, Li J, Huang B, Wen H, Ren J. Cascade signal enhancement by integrating DNA walking and RCA reaction-assisted "silver-link" crossing electrode for ultrasensitive electrochemical detection of Staphylococcus aureus. Biosens Bioelectron 2022; 217:114716. [PMID: 36126557 DOI: 10.1016/j.bios.2022.114716] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/28/2022] [Accepted: 09/10/2022] [Indexed: 11/17/2022]
Abstract
The key factor to control the incidence rate of diseases caused by bacteria is rapid detection and early diagnosis. Herein, we proposed a new electrochemical bacterial sensor by coupling DNA walking and rolling circle amplification (RCA) reaction-assisted "silver-link" crossing electrode. Staphylococcus aureus (S. aureus) was detected using this proof-of concept strategy. Aptamer/DNA walker and auxiliary sequence (AS)/RCA reaction probe (RP) duplexes were modified on the electrode surface. The binding of S. aureus with its aptamer caused the disintegration of aptamer/DNA walker and released DNA walker. With the help of Exo III, DNA walker moved along the electrode surface and AS in AS/RP duplex was continuously digested to release RP. By introducing phi29 DNA polymerase, RCA reaction was performed using RP as the reaction primer to form long single-strand RCA extension products between the electrodes. The "silver-link" crossing electrode was formed by metallization of "gene-link", significant conductivity was thus acquired for bacteria detection. The limit of detection (LOD) was 10 CFU/mL and detection time was 2 h. The proposed sensor has high efficiency, good stability and low background signal, human serum and milk samples were successfully detected, which emerged a promising potential in the food monitoring and clinical diagnosis.
Collapse
Affiliation(s)
- Jialin Zhang
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Yaqi Fan
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Jinhui Li
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Bin Huang
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Herui Wen
- Jiangxi Provincial Key Laboratory of Functional Molecular Materials Chemistry, School of Chemistry and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou, 341000, PR China
| | - Jiali Ren
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Changsha, 410004, PR China.
| |
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Flamme M, Katkevica D, Pajuste K, Katkevics M, Sabat N, Hanlon S, Marzuoli I, Püntener K, Sladojevich F, Hollenstein M. Benzoyl and pivaloyl as efficient protecting groups for controlled enzymatic synthesis of DNA and XNA oligonucleotides. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marie Flamme
- Institut Pasteur Structrual Biology and Chemistry FRANCE
| | - Dace Katkevica
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Karlis Pajuste
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Nazarii Sabat
- Institut Pasteur Structural Biology and Chemistry FRANCE
| | - Steven Hanlon
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | - Irene Marzuoli
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | - Kurt Püntener
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | | | - Marcel Hollenstein
- Institut Pasteur Department of Structural Biology and Chemistry 28 Rue du Dr. Roux 75015 Paris FRANCE
| |
Collapse
|
33
|
Hoshika S, Shukla MS, Benner SA, Georgiadis MM. Visualizing "Alternative Isoinformational Engineered" DNA in A- and B-Forms at High Resolution. J Am Chem Soc 2022; 144:15603-15611. [PMID: 35969672 DOI: 10.1021/jacs.2c05255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A fundamental property of DNA built from four informational nucleotide units (GCAT) is its ability to adopt different helical forms within the context of the Watson-Crick pair. Well-characterized examples include A-, B-, and Z-DNA. For this study, we created an isoinformational biomimetic polymer, built (like standard DNA) from four informational "letters", but with the building blocks being artificial. This ALternative Isoinformational ENgineered (ALIEN) DNA was hypothesized to support two nucleobase pairs, the P:Z pair matching 2-amino-imidazo-[1,2a]-1,3,5-triazin-[8H]-4-one with 6-amino-3-5-nitro-1H-pyridin-2-one and the B:S pair matching 6-amino-4-hydroxy-5-1H-purin-2-one with 3-methyl-6-amino-pyrimidin-2-one. We report two structures of ALIEN DNA duplexes at 1.2 Å resolution and a third at 1.65 Å. All of these are built from a single self-complementary sequence (5'-CTSZZPBSBSZPPBAG) that includes 12 consecutive ALIEN nucleotides. We characterized the helical, nucleobase pair, and dinucleotide step parameters of ALIEN DNA in these structures. In addition to showing that ALIEN pairs retain basic Watson-Crick pairing geometry, two of the ALIEN DNA structures are characterized as A-form DNA and one as B-form DNA. We identified parameters that map differences effecting the transition between the two helical forms; these same parameters distinguish helical forms of isoinformational natural DNA. Collectively, our analyses suggest that ALIEN DNA retains essential structural features of natural DNA, not only its information density and Watson-Crick pairing but also its ability to adopt two canonical forms.
