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Huang Q, Chen X, Meng QF, Yue L, Jiang W, Zhao XZ, Rao L, Chen X, Chen S. Microfluidics-Assisted Fluorescence Mapping of DNA Phosphorothioation. Anal Chem 2022; 94:10479-10486. [PMID: 35834188 DOI: 10.1021/acs.analchem.2c01752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As the key player of a new restriction modification system, DNA phosphorothioate (PT) modification, which swaps oxygen for sulfur on the DNA backbone, protects the bacterial host from foreign DNA invasion. The identification of PT sites helps us understand its physiological defense mechanisms, but accurately quantifying this dynamic modification remains a challenge. Herein, we report a simple quantitative analysis method for optical mapping of PT sites in the single bacterial genome. DNA molecules are fully stretched and immobilized in a microfluidic chip by capillary flow and electrostatic interactions, improving the labeling efficiency by maximizing exposure of PT sites on DNA while avoiding DNA loss and damage. After screening 116 candidates, we identified a bifunctional chemical compound, iodoacetyl-polyethylene glycol-biotin, that can noninvasively and selectively biotinylate PT sites, enabling further labeling with streptavidin fluorescent nanoprobes. With this method, PT sites in PT+ DNA can be easily detected by fluorescence, while almost no detectable ones were found in PT- DNA, achieving real-time visualization of PT sites on a single DNA molecule. Collectively, this facile genome-wide PT site detection method directly characterizes the distribution and frequency of DNA modification, facilitating a better understanding of its modification mechanism that can be potentially extended to label DNAs in different species.
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Affiliation(s)
- Qinqin Huang
- The Second Affiliated Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xingxiang Chen
- The Second Affiliated Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Qian-Fang Meng
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ludan Yue
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore 119074, Singapore
| | - Wei Jiang
- The Second Affiliated Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Xing-Zhong Zhao
- School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lang Rao
- The Second Affiliated Hospital of Zhengzhou University, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China.,Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore 119074, Singapore.,Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore.,Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,Department of Burn and Plastic Surgery, Biomedical Research Center, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
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Liu Y, Zhang J, Guo Y, Wang P, Su Y, Jin X, Zhu X, Zhang C. Drug‐grafted DNA as a novel chemogene for targeted combinatorial cancer therapy. EXPLORATION 2022; 2:20210172. [PMCID: PMC10190944 DOI: 10.1002/exp.20210172] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/09/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Yuhe Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Sixth people's Hospital, School of Medicine, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai China
| | - Jiao Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Sixth people's Hospital, School of Medicine, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai China
| | - Yuanyuan Guo
- Department of Radiology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Ping Wang
- Weigao Research Center Shanghai China
| | - Yue Su
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Sixth people's Hospital, School of Medicine, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai China
| | - Xin Jin
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Sixth people's Hospital, School of Medicine, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Sixth people's Hospital, School of Medicine, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Molecular Medicine, Sixth people's Hospital, School of Medicine, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai China
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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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Wang J, Shang J, Qin Z, Tong A, Xiang Y. Selective and sensitive fluorescence "turn-on" detection of 4-thiouridine in nucleic acids via oxidative amination. Chem Commun (Camb) 2019; 55:13096-13099. [PMID: 31612162 DOI: 10.1039/c9cc06312a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fluorescence "turn-on" method for digestion-free analysis of 4-thiouridine (s4U) in nucleic acids was developed in this work based on the oxidative amination of s4U by fluoresceinamine (FAM-NH2) and periodate (IO4-). It was 125-fold more sensitive for s4U detection than the traditional UV330 absorption method, and showed excellent selectivity to s4U over 2-thiouridine (s2U) analogues and biological thiols.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Zichen Qin
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China.
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Zhang J, Guo Y, Ding F, Pan G, Zhu X, Zhang C. A Camptothecin‐Grafted DNA Tetrahedron as a Precise Nanomedicine to Inhibit Tumor Growth. Angew Chem Int Ed Engl 2019; 58:13794-13798. [DOI: 10.1002/anie.201907380] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Jiao Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yuanyuan Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Fei Ding
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Gaifang Pan
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Xinyuan Zhu
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Chuan Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
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6
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Zhang J, Guo Y, Ding F, Pan G, Zhu X, Zhang C. A Camptothecin‐Grafted DNA Tetrahedron as a Precise Nanomedicine to Inhibit Tumor Growth. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907380] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jiao Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yuanyuan Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Fei Ding
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Gaifang Pan
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Xinyuan Zhu
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Chuan Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
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Chen Y, Zheng T, Li J, Cui J, Deng Z, You D, Yang L. Novel Iodine-induced Cleavage Real-time PCR Assay for Accurate Quantification of Phosphorothioate Modified Sites in Bacterial DNA. Sci Rep 2019; 9:7485. [PMID: 31097783 PMCID: PMC6522622 DOI: 10.1038/s41598-019-44011-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/17/2019] [Indexed: 12/16/2022] Open
Abstract
DNA Phosphorothioate (PT), replacing a non-bridging phosphate oxygen atom with a sulfur atom, is one kind of common DNA modification in bacteria. Whole genome scale description of the location and frequency of PT modification is the key to understand its biological function. Herein we developed a novel method, named with iodine-induced cleavage quantitative real-time PCR (IC-qPCR), to evaluate the frequency of PT modification at a given site in bacterial DNA. The efficiency, dynamic range, sensitivity, reproducibility and accuracy of IC-qPCR were well tested and verified employing an E. coli B7A strain as example. The amplification efficiency of IC-qPCR assay ranged from 91% to 99% with a high correlation coefficient ≥0.99. The limit of quantification was determined as low as 10 copies per reaction for the 607710 and 1818096 sites, and 5 copies for the 302695 and 4120753 sites. Based on the developed IC-qPCR method, the modification frequency of four PTs in E. coli B7A was determined with high accuracy, and the results showed that the PT modification was partial and that the modification frequency varied among investigated PT sites. All these results showed that IC-qPCR was suitable for evaluating the PT modification, which would be helpful to further understand the biological function of PT modification.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinjie Cui
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Litao Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China.
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Fan C, Tamiya E. Editorial: Translating the advances of biosensors from bench to bedside. Biotechnol J 2017; 11:727-8. [PMID: 27273841 DOI: 10.1002/biot.201676010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biosensors have been found with numerous applications in many areas including genetic analysis, detection of infectious diseases, environmental monitoring and forensic analysis. We have witnessed rapid advances in this field, especially with the emergence of nanotechnology in the past decade.
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