1
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Yu H, Han X, Wang W, Zhang Y, Xiang L, Bai D, Zhang L, Weng Z, Lv K, Song L, Luo W, Yin N, Zhang Y, Feng T, Wang L, Xie G. Modified Unit-Mediated Strand Displacement Reactions for Direct Detection of Single Nucleotide Variants in Active Double-Stranded DNA. ACS NANO 2024; 18:12401-12411. [PMID: 38701333 DOI: 10.1021/acsnano.4c01511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Accurate identification of single nucleotide variants (SNVs) in key driver genes holds a significant value for disease diagnosis and treatment. Fluorescent probes exhibit tremendous potential in specific, high-resolution, and rapid detection of SNVs. However, additional steps are required in most post-PCR assays to convert double-stranded DNA (dsDNA) products into single-stranded DNA (ssDNA), enabling them to possess hybridization activity to trigger subsequent reactions. This process not only prolongs the complexity of the experiment but also introduces the risk of losing target information. In this study, we proposed two strategies for enriching active double-stranded DNA, involving PCR based on obstructive groups and cleavable units. Building upon this, we explored the impact of modified units on the strand displacement reaction (SDR) and assessed their discriminatory efficacy for mutations. The results showed that detection of low variant allele frequencies (VAF) as low as 0.1% can be achieved. The proposed strategy allowed orthogonal identification of 45 clinical colorectal cancer tissue samples with 100% specificity, and the results were generally consistent with sequencing results. Compared to existing methods for enriching active targets, our approach offers a more diverse set of enrichment strategies, characterized by the advantage of being simple and fast and preserving original information to the maximum extent. The objective of this study is to offer an effective solution for the swift and facile acquisition of active double-stranded DNA. We anticipate that our work will facilitate the practical applications of SDR based on dsDNA.
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Affiliation(s)
- Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yangli Zhang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Linguo Xiang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Zhi Weng
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ke Lv
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Na Yin
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yaoyi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Tong Feng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, Biobank Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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2
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Xiong E, Liu P, Deng R, Zhang K, Yang R, Li J. Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro. Natl Sci Rev 2024; 11:nwae118. [PMID: 38742234 PMCID: PMC11089818 DOI: 10.1093/nsr/nwae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/16/2024] Open
Abstract
Single-nucleotide variants (SNVs) are the most common type variation of sequence alterations at a specific location in the genome, thus involving significant clinical and biological information. The assay of SNVs has engaged great awareness, because many genome-wide association studies demonstrated that SNVs are highly associated with serious human diseases. Moreover, the investigation of SNV expression levels in single cells are capable of visualizing genetic information and revealing the complexity and heterogeneity of single-nucleotide mutation-related diseases. Thus, developing SNV assay approaches in vitro, particularly in single cells, is becoming increasingly in demand. In this review, we summarized recent progress in the enzyme-free and enzyme-mediated strategies enabling SNV assay transition from sensing interface to the test tube and single cells, which will potentially delve deeper into the knowledge of SNV functions and disease associations, as well as discovering new pathways to diagnose and treat diseases based on individual genetic profiles. The leap of SNV assay achievements will motivate observation and measurement genetic variations in single cells, even within living organisms, delve into the knowledge of SNV functions and disease associations, as well as open up entirely new avenues in the diagnosis and treatment of diseases based on individual genetic profiles.
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Affiliation(s)
- Erhu Xiong
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Pengfei Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Ronghua Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Jinghong Li
- Department of Chemistry, Center for Bioanalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Beijing Institute of Life Science and Technology, Beijing 102206, China
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3
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Wang X, Chen T, Ping Y, Dai Y, Yu P, Xie Y, Liu Z, Sun B, Duan X, Tao Z. Sequence-Guided Localization of DNA Hybridization Enables Highly Selective and Robust Genotyping. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307985. [PMID: 38084466 DOI: 10.1002/smll.202307985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/28/2023] [Indexed: 05/18/2024]
Abstract
Genetic variations are always related to human diseases or susceptibility to therapies. Nucleic acid probes that precisely distinguish closely related sequences become an indispensable requisite both in research and clinical applications. Here, a Sequence-guided DNA LOCalization for leaKless DNA detection (SeqLOCK) is introduced as a technique for DNA hybridization, where the intended targets carrying distinct "guiding sequences" act selectively on the probes. In silicon modeling, experimental results reveal considerable agreement (R2 = 0.9228) that SeqLOCK is capable of preserving high discrimination capacity at an extraordinarily wide range of target concentrations. Furthermore, SeqLOCK reveals high robustness to various solution conditions and can be directly adapted to nucleic acid amplification techniques (e.g., polymerase chain reaction) without the need for laborious pre-treatments. Benefiting from the low hybridization leakage of SeqLOCK, three distinct variations with a clinically relevant mutation frequency under the background of genomic DNA can be discriminated simultaneously. This work establishes a reliable nucleic acid hybridization strategy that offers great potential for constructing robust and programmable systems for molecular sensing and computing.
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Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Tao Chen
- Department of Blood Transfusion, Zhejiang Hospital, Hangzhou, 310052, China
| | - Ying Ping
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Yibei Dai
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Pan Yu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Yiyi Xie
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Zhenping Liu
- Department of Laboratory Medicine, Yuhang Branch of the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310058, China
| | - Bohao Sun
- Department of Pathology, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310009, China
| | - Xiuzhi Duan
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
| | - Zhihua Tao
- Department of Laboratory Medicine, the Second Affiliated Hospital of Zhejiang University, Hangzhou, 310000, China
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4
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Liu S, Wu J, Li S, Wang L. DNA Polymerase-Steered Self-Propelled and Self-Enhanced DNA Walker for Rapid and Distinctly Amplified Electrochemical Sensing. Anal Chem 2024; 96:828-838. [PMID: 38158364 DOI: 10.1021/acs.analchem.3c04340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The development of a simple, rapid, easy-to-operate, and ultrasensitive DNA walker-based sensing system is challenging but would be very intriguing for the enormous applications in biological analysis and disease monitoring. Herein, a new self-propelled and self-enhanced DNA walking strategy was developed on the basis of a simple DNA polymerase-steered conversion from a typical alternate DNA assembly process. The sensing platform was fabricated easily by immobilizing only one hairpin probe (H1) and the sensing process was based on a simple one-step mixing with another hairpin-like DNA probe (H2) and DNA polymerase. The DNA polymerization could achieve target recycling and successive DNA walking steps. Interestingly, along with each DNA walking step, the new DNA walker sequence could be autonomously accumulated for a self-enhanced DNA walking effect. This provided a multilevel signal amplification ability for the ultrasensitive detection of the target with a low detection limit of 0.18 fM. Moreover, it could greatly reduce the reaction time with the sensing process finished within 1 h. The detection selectivity and the applicative potential in a complicated biological matrix were also demonstrated. Furthermore, the flexible control of sensing modes (self-enhanced DNA walking or the alternate DNA assembly) by using DNA polymerase or not offered a powerful means for sensing performance modulation. It thus opens a new avenue toward the development of a DNA walker-based sensing platform with both rapid and ultrasensitive features and might hold a huge potential for point-of-care diagnostic applications.