Collapse
Affiliation(s)
- Shuichi Hoshika
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Madhura S Shukla
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| | - Steven A Benner
- Foundation for Molecular Evolution, 13709 Progress Boulevard, No. 7, Alachua, Florida 32615, United States
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, Indiana 46202, United States
| |
Collapse
|
34
|
Shen C, Li J, Li R, Ma Z, Tao Y, Zhang Q, Wang Z. Effects of Tumor-Derived DNA on CXCL12-CXCR4 and CCL21-CCR7 Axes of Hepatocellular Carcinoma Cells and the Regulation of Sinomenine Hydrochloride. Front Oncol 2022; 12:901705. [PMID: 35860597 PMCID: PMC9289293 DOI: 10.3389/fonc.2022.901705] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Currently, chemokines and their receptors, CXCL12-CXCR4 and CCL21-CCR7 axes, are deemed vital factors in the modulation of angiogenesis and are crucial for the growth and development of liver cancer. Tumor-derived DNA can be recognized by immune cells to induce an autoimmune response. In this study, we demonstrated the mechanism of tumor-derived DNA on the CXCL12-CXCR4 and CCL21-CCR7 axes of hepatocellular carcinoma (HCC) cells and the regulatory effect of sinomenine hydrochloride. Tumor-derived DNA was separated from HCCLM cell lines. Tumor-derived DNA was transfected into SK-Hep1 cells by Lipofectamine 2000. We found that sinomenine hydrochloride reduced the expression of CXCR4, CXCR12, CCR7, and CCL21 in HCC cells, suppressed the growth and invasion of HCC cells, and increased apoptosis. In contrast to the controls, the protein expressions of CXCR4, CXCL12, CCR7, CCL21, P-ERK1/2, MMP-9, and MMP-2 in SK-Hep1 cells were significantly increased after transfection of tumor-derived DNA, while the increase was reversed by sinobine hydrochloride. Acid sinomenine interferes with tumor-derived DNA and affects ERK/MMP signaling via the CXCL12/CXCR4 axis in HCC cells. CXCR4 siRNA and CCR7 siRNA attenuated tumor-derived DNA activation of ERK1/2/MMP2/9 signaling pathways in HCC cells. CXCR4-oe and CCR7-OE enhance the stimulation of erK1/2/MMP2/9 signaling pathway by tumor-derived DNA in HCC cells. Tumor-derived DNA reduced apoptosis and increased invasion of SK-Hep1 cells by CXCL12-CXCR4 axis and CCL21-CCR7 axis, and sinobine hydrochloride reversed this regulation. These results strongly suggest that tumor-derived DNA can increase the growth and invasion of oncocytes via the upregulation of the expression of CXCL12-CXCR4 and CCL21-CCR7 axis and through ERK1/2/MMP2/9 signaling pathway in HCC cells, and sinobine hydrochloride can inhibit this signaling pathway, thus inhibiting HCC cells. These results provide new potential therapeutic targets for blocking the progression of HCC induced by CXCL12-CXCR4 axis and CCL21-CCR7.
