1
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Adams MC, Milam VT. Uncovering Molecular Quencher Effects on FRET Phenomena in Microsphere-Immobilized Probe Systems. Anal Chem 2023; 95:13796-13803. [PMID: 37651319 PMCID: PMC10515108 DOI: 10.1021/acs.analchem.3c01064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023]
Abstract
Double-stranded (ds) oligonucleotide probes composed of quencher-dye sequence pairs outperform analogous single-stranded (ss) probes due to their superior target sequence specificity without any prerequisite target labeling. Optimizing sequence combinations for dsprobe design requires promoting a fast, accurate response to a specific target sequence while minimizing spontaneous dsprobe dissociation events. Here, flow cytometry is used to rapidly interrogate the stability and selective responsiveness of 20 candidate LNA and DNA dsprobes to a 24 base-long segment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and ∼243 degenerate RNA sequences serving as model variants. Importantly, in contrast to quantifying binding events of dye-labeled targets via flow cytometry, the current work employs the Förster resonance energy transfer (FRET)-based detection of unlabeled RNA targets. One DNA dsprobe with a 15-base-long hybridization partner containing a central abasic site emerged as very stable yet responsive only to the SARS-CoV-2 RNA segment. Separate displacement experiments, however, indicated that ∼12% of these quencher-capped hybridization partners remain bound, even in the presence of an excess SARS-CoV-2 RNA target. To examine their quenching range, additional titration studies varied the ratios and spatial placement of nonquencher and quencher-capped hybridization partners in the dsprobes. These titration studies indicate that these residual, bound quencher-capped partners, even at low percentages, act as nodes, enabling both static quenching effects within each residual dsprobe as well as longer-range quenching effects on neighboring FAM moieties. Overall, these studies provide insight into practical implications for rapid dsprobe screening and target detection by combining flow cytometry with FRET-based detection.
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Affiliation(s)
- Mary Catherine Adams
- School
of Materials Science and Engineering, Parker H. Petit Institute for Bioengineering, Bioscience Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245 United States
| | - Valeria T. Milam
- School
of Materials Science and Engineering, Parker H. Petit Institute for Bioengineering, Bioscience Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245 United States
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2
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Toehold-mediated biosensors: Types, mechanisms and biosensing strategies. Biosens Bioelectron 2022; 220:114922. [DOI: 10.1016/j.bios.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
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3
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Li S, Cheng Y, Qin M, Zhou G, Li P, Yang L. Intelligent and robust DNA robots capable of swarming into leakless nonlinear amplification in response to a trigger. NANOSCALE HORIZONS 2022; 7:634-643. [PMID: 35527720 DOI: 10.1039/d2nh00018k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Nonlinear DNA signal amplification with an enzyme-free isothermal self-assembly process is uniquely useful in nanotechnology and nanomedicine. However, progress in this direction is hampered by the lack of effective design models of leak-resistant DNA building blocks. Here, we propose two conceptual models of intelligent and robust DNA robots to perform a leakless nonlinear signal amplification in response to a trigger. Two conceptual models are based on super-hairpin nanostructures, which are designed by innovating novel principles in methodology and codifying them into embedded programs. The dynamical and thermodynamical analyses reveal the critical elements and leak-resistant mechanisms of the designed models, and the leak-resistant behaviors of the intelligent DNA robots and morphologies of swarming into nonlinear amplification are separately verified. The applications of the designed models are also illustrated in specific signal amplification and targeted payload enrichment via integration with an aptamer, a fluorescent molecule and surface-enhanced Raman spectroscopy. This work has the potential to serve as design guidelines of intelligent and robust DNA robots and leakless nonlinear DNA amplification, and also as the design blueprint of cargo delivery robots with the performance of swarming into nonlinear amplification in response to a target automatically, facilitating their future applications in biosensing, bioimaging and biomedicine.
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Affiliation(s)
- Shaofei Li
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- School of Life Science, Anhui University, Hefei 230601, Anhui, China
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Yizhuang Cheng
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Miao Qin
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Guoliang Zhou
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- University of Science & Technology of China, Hefei 230026, Anhui, China
| | - Pan Li
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
| | - Liangbao Yang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, Anhui, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui, China
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4
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Eze NA, Milam VT. Quantitative Analysis of In Situ Locked Nucleic Acid and DNA Competitive Displacement Events on Microspheres. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6871-6881. [PMID: 35617467 DOI: 10.1021/acs.langmuir.2c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Synthetic analogues of natural oligonucleotides known as locked nucleic acids (LNAs) offer superior nuclease resistance and cytocompatibility for numerous scenarios ranging from in vitro detection to intracellular imaging of nucleic acids. While recognized as stronger hybridization partners than equivalent DNA residues, quantitative analysis of LNA hybridization activity is lacking, especially with respect to competitive displacement of the original hybridization partner by another oligonucleotide. In the current study, we perform in situ measurements of toehold-mediated competitive displacement of soluble, fluorescently labeled primary targets from probe strands immobilized on microspheres using high throughput flow cytometry. Both LNA-DNA hybrid sequences and pure DNA sequences are employed as the immobilized strands, as soluble, fluorescently labeled 9-base-long primary targets, and as unlabeled 15-base-long secondary or competitive targets. In addition to comparing chemically substituted and unsubstituted sequences, we explore the effects of mismatched primary targets and the location of the toehold segment within the primary duplexes on the resulting displacement profiles. The primary duplex or double-stranded probe (dsprobe) systems implemented here exhibited varying responses to unlabeled secondary targets ranging from surprisingly modest primary target displacement activity despite the presence of a six base-long nucleotide toehold segment at the dsprobe free end to distinctive displacement profiles sensitive to LNA substitutions and the placement of the toehold segment closer to the microsphere surface.