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Affiliation(s)
- Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Jialiang Wu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Shuang Li
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Li Wang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
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5
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Huang Y, Cheng Z, Xu LP, Zhang X, Liu G. Lateral flow DNA biosensor for visual detection of nucleic acid with triple-helix DNA functionalized carbon nanotube. Anal Chim Acta 2023; 1276:341604. [PMID: 37573103 DOI: 10.1016/j.aca.2023.341604] [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: 05/05/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 08/14/2023]
Abstract
We describe a novel lateral flow DNA biosensor (LFDB) based on carbon nanotube (CNT) and triple helix DNA (THD). The carboxylated CNT was first conjugated with amine-modified auxiliary single-stranded DNA probe (P1) by dehydration reaction and used as signal probe. A main DNA probe (P0) was introduced to react with the P1 and formed the THD on the CNT surface. Because of the large spatial effect, P1 was in an inactive state and cannot hybridize with the capture DNA probe (P2) fixed on the LFDB test area. When the target DNA was present, P0 in the triple helix DNA hybridized with the target DNA due to the stronger base action, and the decomposition of the triple helix structure exposed P1. Therefore, P1 on CNT surface was activated to hybridize with P2. The CNT along with P1 was thus captured at the test area and accumulated to show a black line, which can be observed by naked eye for qualitative analysis and recorded with a portable grayscale reader for quantitative analysis. Single-stranded DNA was used as a target to prove the feasibility of the model. Under the best experimental conditions, the THD-CNT based LFDB was able to detect the lowest DNA concentration of 15 pM, which is 2.67 times better than that of the traditional duplex CNT-based LFDB. It should be noted that the LFDB based on THD functionalized CNT can differentiate between one-base-mismatched DNA and the complementary target DNA, can detected target DNA in 10% human serum, and can be employed as a versatile platform to detect various target (proteins, small molecular) by changing the sequence of P0. This biosensor platform has enormous potential in the point-of-care detection of a rich diversity of analytes for clinical diagnosis and biomedical research.
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Affiliation(s)
- Yan Huang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Zhihao Cheng
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Li-Ping Xu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Guodong Liu
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, Shandong, 276005, China.
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6
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Hybridization chain reaction-mediated Fe2MoO4 bimetallic nanozyme for colorimetric risk prediction of bladder cancer. Biosens Bioelectron 2022; 210:114272. [DOI: 10.1016/j.bios.2022.114272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022]
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7
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Chen L, Huang H, Wang Z, Deng K, Huang H. Sensitive fluorescence detection of pathogens based on target nucleic acid sequence-triggered transcription. Talanta 2022; 243:123352. [DOI: 10.1016/j.talanta.2022.123352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022]
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8
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The Mechanistic Integration and Thermodynamic Optimality of a Nanomotor. Symmetry (Basel) 2022. [DOI: 10.3390/sym14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
The performance of artificial nanomotors is still far behind nature-made biomolecular motors. A mechanistic disparity between the two categories exists: artificial motors often rely on a single mechanism to rectify directional motion, but biomotors integrate multiple mechanisms for better performance. This study proposes a design for a motor-track system and shows that by introducing asymmetric compound foot-track interactions, both selective foot detachment and biased foot-track binding arise from the mechanics of the system. The two mechanisms are naturally integrated to promote the motility of the motor towards being unidirectional, while each mechanism alone only achieves 50% directional fidelity at most. Based on a reported theory, the optimization of the motor is conducted via maximizing the directional fidelity. Along the optimization, the directional fidelity of the motor is raised by parameters that concentrate more energy on driving selective-foot detachment and biased binding, which in turn promotes work production due to the two energies converting to work via a load attached. However, the speed of the motor can drop significantly after the optimization because of energetic competition between speed and directional fidelity, which causes a speed-directional fidelity tradeoff. As a case study, these results test thermodynamic correlation between the performances of a motor and suggest that directional fidelity is an important quantity for motor optimization.
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9
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Na HK, Shon HK, Son HY, Jang E, Joh S, Huh YM, Castner DG, Lee TG. Utilization of chromogenic enzyme substrates for signal amplification in multiplexed detection of biomolecules using surface mass spectrometry. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 332:129452. [PMID: 33519092 PMCID: PMC7845929 DOI: 10.1016/j.snb.2021.129452] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
MicroRNAs (miRNAs) are important post-transcriptional gene regulators and can serve as potential biomarkers for many diseases. Most of the current miRNA detection techniques require purification from biological samples, amplification, labeling, or tagging, which makes quantitative analysis of clinically relevant samples challenging. Here we present a new strategy for the detection of miRNAs with uniformity over a large area based on signal amplification using enzymatic reactions and measurements using time-of-flight secondary ion mass spectrometry (ToF-SIMS), a sensitive surface analysis tool. This technique has high sequence specificity through hybridization with a hairpin DNA probe and allows the identification of single-base mismatches that are difficult to distinguish by conventional mass spectrometry. We successfully detected target miRNAs in biological samples without purification, amplification, or labeling of target molecules. In addition, by adopting a well-known chromogenic enzymatic reaction from the field of biotechnology, we extended the use of enzyme-amplified signal enhancement ToF (EASE-ToF) to protein detection. Our strategy has advantages with respect to scope, quantification, and throughput over the currently available methods, and is amenable to multiplexing based on the outstanding molecular specificity of mass spectrometry (MS). Therefore, our technique not only has the potential for use in clinical diagnosis, but also provides evidence that MS can serve as a useful readout for biosensing to perform multiplexed analysis extending beyond the limitations of existing technology.
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Affiliation(s)
- Hee-Kyung Na
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
| | - Hyun Kyong Shon
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
| | - Hye Young Son
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Korea
| | - Eunji Jang
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Korea
| | - Sunho Joh
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
- Department of Nano Science, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Yong-Min Huh
- Department of Radiology, College of Medicine, Yonsei University, Seoul 03722, Korea
| | - David G. Castner
- National ESCA and Surface Analysis Center for Biomedical Problems, Departments of Bioengineering and Chemical Engineering, University of Washington, Seattle, WA 98195-1653, USA
| | - Tae Geol Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea
- Department of Nano Science, University of Science and Technology (UST), Daejeon 34113, Korea
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10
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Wang GA, Xie X, Mansour H, Chen F, Matamoros G, Sanchez AL, Fan C, Li F. Expanding detection windows for discriminating single nucleotide variants using rationally designed DNA equalizer probes. Nat Commun 2020; 11:5473. [PMID: 33122648 PMCID: PMC7596233 DOI: 10.1038/s41467-020-19269-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications. Herein, we introduce a DNA equalizer gate (DEG) approach, a class of simulation-guided nucleic acid hybridization probes that drastically expand detection windows for discriminating single nucleotide variants in double-stranded DNA (dsDNA) via the user-definable transformation of the quantitative relationship between the detection signal and target concentrations. A thermodynamic-driven theoretical model was also developed, which quantitatively simulates and predicts the performance of DEG. The effectiveness of DEG for expanding detection windows and improving sequence selectivity was demonstrated both in silico and experimentally. As DEG acts directly on dsDNA, it is readily adaptable to nucleic acid amplification techniques, such as polymerase chain reaction (PCR). The practical usefulness of DEG was demonstrated through the simultaneous detection of infections and the screening of drug-resistance in clinical parasitic worm samples collected from rural areas of Honduras.