Collapse
|
35
|
Hu M, Zhang W, Chen W, Chen Y, Huang Q, Bao Q, Lin T, Wang L, Zhang S. Construction and Biological Evaluation of Multiple Modification Hollow Mesoporous Silicone Doxorubicin Nanodrug Delivery System. AAPS PharmSciTech 2022; 23:180. [PMID: 35761120 DOI: 10.1208/s12249-022-02226-8] [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: 11/01/2021] [Accepted: 01/25/2022] [Indexed: 11/30/2022] Open
Abstract
The combination of functionalized nanoparticles and chemotherapy drugs can effectively target tumor tissue, which can improve efficacy and reduce toxicity. In this article, pPeptide-PDA@HMONs-DOX nanoparticles (phosphopeptide-modified polydopamine encapsulates doxorubicin-loaded hollow mesoporous organosilica nanoparticles) were constructed that based on multiple modification hollow mesoporous organosilica nanoparticles (HMONs). The pPeptide-PDA@HMONs-DOX nanoparticles retain the biological functions of phosphorylated peptide while exhibiting biological safety that are suitable for effective drug delivery and stimulus responsive release. The degradation behaviors showed that pPeptide-PDA@HMONs-DOX has dual-responsive to drug release characteristics of pH and glutathione (GSH). In addition, the prepared pPeptide-PDA@HMONs-DOX nanoparticles have good biological safety, and their anti-tumor efficacy was significantly better than doxorubicin (DOX). This provided new research ideas for the construction of targeted nanodrug delivery systems based on mesoporous silicon. Scheme 1 The preparation of pPeptide-PDA@HMONs-DOX and the process of drug release under multiple responses. (A) Schematic diagram of the synthesis process of pPeptide-PDA@HMONs-DOX. (B) The process in which nanoparticles enter the cell and decompose and release DOX in response to pH and GSH.
Collapse
Affiliation(s)
- Mengru Hu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, Anhui, China
| | - Wenjing Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, Anhui, China
| | - Weidong Chen
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, Anhui, China.,Anhui Province Key Laboratory of Pharmaceutical Preparation Technology and Application, Heifei, 230012, Anhui, China
| | - Yunna Chen
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, Anhui, China
| | - Qianqian Huang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, Anhui, China
| | - Qianqian Bao
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China.,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, Anhui, China
| | - Tongyuan Lin
- The Second People's Hospital of Wuhu, Wuhu, 241000, Anhui, China
| | - Lei Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China. .,Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, Anhui, China. .,Anhui Province Key Laboratory of Pharmaceutical Preparation Technology and Application, Heifei, 230012, Anhui, China.
| | - Shantang Zhang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, Anhui, China. .,The First Affiliated Hospital of USTC, Hefei, 230001, Anhui, China.
| |
Collapse
|
36
|
Wang M, Li X, He F, Li J, Wang HH, Nie Z. The Advances in Designer DNA Nanorobots Enabling Programmable Functions. Chembiochem 2022; 23:e202200119. [DOI: 10.1002/cbic.202200119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Fang He
- Hunan University College of Chemistry and Chemical Engineering CHINA
| | - Juan Li
- Hunan University College of Biology CHINA
| | - Hong-Hui Wang
- Hunan University College of Biology 410082 Changsha CHINA
| | - Zhou Nie
- Hunan University College of Chemistry and Chemical Engineering Yuelushan, Changsha, Hunan, 410082, P.R.China 410082 Changsha CHINA
| |
Collapse
|
37
|
Aliouat H, Peng Y, Waseem Z, Wang S, Zhou W. Pure DNA scaffolded drug delivery systems for cancer therapy. Biomaterials 2022; 285:121532. [DOI: 10.1016/j.biomaterials.2022.121532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/04/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023]
|
38
|
Okamura H, Trinh GH, Dong Z, Masaki Y, Seio K, Nagatsugi F. Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface. Nucleic Acids Res 2022; 50:3042-3055. [PMID: 35234916 PMCID: PMC8989583 DOI: 10.1093/nar/gkac140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/27/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Unnatural base pairs (UBPs) which exhibit a selectivity against pairing with canonical nucleobases provide a powerful tool for the development of nucleic acid-based technologies. As an alternative strategy to the conventional UBP designs, which involve utility of different recognition modes at the Watson–Crick interface, we now report that the exclusive base pairing can be achieved through the spatial separation of recognition units. The design concept was demonstrated with the alkynylated purine (NPu, OPu) and pyridazine (NPz, OPz) nucleosides endowed with nucleobase-like 2-aminopyrimidine or 2-pyridone (‘pseudo-nucleobases’) on their major groove side. These alkynylated purines and pyridazines exhibited exclusive and stable pairing properties by the formation of complementary hydrogen bonds between the pseudo-nucleobases in the DNA major groove as revealed by comprehensive Tm measurements, 2D-NMR analyses, and MD simulations. Moreover, the alkynylated purine-pyridazine pairs enabled dramatic stabilization of the DNA duplex upon consecutive incorporation while maintaining a high sequence-specificity. The present study showcases the separation of the recognition interface as a promising strategy for developing new types of UBPs.
