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Nucleic Acids Analysis SCIENCE CHINA SCIENCE CHINA Chemistry •INVITED REVIEWS• February 2021 Vol.64 No.2: 171–203 https://doi.org/10.1007/s11426-020-9864-7 Nucleic acids analysis Yongxi Zhao1†, Xiaolei Zuo2†, Qian Li3†, Feng Chen1, Yan-Ru Chen4, Jinqi Deng5, Da Han2, Changlong Hao6, Fujian Huang7, Yanyi Huang8, Guoliang Ke9, Hua Kuang6, Fan Li2, Jiang Li10,11, Min Li2, Na Li12, Zhenyu Lin13, Dingbin Liu14, Juewen Liu15, Libing Liu16, Xiaoguo Liu3, Chunhua Lu13, Fang Luo13, Xiuhai Mao2, Jiashu Sun5, Bo Tang12, Fei Wang3, Jianbin Wang17, Lihua Wang10,11, Shu Wang15, Lingling Wu2, Zai-Sheng Wu4, Fan Xia7, Chuanlai Xu6, Yang Yang2, Bi-Feng Yuan18, Quan Yuan9, Chao Zhang2, Zhi Zhu19, Chaoyong Yang2,19*, Xiao-Bing Zhang9*, Huanghao Yang13*, Weihong Tan2,9* & Chunhai Fan2,3* 1Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China; 2Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; 3School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China; 4Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China; 5CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China; 6State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; 7Faculty of Materials Science and Chemistry, Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan 430074, China; 8College of Chemistry and Molecular Engineering, Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; 9State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China; 10Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; 11Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; 12College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, China; 13Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, College of Chemistry, Fuzhou University, Fuzhou 350116, China; 14College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, and Tianjin Key Laboratory of Molecular Recognition and Biosensing, Nankai University, Tianjin 300071, China; 15Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada; 16Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; College of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, China; 17School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology (ICSB), †These authors contributed equally to this work. *Corresponding authors (email: [email protected]; [email protected]; [email protected]; [email protected]; [email protected]) © Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2020 chem.scichina.com link.springer.com 172 Zhao et al. Sci China Chem February (2021) Vol.64 No.2 Chinese Institute for Brain Research (CIBR), Tsinghua University, Beijing 100084, China; 18Department of Chemistry, Wuhan University, Wuhan 430072, China; 19The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China Received July 9, 2020; accepted September 4, 2020; published online December 2, 2020 Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided. nucleic acids analysis, signal amplification, DNA nanotechnology, aptamer, biosensing Citation: Zhao Y, Zuo X, Li Q, Chen F, Chen YR, Deng J, Han D, Hao C, Huang F, Huang Y, Ke G, Kuang H, Li F, Li J, Li M, Li N, Lin Z, Liu D, Liu J, Liu L, Liu X, Lu C, Luo F, Mao X, Sun J, Tang B, Wang F, Wang J, Wang L, Wang S, Wu L, Wu ZS, Xia F, Xu C, Yang Y, Yuan BF, Yuan Q, Zhang C, Zhu Z, Yang C, Zhang XB, Yang H, Tan W, Fan C. Nucleic acids analysis. Sci China Chem, 2021, 64: 171–203, https://doi.org/10.1007/s11426-020-9864-7 1 Introduction Moreover, high-throughput detection techniques, including microarray chip [10,11] and next-generation sequencing Nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic (NGS) [12,13], have been developed for simultaneous de- acid (RNA), are natural biopolymers of nucleotides that tection of thousands of and even more nucleic acid sequences store, encode, transmit and express genetic information [1,2]. of interest. The NGS technique can also be expanded for DNA is composed of a phosphate-deoxyribose sugar back- other biological and biomedical applications, including the bone and the nitrogenous bases adenine (A), cytosine (C), analysis of non-nucleic acid targets [14] and the rapid guanine (G), and thymine (T), while RNA has a ribose sugar screening of small-molecule drugs [15]. Several amplifica- backbone and another base uracil (U) instead of T. Single- tion methods have been utilized to improve the quality of stranded nucleic acids can form double helix structures when sequencing library [16–18]. Furthermore, these nucleic acid hybridizing to complementary sequences, following the techniques play important roles in cellular and in vivo ap- Watson-Crick base-pairing rules (A:T or A:U, G:C) [3]. Both plications. Live-cell imaging analysis with high signal gain DNA sequences and RNA transcripts play crucial roles in has been realized by enzymatic or enzyme-free amplification diverse biological events, which can be exploited to serve as methods [19–25]. Single-molecule visualization of nucleic biomarkers for biological studies and clinical diagnosis. acids or proteins in fixed cells or tissues has also been re- Electrophoresis and blotting are the most widely used ana- ported based on in situ DNA amplification methods [26–29]. lytical techniques for analyzing nucleic acids, which remain DNA or RNA oligonucleotides have been selected as re- to be used to analyze the length or structure and sequence, cognition probes such as aptamers and DNAzymes by the respectively. Their sensitivities, however, are limited to the systematic evolution of ligands by exponential enrichment sub-microgram regime. (SELEX) [30,31]. Most of these probes bind to target mo- Inspired by intracellular DNA replication and RNA tran- lecules (proteins, small molecules, ions, etc.) with equal or scription, in vitro nucleic acid amplification techniques have even higher affinity and specificity than those of antibodies. been developed to improve signal response and detection Innovative bioanalysis methods based on aptamers or sensitivity. They can be in general classified into two cate- DNAzymes have been proposed to enhance detection per- gories, thermal-cycle amplification such as best-known formance [32,33]. Unnatural nucleic acids, such as locked polymerase chain reaction (PCR) [4] and isothermal ampli- nucleic acids (LNAs) and peptide nucleic acids (PNAs), have fication [1,5,6]. The later one is especially useful for tem- been synthesized to improve the hybridization or binding perature-sensitive targets such as live cells and proteins. stability and nuclease resistance [34,35]. Nucleic acids also Bioanalysis at single-cell
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