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Affiliation(s)
- Guan A Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Xiaoyu Xie
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Hayam Mansour
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Department of Cell Biology, National Research Centre, Cairo, 12622, Egypt
| | - Fangfang Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Gabriela Matamoros
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Microbiology Research Institute, National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - Ana L Sanchez
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Microbiology Research Institute, National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 201240, Shanghai, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China.
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada.
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11
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Zhao Y, Feng Y, Zhang Y, Xia P, Xiao Z, Wang Z, Yan H. Combining competitive sequestration with nonlinear hybridization chain reaction amplification: an ultra-specific and highly sensitive sensing strategy for single-nucleotide variants. Anal Chim Acta 2020; 1130:107-116. [PMID: 32892930 DOI: 10.1016/j.aca.2020.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022]
Abstract
Highly specific and sensitive detection of single-nucleotide variants (SNVs) is of central importance in disease diagnosis and pharmacogenomics. However, it remains a great challenge to successfully detect very low amounts of mutant SNV sequences in real samples in which a SNV sequence may be surrounded by high levels of closely related wild-type sequences. Herein, we propose an ultra-specific and highly sensitive SNV sensing strategy by combining the competitive sequestration with the nonlinear hybridization chain reaction (HCR) amplification. The rationally designed sequestration hairpin can effectively sequester the large amount of wild-type sequence and thus dramatically improve the hybridization specificity in recognizing SNVs. To improve the detection sensitivity, a new fluorescent signal probe is fabricated by intercalating SYBR Green I dye into the nonlinear HCR based DNA dendrimer to further bind with SNVs for signal amplification. The hyperbranched DNA dendrimer possesses large numbers of DNA duplexes for dye intercalation, thus the signal probe shows strong fluorescence intensity, leading to large fluorescence signal amplification. Taking advantage of the improved hybridization specificity of the competitive sequestration and the enhanced fluorescence response of the nonlinear HCR amplification, the developed sensing strategy enables ultra-specific and highly sensitive detection of SNVs. Taking human pancreatic cancers and colorectal carcinomas related KRAS gene mutations as models, the developed strategy shows remarkably high specificity against 17 SNVs (discrimination factors ranged from 126 to 1001 with a median of 310), and achieves high sensitivity for 6 KRAS mutations (the best resultant detection limit reached 15 pM for KRAS G13D (c.38G > A)). Notably, combined with PCR amplification, our SNV sensing strategy could detect KRAS G12D (c.35G > A) from extracted human genomic DNA samples at abundance as low as 0.05%. This work expands the rule set of designing specific and sensitive SNV sensing strategies and shows promising potential application in clinical diagnosis.
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Affiliation(s)
- Yan Zhao
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
| | - Yuanbo Feng
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Yuanbo Zhang
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Pu Xia
- Key Laboratory of Spectral Imaging Technology, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an, 710119, China
| | - Zihan Xiao
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Ziheng Wang
- Queen Mary University of London Engineering School, NPU, Northwestern Polytechnical University, Xi'an, 710129, China
| | - Hongxia Yan
- MOE Key Laboratory of Material Physics and Chemistry Under Extraordinary Conditions, School of Science, Northwestern Polytechnical University, Xi'an, 710129, China.
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12
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Bai S, Xu B, Zhang Y, Zhang Y, Dang H, Yang S, Zuo C, Zhang L, Li J, Xie G. Tuning the specificity of DNA probes using bulge-loops for low-abundance SNV detection. Biosens Bioelectron 2020; 154:112092. [DOI: 10.1016/j.bios.2020.112092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 12/15/2022]
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13
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Canady TD, Berlyoung AS, Martinez JA, Emanuelson C, Telmer CA, Bruchez MP, Armitage BA. Enhanced Hybridization Selectivity Using Structured GammaPNA Probes. Molecules 2020; 25:molecules25040970. [PMID: 32098111 PMCID: PMC7070858 DOI: 10.3390/molecules25040970] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 11/30/2022] Open
Abstract
High affinity nucleic acid analogues such as gammaPNA (γPNA) are capable of invading stable secondary and tertiary structures in DNA and RNA targets but are susceptible to off-target binding to mismatch-containing sequences. We introduced a hairpin secondary structure into a γPNA oligomer to enhance hybridization selectivity compared with a hairpin-free analogue. The hairpin structure features a five base PNA mask that covers the proximal five bases of the γPNA probe, leaving an additional five γPNA bases available as a toehold for target hybridization. Surface plasmon resonance experiments demonstrated that the hairpin probe exhibited slower on-rates and faster off-rates (i.e., lower affinity) compared with the linear probe but improved single mismatch discrimination by up to a factor of five, due primarily to slower on-rates for mismatch vs. perfect match targets. The ability to discriminate against single mismatches was also determined in a cell-free mRNA translation assay using a luciferase reporter gene, where the hairpin probe was two-fold more selective than the linear probe. These results validate the hairpin design and present a generalizable approach to improving hybridization selectivity.
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Affiliation(s)
- Taylor D. Canady
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - April S. Berlyoung
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - Joe A. Martinez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - Cole Emanuelson
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
| | - Cheryl A. Telmer
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA;
| | - Marcel P. Bruchez
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA;
| | - Bruce A. Armitage
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA; (T.D.C.); (A.S.B.); (J.A.M.); (C.E.); (M.P.B.)
- Correspondence:
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14
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Zhu M, Yu Y, Zhu J, Zhou Y, Su G, Zhu H, Chen Y, Liu M. Single nucleotide variant discrimination by toehold exchange spherical nucleic acids modulated on hierarchical molybdenum disulfide acanthospheres. Chem Commun (Camb) 2020; 56:8599-8602. [DOI: 10.1039/d0cc03425h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Toehold exchange spherical nucleic acids (TESNA) modulated on molybdenum disulfide acanthospheres are proposed for the discrimination of single nucleotide variants (SNVs) with significantly improved sensitivity and specificity.
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Affiliation(s)
- Min Zhu
- School of Pharmacy
- Nantong University
- Nantong
- China
| | - Yanyan Yu
- School of Pharmacy
- Nantong University
- Nantong
- China
| | - Junfeng Zhu
- School of Pharmacy
- Nantong University
- Nantong
- China
| | - Yao Zhou
- School of Pharmacy
- Nantong University
- Nantong
- China
| | - Gaoxing Su
- School of Pharmacy
- Nantong University
- Nantong
- China
| | - Hongyan Zhu
- School of Pharmacy
- Nantong University
- Nantong
- China
| | - Yong Chen
- School of Pharmacy
- Nantong University
- Nantong
- China
| | - Mingkai Liu
- School of Chemistry and Chemical Engineering
- Jiangsu Key Laboratory of Green Synthetic Chemistry for Functional Materials
- Jiangsu Normal University
- Xuzhou
- China
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15
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Liu JB, Wu C, Chen F, Leung CH, Ma DL. A simple iridium(III) dimer as a switch-on luminescent chemosensor for carbon disulfide detection in water samples. Anal Chim Acta 2019; 1083:166-171. [DOI: 10.1016/j.aca.2019.07.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022]
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16
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Shigeto H, Ohtsuki T, Iizuka A, Akiyama Y, Yamamura S. Imaging analysis of EGFR mutated cancer cells using peptide nucleic acid (PNA)-DNA probes. Analyst 2019; 144:4613-4621. [PMID: 31241068 DOI: 10.1039/c9an00725c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung cancer cells harbor various gene mutations in the mRNA sequence of the Epidermal Growth Factor Receptor (EGFR), especially the mutations of exon19del E746-A750, T790M, and L858R. This results in cancer progression and resistance to anticancer drugs (tyrosine kinase inhibitor; TKI). Therefore, the imaging analysis of EGFR mutations is required for the treatment planning for non-small cell lung cancers. This study focused on the imaging analysis of a single nucleotide substitute in EGFR mutated cancer cells. We developed three novel peptide nucleic acid (PNA)-DNA probes for recognizing and detecting the following three gene mutations in EGFR gene mutations. The PNA-DNA probes consist of fluorescein isothiocyanate (FITC) conjugated PNA as a detection probe and Dabcyl conjugated DNA as a quencher probe. The PNA-DNA probes were used to validate the feasibility for detecting three EGFR mutated sequences: exon19del E746-A750, T790M, and L858R. The three probes emitted fluorescent dose-dependent signals against three target DNA and RNA. Using the three PNA-DNA probes, we succeeded in distinguishing three kinds of lung-cancer cell lines (H1975, PC-9, and A549) which have different EGFR mutations by the fluorescence in situ hybridization (FISH) method.