Collapse
Affiliation(s)
- Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Giang Hoang Trinh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Zhuoxin Dong
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| |
Collapse
|
39
|
Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
Collapse
Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| |
Collapse
|
40
|
Guo Y, Cao X, Zheng X, Abbas SJ, Li J, Tan W. Construction of nanocarriers based on nucleic acids and their application in nanobiology delivery systems. Natl Sci Rev 2022; 9:nwac006. [PMID: 35668748 PMCID: PMC9162387 DOI: 10.1093/nsr/nwac006] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/23/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
In recent years, nanocarriers based on nucleic acids (NCNAs) have emerged as powerful and novel nanocarriers that are able to meet the demand for cancer cell-specific targeting. Functional dynamics analysis revealed good biocompatibility, low toxicity, and programmable structures, and their advantages include controllable size and modifiability. The development of novel hybrids has focused on the distinct roles of biosensing, drug and gene delivery, vaccine transport, photosensitization, counteracting drug resistance and functioning as carriers and logic gates. This review is divided into three parts: (1) DNA nanocarriers, (2) RNA nanocarriers, and (3) DNA/RNA hybrid nanocarriers and their biological applications. We also provide perspectives on possible future directions for growth in this field.
Collapse
Affiliation(s)
- Yingshu Guo
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Xiuping Cao
- School of Chemistry and Chemical Engineering, Linyi University, Linyi276005, China
| | - Xiaofei Zheng
- School of Chemistry and Chemical Engineering, Linyi University, Linyi276005, China
| | - Sk Jahir Abbas
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, Shanghai Jiao Tong University School of Medicine, College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Juan Li
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310022, China
| | - Weihong Tan
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou310022, China
| |
Collapse
|
41
|
Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
Collapse
Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
42
|
Liu S, Wang Z, Chen Y, Cao T, Zhao G. Recognition and Selectivity Analysis Monitoring of Multicomponent Steroid Estrogen Mixtures in Complex Systems Using a Group-Targeting Environmental Sensor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14115-14125. [PMID: 34460232 DOI: 10.1021/acs.est.1c03683] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The same class of steroid estrogen mixtures, coexisting in the environment of 17β-estradiol, estrone (E1), and ethinyl estradiol (EE2), have strong ability to disrupt the human endocrine system and are seriously prejudicial to the health of the organism and environmental safety. Herein, a highly sensitive and group-targeting environmental monitoring sensor was fabricated for a comprehensive analysis of multicomponent steroid estrogens (multi-SEs) in complex systems. This breakthrough was based on the highly sensitive photoelectrochemical response composite material CdSe NPs-TiO2 nanotube and highly group-specific aptamers. The optimized procedure exhibited not only high sensitivity in a wide range of concentrations from 0.1 to 50 nM, indeed, the minimum detection limit was 33 pM, but also strong resistance to interference. The affinity and consistent action pockets of this sensor enable selective detection of multi-SEs in complex systems. It subsequently was applied for the analysis of multi-SEs from three real samples in the environment including medical wastewater, river water, and tap water to provide a means to clarify the fate of multi-SEs in the process of migration and transformation. This monitoring sensor has a brilliant application prospect for the identification and monitoring of the same class of endocrine-disrupting chemical mixtures in environmental complex systems.