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5
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Zou C, Zhang Q, Zhou C, Cao W. A nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit. NANOSCALE 2022; 14:6585-6599. [PMID: 35421885 DOI: 10.1039/d1nr06861j] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The DNA toehold mediated strand displacement reaction is one of the semi-synthetic biology technologies for next-generation computers. In this article, we present a framework for a novel nonlinear neural network based on an engineered biochemical circuit, which is constructed by several reaction modules including catalysis, degradation and adjustment reaction modules. The proposed neural network possesses an architecture that is similar to that of an error back propagation neural network, and is built of an input layer, hidden layer and output layer. As a proof of concept, we utilize this nonlinear neural network based on an analog DNA toehold mediated strand displacement reaction circuit to learn the standard quadratic form function and analyze the robustness of the nonlinear neural network toward DNA strand concentration detection, DNA strand displacement reaction rate and noise. Unlike in error back propagation neural networks, the adaptive behavior of this DNA molecular neural network system endows it with supervised learning capability. This investigation will highlight the potential of analog DNA displacement reaction circuits for implementing artificial intelligence.
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Affiliation(s)
- Chengye Zou
- School of Mathematics and Statistics, Anyang Normal University, Anyang 455000, China
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China.
- Informedia Electronic Co., Ltd, Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China.
| | - Changjun Zhou
- College of Mathematics and Computer Science, Zhejiang Normal University, Jinhua 321000, China.
| | - Wenyu Cao
- Institution of Information Management and Information system, Dalian University of Technology, Dalian 116024, China
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6
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Xing C, Zheng X, Zhang Q. Constructing DNA logic circuits based on the toehold preemption mechanism. RSC Adv 2021; 12:338-345. [PMID: 35424506 PMCID: PMC8978688 DOI: 10.1039/d1ra08687a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/14/2021] [Indexed: 11/21/2022] Open
Abstract
Strand displacement technology and ribozyme digestion technology have enriched the intelligent toolbox of molecular computing and provided more methods for the construction of DNA logic circuits. In recent years, DNA logic circuits have developed rapidly, and their scalability and accuracy in molecular computing and information processing have been fully demonstrated. However, existing DNA logic circuits still have some problems such as high complexity of DNA strands (number of DNA strands) hindering the expansion of practical computing tasks. In view of the above problems, we presented a toehold preemption mechanism and applied it to construct DNA logic circuits using E6-type DNAzymes, such as half adder circuit, half subtractor circuit, and 4-bit square root logic circuit. Different from the dual-track logic expressions, all the signals in the circuits of this study were monorail which substantially reduced the number of DNA strands in the DNA logic circuits. The presented preemption mechanism provides a way to simplify the implementation of large and complex DNA integrated circuits.
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Affiliation(s)
- Cuicui Xing
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education Dalian 116622 China
| | - Xuedong Zheng
- College of Computer Science, Shenyang Aerospace University Shenyang 110136 China
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education Dalian 116622 China
- School of Computer Science and Technology, Dalian University of Technology Dalian 116024 China
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7
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Kundu N, Young BE, Sczepanski JT. Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes. Nucleic Acids Res 2021; 49:6114-6127. [PMID: 34125895 PMCID: PMC8216467 DOI: 10.1093/nar/gkab499] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Dynamic DNA nanodevices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation remains challenging due to nuclease degradation and other cellular factors. Use of l-DNA, the nuclease resistant enantiomer of native d-DNA, provides a promising solution. On this basis, we recently developed a strand displacement methodology, referred to as ‘heterochiral’ strand displacement, that enables robust l-DNA nanodevices to be sequence-specifically interfaced with endogenous d-nucleic acids. However, the underlying reaction – strand displacement from PNA–DNA heteroduplexes – remains poorly characterized, limiting design capabilities. Herein, we characterize the kinetics of strand displacement from PNA–DNA heteroduplexes and show that reaction rates can be predictably tuned based on several common design parameters, including toehold length and mismatches. Moreover, we investigate the impact of nucleic acid stereochemistry on reaction kinetics and thermodynamics, revealing important insights into the biophysical mechanisms of heterochiral strand displacement. Importantly, we show that strand displacement from PNA–DNA heteroduplexes is compatible with RNA inputs, the most common nucleic acid target for intracellular applications. Overall, this work greatly improves the understanding of heterochiral strand displacement reactions and will be useful in the rational design and optimization of l-DNA nanodevices that operate at the interface with biology.