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Affiliation(s)
- Hajime Shigeto
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan.
| | - Takashi Ohtsuki
- Department of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
| | - Akira Iizuka
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka 411-8777, Japan
| | - Shohei Yamamura
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan.
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17
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Zhao H, Shao X, Qing Z, Wang T, Chen X, Yang H, Zhai H. Cobalt‐Catalyzed 2‐(1‐Methylhydrazinyl)pyridine‐Assisted Direct C−H/N−H Functionalization of Benzoyl Hydrazide with Isocyanide: Efficient Synthesis of Iminoisoindolinone Derivatives. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Hua Zhao
- The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking University Shenzhen 518055 People's Republic of China
| | - Xiaoru Shao
- The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking University Shenzhen 518055 People's Republic of China
| | - Zhineng Qing
- The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking University Shenzhen 518055 People's Republic of China
| | - Taimin Wang
- The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking University Shenzhen 518055 People's Republic of China
| | - Xiaoming Chen
- The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking University Shenzhen 518055 People's Republic of China
| | - Hongjian Yang
- The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking University Shenzhen 518055 People's Republic of China
| | - Hongbin Zhai
- The State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking University Shenzhen 518055 People's Republic of China
- The State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical EngineeringLanzhou University Lanzhou 730000 People's Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300071 People's Republic of China
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18
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Zhang X, Yang L, Wang F, Liu Z, Liu R, Ying Q, Fan C, Wu X. Development of a Simple and Cost-Effective Method Based on T7 Endonuclease Cleavage for Detection of Single Nucleotide Polymorphisms. Genet Test Mol Biomarkers 2018; 22:719-723. [PMID: 30484704 DOI: 10.1089/gtmb.2018.0181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIMS Single nucleotide polymorphisms (SNP) can be used as genetic markers and for risk assessment of allele-linked diseases, which can provide information for clinical diagnosis. Large-scale microarray and next-generation sequencing methods have made genome-wide SNP genotyping possible. However, in addition to their high cost, these techniques are dependent on having specialized equipment. Thus, there is a need for a simple genotyping method that can be implemented in a resource-limited environment. METHODS We developed a strategy for SNP genotyping based on T7 Endonuclease I cleavage and an enzyme-linked microparticle immune assay. Using this method, we genotyped two common SNP sites (rs11526468 and rs12979860). The quality of the genotyping process was validated. RESULTS Although a 70% false-negative rate was observed, no false-positive reactions were found. Therefore, multiple parallel repeat reactions can offset the possibility of mutation detection failure. DISCUSSION This method employs a duplicate reagent-dependent procedure, and therefore has the potential for integration into a portable kit for field utilization.
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Affiliation(s)
- Xiaoxiao Zhang
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Lina Yang
- 2 Institute for Hygiene of Ordernance Industry, Xi'an, China
| | - Fang Wang
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Ziyu Liu
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Rongrong Liu
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Qikang Ying
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
| | - Chao Fan
- 3 Department of Infectious Diseases and Center of Liver Diseases, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xingan Wu
- 1 Department of Microbiology, Fourth Military Medical University, Xi'an, China
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19
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Thorat VH, Upadhyay NS, Cheng CH. Nickel-Catalyzed Denitrogenativeortho-Arylation of Benzotriazinones with Organic Boronic Acids: an Efficient Route to Losartan and Irbesartan Drug Molecules. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800923] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | - Chien-Hong Cheng
- Department of Chemistry; National Tsing Hua University; Hsinchu 30013 Taiwan
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20
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Zhong W, Tang W, Fan J, Zhang J, Zhou X, Liu Y. A domain-based DNA circuit for smart single-nucleotide variant identification. Chem Commun (Camb) 2018; 54:1311-1314. [PMID: 29177325 DOI: 10.1039/c7cc07733e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
According to the differential information of four homologous oligonucleotides, two domain-based encoders have been constructed with the molecular information as the input. Based on the one-to-one correspondence between the input and output, SNVs can be identified and their sites can be located at the domain level.
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Affiliation(s)
- Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, P. R. China.
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21
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Li Y, Wang GA, Mason SD, Yang X, Yu Z, Tang Y, Li F. Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants. Chem Sci 2018; 9:6434-6439. [PMID: 30310573 PMCID: PMC6115701 DOI: 10.1039/c8sc02761g] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 06/30/2018] [Indexed: 12/15/2022] Open
Abstract
Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity. We also introduced an auxiliary probe, a molecular fuel capable of tuning the device in solution via noncovalent catalysis. Collectively, our device produced discrimination factors comparable with commonly used molecular probes but improved the assay sensitivity by ∼100 times. Our results also demonstrate that rationally designed DNA probes through computer simulation can be used to quantitatively improve the design and operation of complexed molecular devices and sensors.
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Affiliation(s)
- Yongya Li
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Guan A Wang
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Sean D Mason
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Xiaolong Yang
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Zechen Yu
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
| | - Yanan Tang
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
- College of Chemistry , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan , China 610064
| | - Feng Li
- Department of Chemistry , Centre for Biotechnology , Brock University , 1812 Sir Isaac Brock Way , St. Catharines , Ontario L2S 3A1 , Canada .