Collapse
Affiliation(s)
- Siyao Liu
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Zhiming Wang
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Yuqing Chen
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Tongcheng Cao
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| | - Guohua Zhao
- School of Chemical Science and Engineering, Shanghai Key Lab of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China
| |
Collapse
|
43
|
Morihiro K, Moriyama Y, Nemoto Y, Osumi H, Okamoto A. anti-syn Unnatural Base Pair Enables Alphabet-Expanded DNA Self-Assembly. J Am Chem Soc 2021; 143:14207-14217. [PMID: 34450012 DOI: 10.1021/jacs.1c05393] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Self-assembly properties and diversity in higher-order structures of DNA enable programmable tools to be used to construct algorithms at the molecular level. However, the utility of DNA-based programmable tools is hampered by the low orthogonality to natural nucleic acids, especially in complex molecular systems. To address this challenge, we report here the orthogonal regulation of DNA self-assembly by using an unnatural base pair (UBP) formation. Our newly designed UBP AnN:SyN is formed in combination with anti and unusual syn glycosidic conformation with high thermal stability and selectivity. Furthermore, AnC worked as a pH-sensitive artificial nucleobase, which forms a strong base pair with cytosine under a weak acidic condition (pH 6.0). The orthogonal AnN:SyN base pair functioned as a trigger for hybridization chain reaction to provide long nicked double-stranded DNA (ca. 1000 base pairs). This work represents the first example of the orthogonal DNA self-assembly that is nonreactive to natural four-letter alphabets DNA trigger and expands the types of programmable tools that work in a complex environment.
Collapse
Affiliation(s)
- Kunihiko Morihiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuya Moriyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yui Nemoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiraki Osumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| |
Collapse
|
44
|
Shen L, Wang P, Ke Y. DNA Nanotechnology-Based Biosensors and Therapeutics. Adv Healthc Mater 2021; 10:e2002205. [PMID: 34085411 DOI: 10.1002/adhm.202002205] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
Collapse
Affiliation(s)
- Luyao Shen
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Pengfei Wang
- Institute of Molecular Medicine Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| |
Collapse
|
45
|
Lv WY, Li CH, Li YF, Zhen SJ, Huang CZ. Hierarchical Hybridization Chain Reaction for Amplified Signal Output and Cascade DNA Logic Circuits. Anal Chem 2021; 93:3411-3417. [DOI: 10.1021/acs.analchem.0c04483] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wen Yi Lv
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Chun Hong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Yuan Fang Li
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Shu Jun Zhen
- Key Laboratory of Luminescent and Real-Time Analytical System (Southwest University), Chongqing Science and Technology Bureau, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| |
Collapse
|
46
|
Mollarasouli F, Badilli U, Bakirhan NK, Ozkan SA, Ozkan Y. Advanced DNA nanomachines: Strategies and bioapplications. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2020.102290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
47
|
Zhou J, Rao L, Yu G, Cook TR, Chen X, Huang F. Supramolecular cancer nanotheranostics. Chem Soc Rev 2021; 50:2839-2891. [PMID: 33524093 DOI: 10.1039/d0cs00011f] [Citation(s) in RCA: 213] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Among the many challenges in medicine, the treatment and cure of cancer remains an outstanding goal given the complexity and diversity of the disease. Nanotheranostics, the integration of therapy and diagnosis in nanoformulations, is the next generation of personalized medicine to meet the challenges in precise cancer diagnosis, rational management and effective therapy, aiming to significantly increase the survival rate and improve the life quality of cancer patients. Different from most conventional platforms with unsatisfactory theranostic capabilities, supramolecular cancer nanotheranostics have unparalleled advantages in early-stage diagnosis and personal therapy, showing promising potential in clinical translations and applications. In this review, we summarize the progress of supramolecular cancer nanotheranostics and provide guidance for designing new targeted supramolecular theranostic agents. Based on extensive state-of-the-art research, our review will provide the existing and new researchers a foundation from which to advance supramolecular cancer nanotheranostics and promote translationally clinical applications.
Collapse
Affiliation(s)
- Jiong Zhou
- State Key Laboratory of Chemical Engineering, Center for Chemistry of High-Performance & Novel Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China.