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Affiliation(s)
- Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Brian E Young
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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8
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Liu C, Liu Y, Zhu E, Zhang Q, Wei X, Wang B. Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement. Nucleic Acids Res 2020; 48:10691-10701. [PMID: 33045746 PMCID: PMC7641751 DOI: 10.1093/nar/gkaa835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 01/19/2023] Open
Abstract
Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.
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Affiliation(s)
- Chanjuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Enqiang Zhu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
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9
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Li S, Li P, Ge M, Wang H, Cheng Y, Li G, Huang Q, He H, Cao C, Lin D, Yang L. Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility. Nucleic Acids Res 2020; 48:2220-2231. [PMID: 32020194 PMCID: PMC7049695 DOI: 10.1093/nar/gkaa016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/30/2019] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
Hybridization chain reaction (HCR) was a significant discovery for the development of nanoscale materials and devices. One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator. Here, we systematically analyze the sources of leakage and refine leak-resistant rule by using molecular thermodynamics and dynamics, biochemical and biophysical methods. Transient melting of DNA hairpin is revealed to be the underlying cause of leakage and that this can be mitigated through careful consideration of the sequence thermodynamics. The transition threshold of the energy barrier is proposed as a testing benchmark of leak-resistance DNA hairpins. The universal design of DNA hairpins is illustrated by the analysis of hsa-miR-21-5p as biomarker when used in conjunction with surface-enhanced Raman spectroscopy. We further extend the strategy for specific signal amplification of miRNA homologs. Significantly, it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification, and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.
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Affiliation(s)
- Shaofei Li
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,School of Life Science, Anhui University, Hefei, Anhui 230601, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Pan Li
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Meihong Ge
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hongzhi Wang
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Yizhuang Cheng
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Gan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huan He
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Chentai Cao
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dongyue Lin
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Liangbao Yang
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China.,Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui 230031, China
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10
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Tang W, Zhong W, Tan Y, Wang GA, Li F, Liu Y. DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants. Top Curr Chem (Cham) 2020; 378:10. [PMID: 31894426 DOI: 10.1007/s41061-019-0274-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023]
Abstract
Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.
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Affiliation(s)
- Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Guan A Wang
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada
| | - Feng Li
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada. .,College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China. .,Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, China.
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11
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Li L, Zhang W, Tang X, Li Z, Wu Y, Xiao X. Fine and bidirectional regulation of toehold-mediated DNA strand displacement by a wedge-like DNA tool. Chem Commun (Camb) 2020; 56:8794-8797. [DOI: 10.1039/d0cc03722b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We established a novel wedge-like tool that could subtly and bidirectionally regulate the DNA strand displacement kinetics.
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Affiliation(s)
- Longjie Li
- Institute of Reproductive Health
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430030
- China
| | - Wenkai Zhang
- Institute of Reproductive Health
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430030
- China
| | - Xiaofeng Tang
- Institute of Reproductive Health
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430030
- China
| | - Zejian Li
- Institute of Reproductive Health
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430030
- China
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- School of Chemistry and Chemical Engineering
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Xianjin Xiao
- Institute of Reproductive Health
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430030
- China
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12
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Bader A, Cockroft SL. Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices. Chem Commun (Camb) 2020; 56:5135-5138. [DOI: 10.1039/d0cc00882f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Simple design principles improve conformational stability and decrease strand leakage by two orders of magnitude.
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Affiliation(s)
- Antoine Bader
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh EH9 3FJ
- UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh EH9 3FJ
- UK
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13
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Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 367] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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14
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Yu W, Tang L, Qiu JH, Zhang Z, Zhou LL, Li JL, Xie GM. Systematic comparison between toehold exchange and toehold displacement: exploration for highly specific and sensitive DNA detection. RSC Adv 2017. [DOI: 10.1039/c7ra07481f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The detection of nucleic acid variations with high specificity and sensitivity is essential for the good practice of precision medicine.
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Affiliation(s)
- Wen Yu
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Lan Tang
- The Public Health Center
- The First Affiliated Hospital of Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Ju-Hui Qiu
- State Key Laboratory of Membrane Biology
- Tsinghua-Peking Center for Life Sciences
- School of Life Sciences
- Tsinghua University
- Beijing 100084
| | - Zhang Zhang
- Department of Laboratory Medicine
- Affiliated Hospital of Southwest Medical University
- Luzhou
- P. R. China
| | - Li-Li Zhou
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Jun-Long Li
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
| | - Guo-Ming Xie
- Key Laboratory of Laboratory Medical Diagnostics of Education
- Department of Laboratory Medicine
- Chongqing Medical University
- Chongqing 400016
- P. R. China
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