- College of Chemistry , Sichuan University , 29 Wangjiang Road , Chengdu , Sichuan , China 610064
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22
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Na HK, Wi JS, Son HY, Ok JG, Huh YM, Lee TG. Discrimination of single nucleotide mismatches using a scalable, flexible, and transparent three-dimensional nanostructure-based plasmonic miRNA sensor with high sensitivity. Biosens Bioelectron 2018; 113:39-45. [DOI: 10.1016/j.bios.2018.04.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/06/2018] [Accepted: 04/16/2018] [Indexed: 01/20/2023]
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23
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Xu J, Fu Y, Xiao Y. Endonuclease IV recognizes single base mismatch on the eighth base 3' to the abasic site in DNA strands for ultra-selective and sensitive mutant-type DNA detection. RSC Adv 2018; 8:27016-27020. [PMID: 35540020 PMCID: PMC9083296 DOI: 10.1039/c8ra04552f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/12/2018] [Indexed: 01/25/2023] Open
Abstract
Since single nucleotide polymorphism (SNP) is related with many diseases and drug metabolic polymorphous and SNP genotyping is rising rapidly in many biological and medical areas, various methods of discriminating SNPs have been developed, one of which is an enzyme-based method. We uncovered a unique property of endonuclease IV due to which it can discriminate single base mismatches in different positions of DNA strands containing an abasic site, and we also discovered a new property: a mismatch in the +8 position could inhibit the cleavage of endonuclease IV. Then, we coupled +8 mismatch with other mismatches along with the discrimination effect of melting temperature to develop a new ultra-selective and sensitive genotyping system, which showed high discrimination factors. The detection limit was as low as 0.05-0.01%. Our new discovery improves the understanding of endonuclease IV. Also, the method could be applied to clinical real samples; thus, it merits further investigation and improvement for application in clinical utilization for early screening of specific diseases.
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Affiliation(s)
- Jiaju Xu
- Department of Anesthesiology, Tongji Hospital, Huazhong University of Science and Technology Wuhan 430030 P. R. China
| | - Yanqiao Fu
- Department of Otorhinolaryngology, Taihe Hospital, Hubei University of Medicine Shiyan 442000 P. R. China
| | - Yan Xiao
- Department of Anesthesiology, Tongji Hospital, Huazhong University of Science and Technology Wuhan 430030 P. R. China
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24
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Dou B, Li J, Jiang B, Yuan R, Xiang Y. Electrochemical screening of single nucleotide polymorphisms with significantly enhanced discrimination factor by an amplified ratiometric sensor. Anal Chim Acta 2018; 1038:166-172. [PMID: 30278899 DOI: 10.1016/j.aca.2018.07.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/14/2018] [Accepted: 07/10/2018] [Indexed: 01/12/2023]
Abstract
The detection of single nucleotide polymorphisms (SNPs) is of great clinical significance to the diagnosis of various genetic diseases and cancers. In this work, the development of an ultrasensitive ratiometric electrochemical sensor for screening SNP with a significantly enhanced discrimination factor is reported. The ferrocene (Fc) and methylene blue (MB) dual-tagged triple helix complex (THC) probes are self-assembled on the gold electrode to construct the sensing interface. The addition of the mutant p53 gene causes the disassembly of the THC probes with the release of the Fc-tagged sequence and the folding of the MB-labeled sequence into a hairpin structure, causing the change in the current response ratio of MB to Fc for monitoring the mutant p53 gene. Such ratio is dramatically enhanced by the toehold-mediated displacement reaction-assisted target recycling amplification with the presence of an assistance hairpin sequence. With the significant signal amplification and the advantageous specificity of the THC probes, sub-femtomolar detection limit and a highly enhanced SNP discrimination factor for the mutant p53 gene can be obtained. Besides, the proof-of-demonstration application of the sensor for diluted real samples has been verified, offering such sensor new opportunities for monitoring various genetic related diseases.
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Affiliation(s)
- Baoting Dou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Jin Li
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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25
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Hu S, Li N, Liu F. Combining cooperativity with sequestration: a novel strategy for discrimination of single nucleotide variants. Chem Commun (Camb) 2018. [PMID: 29528359 DOI: 10.1039/c8cc00838h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a novel strategy for the discrimination of single nucleotide variants (SNVs) by combining cooperativity with sequestration, which displays remarkably high specificity (discrimination factors ranging from 67 to 618 with a median of 194) against 12 model SNVs and can be easily integrated with PCR amplification to detect KRAS G12D mutation.
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Affiliation(s)
- Shichao Hu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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26
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Pei X, Lai T, Tao G, Hong H, Liu F, Li N. Ultraspecific Multiplexed Detection of Low-Abundance Single-Nucleotide Variants by Combining a Masking Tactic with Fluorescent Nanoparticle Counting. Anal Chem 2018; 90:4226-4233. [PMID: 29504392 DOI: 10.1021/acs.analchem.8b00685] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To be able to detect simultaneously multiple single-nucleotide variants (SNVs) with both ultrahigh specificity and low-abundance sensitivity is of pivotal importance for molecular diagnostics and biological research. In this contribution, we for the first time developed a multiplex SNV detection method that combines the masking tactic with fluorescent nanoparticle (FNP) counting based on the sandwich design. The method presents a rivaling performance due to its advantageous features: the masking reagent was designed to hybridize with an extremely large amount of the wild-type sequence to render the assay with high specificity; FNP counting provides a sensitive multiplexed SNV detection; the sandwich design facilitates an easy separation to make the detection free of interferences from the matrix. For single SNV target discrimination, including the 6 most frequently occurring DNA KRAS gene mutations and 2 possible RNA KRAS gene mutations as well as 11 artificial mutations, the discrimination factor ranged from 204 to 1177 with the median being 545. Among the tested 19 SNVs, abundances as low as 0.05% were successfully identified in 14 cases, and an abundance as low as 0.1% was identified for the remaining 5 cases. For multiplexed detection of SNVs in the KRAS gene, abundances as low as 0.05-0.1% were achieved for multiple SNVs occurring at the same and different codons. As low as 0.05% low-abundance detection sensitivity was also achieved for PCR amplicons of human genomic DNA extracted from cell samples. This proposed method presents the potential for ultrahigh specific multiplexed detection of SNVs with low-abundance detection capability, which may be applied to practical applications.
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Affiliation(s)
- Xiaojing Pei
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Tiancheng Lai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Guangyu Tao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Hu Hong
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , P. R. China
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27
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Wu T, Chen W, Yang Z, Tan H, Wang J, Xiao X, Li M, Zhao M. DNA terminal structure-mediated enzymatic reaction for ultra-sensitive discrimination of single nucleotide variations in circulating cell-free DNA. Nucleic Acids Res 2018; 46:e24. [PMID: 29190359 PMCID: PMC5829738 DOI: 10.1093/nar/gkx1218] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 11/08/2017] [Accepted: 11/23/2017] [Indexed: 12/18/2022] Open
Abstract
Sensitive detection of the single nucleotide variants in cell-free DNA (cfDNA) may provide great opportunity for minimally invasive diagnosis and prognosis of cancer and other related diseases. Here, we demonstrate a facile new strategy for quantitative measurement of cfDNA mutations at low abundance in the cancer patients' plasma samples. The method takes advantage of a novel property of lambda exonuclease which effectively digests a 5'-fluorophore modified dsDNA with a 2-nt overhang structure and sensitively responds to the presence of mismatched base pairs in the duplex. It achieves a limit of detection as low as 0.02% (percentage of the mutant type) for BRAFV600E mutation, NRASQ61R mutation and three types of EGFR mutations (G719S, T790M and L858R). The method enabled identification of BRAFV600E and EGFRL858R mutations in the plasma of different cancer patients within only 3.5 h. Moreover, the terminal structure-dependent reaction greatly simplifies the probe design and reduces the cost, and the assay only requires a regular real-time PCR machine. This new method may serve as a practical tool for quantitative measurement of low-abundance mutations in clinical samples for providing genetic mutation information with prognostic or therapeutic implications.