| | | | | | | | | | | |
Collapse
|
48
|
Huang X, Blum NT, Lin J, Shi J, Zhang C, Huang P. Chemotherapeutic drug-DNA hybrid nanostructures for anti-tumor therapy. MATERIALS HORIZONS 2021; 8:78-101. [PMID: 34821291 DOI: 10.1039/d0mh00715c] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Compared to traditional drug delivery systems, DNA nanostructure-based drug delivery systems have several advantages including programmable sequences, precise size and shape, high drug payloads, excellent biocompatibility and biodegradability. To date, a wide range of chemotherapeutic drug-DNA hybrid nanostructures have been developed for anti-tumor therapy. In this review, the constructions of various DNA nanostructures for anticancer drug delivery are firstly summarized. Next, the anticancer drug loading methods for DNA nanostructures are presented. Then, the recent applications of chemotherapeutic drug-DNA hybrid nanostructures for drug delivery are highlighted. In the end, the challenges and opportunities of the chemotherapeutic drug-DNA hybrid nanostructure-based delivery system are discussed. The designs of drug-DNA hybrid systems, including the constructions of nanostructures and the strategies for drug loading, largely influence the efficiency of drug delivery. Recent studies have focused on the development of novel drug-DNA hybrid systems to acquire more precise and efficient therapy for various diseases. A systematic review of the design strategies of chemotherapeutic drug-DNA hybrid nanostructures will benefit the innovation and development of the chemotherapeutic drug-based chemotherapy in clinics.
Collapse
Affiliation(s)
- Xiangang Huang
- Marshall Laboratory of Biomedical Engineering, International Cancer Center, Laboratory of Evolutionary Theranostics (LET), School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518060, China.
| | | | | | | | | | | |
Collapse
|
49
|
Zhang K, Li H, Wang W, Cao J, Gan N, Han H. Application of Multiplexed Aptasensors in Food Contaminants Detection. ACS Sens 2020; 5:3721-3738. [PMID: 33284002 DOI: 10.1021/acssensors.0c01740] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The existence of contaminants in food poses a serious threat to human health. In recent years, aptamer sensors (aptasensors) have been developed rapidly for the detection of food contaminants because of their high specificity, design flexibility, and high efficiency. However, the development of high-throughput, highly sensitive, on-site, and cost-effective methods for simultaneous detection of food contaminants is still restricted due to multiple signal overlap or mutual interference and cross-reaction between different analytes with similar molecular structures. To overcome these problems, this Review summarizes some effective strategies from the articles published in recent years about multiplexed aptasensors for the simultaneous detection of food contaminants. This work focuses on the application of multiplexed aptasensors to simultaneously detect antibiotics, pathogens, and mycotoxins in food. These aptasensors mainly contain fluorescent aptasensors, electrochemical aptasensors, surface-enhanced Raman scattering-based aptasensors, microfluidic chip aptasensors, and paper-based multiplexed aptasensors. In addition, this Review also covers the application of nucleic acid cycle amplification and nanomaterial amplification strategies to improve the detection sensitivity. Finally, the limitations and challenges in the design of multiplexed aptasensor are also taken into account.
Collapse
Affiliation(s)
- Kai Zhang
- The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, P.R. China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Hongyang Li
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, Henan, P.R. China
| | - Wenjing Wang
- The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, P.R. China
| | - Jinxuan Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Ning Gan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Faculty of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, P.R. China
| | - Heyou Han
- The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, College of Science, Huazhong Agricultural University, Wuhan 430070, Hubei, P.R. China
| |
Collapse
|
50
|
Fu Z, Xiang J. Aptamer-Functionalized Nanoparticles in Targeted Delivery and Cancer Therapy. Int J Mol Sci 2020; 21:ijms21239123. [PMID: 33266216 PMCID: PMC7730239 DOI: 10.3390/ijms21239123] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/13/2022] Open
Abstract
Using nanoparticles to carry and delivery anticancer drugs holds much promise in cancer therapy, but nanoparticles per se are lacking specificity. Active targeting, that is, using specific ligands to functionalize nanoparticles, is attracting much attention in recent years. Aptamers, with their several favorable features like high specificity and affinity, small size, very low immunogenicity, relatively low cost for production, and easiness to store, are one of the best candidates for the specific ligands of nanoparticle functionalization. This review discusses the benefits and challenges of using aptamers to functionalize nanoparticles for active targeting and especially presents nearly all of the published works that address the topic of using aptamers to functionalize nanoparticles for targeted drug delivery and cancer therapy.
Collapse
Affiliation(s)
- Zhaoying Fu
- Institute of Molecular Biology and Immunology, College of Medicine, Yanan University, Yanan 716000, China
- Correspondence: (Z.F.); (J.X.)
| | - Jim Xiang
- Division of Oncology, University of Saskatchewan, Saskatoon, SK S7N 4H4, Canada
- Correspondence: (Z.F.); (J.X.)
| |
Collapse
|