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Affiliation(s)
- Tongbo Wu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Haocheng Tan
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiayu Wang
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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28
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Zhang Z, Hsing IM. Nucleic Acid Self-Assembly Circuitry Aided by Exonuclease III for Discrimination of Single Nucleotide Variants. Anal Chem 2017; 89:12466-12471. [DOI: 10.1021/acs.analchem.7b03564] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zhuo Zhang
- Division
of Biomedical Engineering and ‡Department of Chemical and Biological
Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Division
of Biomedical Engineering and ‡Department of Chemical and Biological
Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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29
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Xiao X, Wu T, Xu L, Chen W, Zhao M. A branch-migration based fluorescent probe for straightforward, sensitive and specific discrimination of DNA mutations. Nucleic Acids Res 2017; 45:e90. [PMID: 28201758 PMCID: PMC5449635 DOI: 10.1093/nar/gkx117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022] Open
Abstract
Genetic mutations are important biomarkers for cancer diagnostics and surveillance. Preferably, the methods for mutation detection should be straightforward, highly specific and sensitive to low-level mutations within various sequence contexts, fast and applicable at room-temperature. Though some of the currently available methods have shown very encouraging results, their discrimination efficiency is still very low. Herein, we demonstrate a branch-migration based fluorescent probe (BM probe) which is able to identify the presence of known or unknown single-base variations at abundances down to 0.3%-1% within 5 min, even in highly GC-rich sequence regions. The discrimination factors between the perfect-match target and single-base mismatched target are determined to be 89-311 by measurement of their respective branch-migration products via polymerase elongation reactions. The BM probe not only enabled sensitive detection of two types of EGFR-associated point mutations located in GC-rich regions, but also successfully identified the BRAF V600E mutation in the serum from a thyroid cancer patient which could not be detected by the conventional sequencing method. The new method would be an ideal choice for high-throughput in vitro diagnostics and precise clinical treatment.
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Affiliation(s)
- Xianjin Xiao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lei Xu
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences and MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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30
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Liu J, Lu Y, Feng L, Wang S, Zhang S, Zhu X, Sheng L, Zhang S, Zhang X. Pinpoint the Positions of Single Nucleotide Polymorphisms by a Nanocluster Dimer. Anal Chem 2017; 89:2622-2627. [DOI: 10.1021/acs.analchem.6b04981] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jie Liu
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Yuexiang Lu
- Institute
of Nuclear and New Energy Technology, Collaborative Innovation Center
of Advanced Nuclear Energy Technology, Beijing Key Lab of Radioactive
Waste Treatment, Tsinghua University, Beijing 100084, P. R. China
| | - Lu Feng
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Song Wang
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Shixi Zhang
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Xuewei Zhu
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Linfeng Sheng
- State
Key Laboratory of Analytical Chemistry for Life Science, Collaborative
Innovation Center of Chemistry for Life Sciences, School of Chemistry
and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Sichun Zhang
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
| | - Xinrong Zhang
- Department
of Chemistry, Tsinghua University, Beijing 100084, P.R. China
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31
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Hu S, Tang W, Zhao Y, Li N, Liu F. Ultra-specific discrimination of single-nucleotide mutations using sequestration-assisted molecular beacons. Chem Sci 2017; 8:1021-1026. [PMID: 28451240 PMCID: PMC5356502 DOI: 10.1039/c6sc03048c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/17/2016] [Indexed: 12/31/2022] Open
Abstract
Reliably distinguishing single-nucleotide mutations (SNMs) at low abundance is of great significance in clinical diagnosis. However, the specificity of most current SNM discrimination methods based on the Watson-Crick hybridization is seriously limited by the cross-reactivity of the probe with closely related unintended sequences. Herein, we propose a sequestration-assisted molecular beacon (MB) strategy for highly specific SNM discrimination. The new SNM discrimination system consists of a target-specific MB and a series of hairpin sequestering agents (SEQs). The rationally designed hairpin SEQs can effectively sequester the corresponding unintended sequences and thus dramatically improve the hybridization specificity of the MB in recognizing SNMs. The developed SNM discrimination method shows remarkably high specificity (discrimination factors ranging from 12 to 1144 with a median of 117) against 20 model SNMs, and can work rapidly and robustly over a wide range of conditions. Notably, our SNM discrimination method can be easily combined with PCR amplification for the detection of KRAS G12D (c.35G>A) and G12V (c.35G>T) mutations at abundance as low as 0.5%. This work expands the rule set of designing hybridization-based SNM discrimination strategies and shows promising potential application in clinical diagnosis.
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Affiliation(s)
- Shichao Hu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Wei Tang
- Institute of Materials , China Academy of Engineering Physics , Mianyang , 621700 , China
| | - Yan Zhao
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Na Li
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences , Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China .
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32
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Li X, Song J, Xue Q, Zhao H, Liu M, Chen B, Liu Y, Jiang W, Li CZ. Sensitive and selective detection of the p53 gene based on a triple-helix magnetic probe coupled to a fluorescent liposome hybridization assembly via rolling circle amplification. Analyst 2017; 142:3598-3604. [DOI: 10.1039/c7an01255a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Developing a sensitive and selective sensing platform for the p53 gene and its mutation analysis is essential and may aid in early cancer screening and assessment of prognosis.
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Affiliation(s)
- Xia Li
- Department of Chemistry
- Liaocheng University
- Liaocheng 252059
- China
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
| | - Juan Song
- Department of Chemistry
- Liaocheng University
- Liaocheng 252059
- China
| | - Qingwang Xue
- Department of Chemistry
- Liaocheng University
- Liaocheng 252059
- China
| | - Haiyan Zhao
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P.R. China
| | - Min Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng 252059
- China
| | - Baoli Chen
- Department of Chemistry
- Liaocheng University
- Liaocheng 252059
- China
| | - Yun Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng 252059
- China
| | - Wei Jiang
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry
- School of Chemistry and Chemical Engineering
- Shandong University
- 250100 Jinan
- P.R. China
| | - Chen-zhong Li
- Department of Chemistry
- Liaocheng University
- Liaocheng 252059
- China
- Nanobioengineering/Bioelectronics Laboratory
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33
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Zacharioudakis E, Cañeque T, Custodio R, Müller S, Cuadro AM, Vaquero JJ, Rodriguez R. Quinolizinium as a new fluorescent lysosomotropic probe. Bioorg Med Chem Lett 2016; 27:203-207. [PMID: 27919658 DOI: 10.1016/j.bmcl.2016.11.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 11/22/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
Abstract
We have synthesized a collection of quinolizinium fluorescent dyes for the purpose of cell imaging. Preliminary biological studies in human U2OS osteosarcoma cancer cells have shown that different functional groups appended to the cationic quinolizinium scaffold efficiently modulate photophysical properties but also cellular distribution. While quinolizinium probes are known nuclear staining reagents, we have identified a particular quinolizinium derivative salt that targets the lysosomal compartment. This finding raises the question of predictability of specific organelle targeting from structural features of small molecules.
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Affiliation(s)
- Emmanouil Zacharioudakis
- Institut Curie, PSL Research University, Organic Synthesis and Cell Biology Group, 26 rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3666, 75005 Paris, France; INSERM U1143, 75005 Paris, France
| | - Tatiana Cañeque
- Institut Curie, PSL Research University, Organic Synthesis and Cell Biology Group, 26 rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3666, 75005 Paris, France; INSERM U1143, 75005 Paris, France.
| | - Raúl Custodio
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Sebastian Müller
- Institut Curie, PSL Research University, Organic Synthesis and Cell Biology Group, 26 rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3666, 75005 Paris, France; INSERM U1143, 75005 Paris, France
| | - Ana M Cuadro
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Juan J Vaquero
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Raphaël Rodriguez
- Institut Curie, PSL Research University, Organic Synthesis and Cell Biology Group, 26 rue d'Ulm, 75248 Paris Cedex 05, France; CNRS UMR3666, 75005 Paris, France; INSERM U1143, 75005 Paris, France
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34
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Stancescu M, Fedotova TA, Hooyberghs J, Balaeff A, Kolpashchikov DM. Nonequilibrium Hybridization Enables Discrimination of a Point Mutation within 5-40 °C. J Am Chem Soc 2016; 138:13465-13468. [PMID: 27681667 DOI: 10.1021/jacs.6b05628] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Detection of point mutations and single nucleotide polymorphisms in DNA and RNA has a growing importance in biology, biotechnology, and medicine. For the application at hand, hybridization assays are often used. Traditionally, they differentiate point mutations only at elevated temperatures (>40 °C) and in narrow intervals (ΔT = 1-10 °C). The current study demonstrates that a specially designed multistranded DNA probe can differentiate point mutations in the range of 5-40 °C. This unprecedentedly broad ambient-temperature range is enabled by a controlled combination of (i) nonequilibrium hybridization conditions and (ii) a mismatch-induced increase of equilibration time in respect to that of a fully matched complex, which we dub "kinetic inversion".
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Affiliation(s)
- Maria Stancescu
- Chemistry Department, University of Central Florida , Orlando, Florida 32816, United States
| | - Tatiana A Fedotova
- Chemistry Department, University of Central Florida , Orlando, Florida 32816, United States
| | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO , Boeretang 200, Mol B-2400, Belgium.,Theoretical Physics, Hasselt University, Campus Diepenbeek , Agoralaan - Building D, Diepenbeek B-3590, Belgium
| | - Alexander Balaeff
- NanoScience Technology Center , 12424 Research Parkway, Suite 400, Orlando, Florida 32826, United States
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida , Orlando, Florida 32816, United States.,National Center for Forensic Science and Burnett School of Biomedical Sciences, University of Central Florida , Orlando, Florida 32816, United States
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35
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Highly specific SNP detection using 2D graphene electronics and DNA strand displacement. Proc Natl Acad Sci U S A 2016; 113:7088-93. [PMID: 27298347 DOI: 10.1073/pnas.1603753113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.
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36
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Lee J, Park G, Min DH. A biosensor for the detection of single base mismatches in microRNA. Chem Commun (Camb) 2016; 51:14597-600. [PMID: 26288854 DOI: 10.1039/c5cc04706d] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Graphene oxide quenches fluorescence corresponding to only a mismatched target due to selective denaturing of the thermo-unstable duplex composed of probe peptide nucleic acid and single base mismatched target RNA and thus, the fluorescence signal only from perfectly matched target RNA is measured.
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Affiliation(s)
- Jieon Lee
- Center for RNA Research, Institute for Basic Science, Seoul National University, Seoul, 151-747, Korea.
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37
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Chen SX, Seelig G. An Engineered Kinetic Amplification Mechanism for Single Nucleotide Variant Discrimination by DNA Hybridization Probes. J Am Chem Soc 2016; 138:5076-86. [PMID: 27010123 DOI: 10.1021/jacs.6b00277] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Even a single-nucleotide difference between the sequences of two otherwise identical biological nucleic acids can have dramatic functional consequences. Here, we use model-guided reaction pathway engineering to quantitatively improve the performance of selective hybridization probes in recognizing single nucleotide variants (SNVs). Specifically, we build a detection system that combines discrimination by competition with DNA strand displacement-based catalytic amplification. We show, both mathematically and experimentally, that the single nucleotide selectivity of such a system in binding to single-stranded DNA and RNA is quadratically better than discrimination due to competitive hybridization alone. As an additional benefit the integrated circuit inherits the property of amplification and provides at least 10-fold better sensitivity than standard hybridization probes. Moreover, we demonstrate how the detection mechanism can be tuned such that the detection reaction is agnostic to the position of the SNV within the target sequence. in contrast, prior strand displacement-based probes designed for kinetic discrimination are highly sensitive to position effects. We apply our system to reliably discriminate between different members of the let-7 microRNA family that differ in only a single base position. Our results demonstrate the power of systematic reaction network design to quantitatively improve biotechnology.
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Affiliation(s)
- Sherry Xi Chen
- Department of Electrical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington , Seattle, Washington 98195, United States.,Department of Computer Science & Engineering, University of Washington , Seattle, Washington 98195, United States
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38
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Wolf‐Preis in Chemie: K. C. Nicolaou und S. L. Schreiber / Preise der Israel Chemical Society: R. Klajn, R. Tenne und M. Kol / Pittcon‐2016‐Preise: S. A. Asher, D. R. Walt, J. Popp, S. Mukamel und R. J. White. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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39
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Wolf Prize in Chemistry: K. C. Nicolaou and S. L. Schreiber / Israel Chemical Society Awards: R. Klajn, R. Tenne, and M. Kol / Pittcon 2016 Award Winners: S. A. Asher, D. R. Walt, J. Popp, S. Mukamel, and R. J. White. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/anie.201601464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Chen X, Zhou D, Shen H, Chen H, Feng W, Xie G. A universal probe design for colorimetric detection of single-nucleotide variation with visible readout and high specificity. Sci Rep 2016; 6:20257. [PMID: 26830326 PMCID: PMC4735751 DOI: 10.1038/srep20257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/31/2015] [Indexed: 01/02/2023] Open
Abstract
Single-nucleotide variation (SNV) is a crucial biomarker for drug resistance-related detection in cancer and bacterial infection. However, the unintended binding of DNA probes limits the specificity of SNV detection, and the need for redesigned sequences compromise the universality of SNV assay. Herein, we demonstrated a universal and low-cost assay for the colorimetric discrimination of drug-resistance related point mutation. By the use of a universal DNA probe and a split G-quadruplex, the signal could be recognized by naked eye at room temperature. The DNA probe was used as a signal reporter which not only improved the universality, but also enabled high specificity of probe hybridization. This assay was successfully applied in the detection of cancer-related SNV in the epidermal growth factor receptor (EGFR) gene, kirsten rat sarcoma viral oncogene homologue (KRAS), and tuberculosis drug-resistance related point mutation in RNA polymerase beta subunit gene (rpoB) with high specificity and visible readout. This method was simple, rapid, high-throughput and effective, which was suitable for point-of-care applications.
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Affiliation(s)
- Xueping Chen
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Dandan Zhou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Huawei Shen
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P. R. China
| | - Wenli Feng
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
| | - Guoming Xie
- Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P. R. China
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41
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Gao P, Hu L, Liu N, Yang Z, Lou X, Zhai T, Li H, Xia F. Functional "Janus" Annulus in Confined Channels. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:460-5. [PMID: 26765675 DOI: 10.1002/adma.201502344] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/30/2015] [Indexed: 05/12/2023]
Abstract
Scattered Au 3D nanoparticles form distinct functional regions with an uncovered internal surface in confined channels, named the "Janus" annulus. Electrochemical impedance spectroscopy responses to the variations in DNA self-assembly and hybridization in the channels decorated by the "Janus" annulus are presented. Single nucleotide mutations are further detected in a linear DNA chain, including terminal base polymorphisms.
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Affiliation(s)
- Pengcheng Gao
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Lintong Hu
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Nannan Liu
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Zekun Yang
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Xiaoding Lou
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Tianyou Zhai
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Huiqiao Li
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Material Sciences and Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
| | - Fan Xia
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
- National Engineering Research Center for Nanomedicine Institute of Material Medical, College of Life Science & Technology, Huazhong University of Science and Technology (HUST), Wuhan, 430074, P. R. China
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42
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Li C, Li Y, Chen Y, Lin R, Li T, Liu F, Li N. Modulating the DNA strand-displacement kinetics with the one-sided remote toehold design for differentiation of single-base mismatched DNA. RSC Adv 2016. [DOI: 10.1039/c6ra17006d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A one-sided remote toehold design was proposed to provide the fine control over strand-displacement reaction kinetics with simplicity and versatility.
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Affiliation(s)
- Chenxi Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Yixin Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Yang Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Ruoyun Lin
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Tian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Feng Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
| | - Na Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education
- Institute of Analytical Chemistry
- College of Chemistry and Molecular Engineering
- Peking University
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43
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Zhang XR, Zhang Y, Chen FT, Li Y, Zhang SS. Visual detection of single-nucleotide polymorphisms and DNA methyltransferase based on cation-exchange of CuS nanoparticles and click chemistry of functionalized gold nanoparticles. Chem Commun (Camb) 2016; 52:13261-13264. [DOI: 10.1039/c6cc06735b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel biosensor was developed based on the cation-exchange of CuS nanoparticles (NPs) and Cu(i)-based click chemistry of functionalized gold nanoparticles (AuNPs).
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Affiliation(s)
- X. R. Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Y. Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - F. T. Chen
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Y. Li
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - S. S. Zhang
- Shandong Province Key Laboratory of Detection Technology for Tumor Makers
- College of Chemistry and Chemical Engineering
- Linyi University
- Linyi 276000
- P. R. China
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44
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Shaikh MUM, Mudaliar SS, Chikhalia KH. An efficient alkynylation of 4-thiazolidinone with terminal alkyne under C–H functionalisation. RSC Adv 2016. [DOI: 10.1039/c6ra05015h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A method of palladium catalysed efficient alkynylation through the cross coupling reaction of terminal alkynes with the slightly more acidic C–H bonds of 4-thiazolidinone has been developed.
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Affiliation(s)
| | | | - Kishor H. Chikhalia
- Department of Chemistry
- School of Science
- Gujarat University
- Ahmedabad 380009
- India
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45
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Huang J, Wang Z, Kim JK, Su X, Li Z. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide. Anal Chem 2015; 87:12254-61. [DOI: 10.1021/acs.analchem.5b03369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiahao Huang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhenyu Wang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jang-Kyo Kim
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public
Health and Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong
| | - Zhigang Li
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Hwang MT, Landon PB, Lee J, Mo A, Meckes B, Glinsky G, Lal R. DNA nano-carrier for repeatable capture and release of biomolecules. NANOSCALE 2015; 7:17397-17403. [PMID: 26439640 DOI: 10.1039/c5nr05124j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA can be manipulated to design nano-machines through specific sequence recognition. We report a switchable DNA carrier for repeatable capture and release of a single stranded DNA. The activity of the carrier was regulated by the interactions among a double-stranded actuator, single stranded target, fuel, and anti-fuel DNA strands. Inosine was used to maintain a stable triple-stranded complex when the actuator's conformation was switched between open (capture) and closed (release) configurations. Time lapse fluorescence measurements show repeatable capture and release of target strands. TEM images also show visible capture of target DNA strands when gold nanoparticles were attached to the DNA carrier and the target DNA strand. The carrier activity was controlled by length of toeholds, number of mismatches, and inosine substitutions. Significantly, unlike in previously published work that reported the devices functioned only when there is a perfect match between the interacting DNA strands, the present device works only when there are mismatches in the fuel strand and the best performance is achieved for 1-3 mismatches. The device was used to successfully capture and release gold nanoparticles when linked to the target single-stranded DNA. In general, this type of devices can be used for transport and delivery of theranostic molecules.
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Affiliation(s)
- Michael T Hwang
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Signaling-Probe Displacement Electrochemical Aptamer-based Sensor (SD-EAB) for Detection of Nanomolar Kanamycin A. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.09.140] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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48
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Zhang X, Zhang J, Wu D, Liu Z, Cai S, Chen M, Zhao Y, Li C, Yang H, Chen J. Ultraselective electrochemiluminescence biosensor based on locked nucleic acid modified toehold-mediated strand displacement reaction and junction-probe. Analyst 2015; 139:6109-12. [PMID: 25299420 DOI: 10.1039/c4an01363h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Locked nucleic acid (LNA) is applied in toehold-mediated strand displacement reaction (TMSDR) to develop a junction-probe electrochemiluminescence (ECL) biosensor for single-nucleotide polymorphism (SNP) detection in the BRCA1 gene related to breast cancer. More than 65-fold signal difference can be observed with perfectly matched target sequence to single-base mismatched sequence under the same conditions, indicating good selectivity of the ECL biosensor.
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Affiliation(s)
- Xi Zhang
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou, Fujian 350108, P R China.
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49
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Min X, Zhuang Y, Zhang Z, Jia Y, Hakeem A, Zheng F, Cheng Y, Tang BZ, Lou X, Xia F. Lab in a Tube: Sensitive Detection of MicroRNAs in Urine Samples from Bladder Cancer Patients Using a Single-Label DNA Probe with AIEgens. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16813-16818. [PMID: 26180929 DOI: 10.1021/acsami.5b04821] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We demonstrate an ultrasensitive microRNA detection method based on an extremely simple probe with only fluorogens but without quencher groups. It avoids complex and difficult steps to accurately design the relative distance between the fluorogens and quencher groups in the probes. Furthermore, the assay could accomplish various detection limits by tuning the reaction temperature due to the different activity of exonuclease III corresponding to the diverse temperature. Specifically, 1 pM miR-21 can be detected in 40 min at 37 °C, and 10 aM (about 300 molecules in 50 μL) miR-21 could be discriminated in 7 days at 4 °C. The great specificity of the assay guarantees that the real 21 urine samples from the bladder cancer patients are successfully detected by our method.
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Affiliation(s)
- Xuehong Min
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuan Zhuang
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhenyu Zhang
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yongmei Jia
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Abdul Hakeem
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fuxin Zheng
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yong Cheng
- ‡National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ben Zhong Tang
- §Department of Chemistry, HKUST Jockey Club Institute for Advanced Study Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong, China
| | - Xiaoding Lou
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Fan Xia
- †Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- ‡National Engineering Research Center for Nanomedicine, Huazhong University of Science and Technology, Wuhan 430074, China
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50
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Spectra, Stability and Labeling of a Novel Carbazole Derivative as a Fluorescent Turn-on DNA Probe. J Fluoresc 2015; 25:1251-8. [DOI: 10.1007/s10895-015-1613-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/30/2015] [Indexed: 01/29/2023]
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