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Jiang P, Dong K, Zhang W, Wang H, Xiao X, Chen N, Cheng Y. A universal probe system for low-abundance point mutation detection based on endonuclease IV. Analyst 2022; 147:1534-1539. [PMID: 35311862 DOI: 10.1039/d1an02003j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single base mutations are closely related to cancer diagnosis and treatment. The fluorescent probe method is one of the important methods to detect single-base mutations. We constructed a universal probe detection system based on endonuclease IV and the DNA strand displacement reaction. The system uses two toehold strand displacement reactions to relay the mutation information to the universal strand. There is no need to design the probe one-by-one for each mutation point during multi-site detection. It has the advantages of simple operation, rapid detection, and low cost. We used this method to detect common clinical mutation sites (PTEN R130Q/EGFR L858R/PTEN rs1473918395), and the detection limit can reach 0.1%-1%. The detection system can provide a new rapid and economical method for clinical single-base mutation detection, and has broad application prospects in diagnosis and prognostic evaluation.
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Affiliation(s)
- Ping Jiang
- Department of Gynecology, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Chen
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yanxiang Cheng
- Department of Gynecology, Renmin Hospital of Wuhan University, Wuhan, China.
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2
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Dong K, Zhang W, Cheng S, Shu W, Zhao R, Wang H. The Progress of the Specific and Rapid Genetic Detection Methods for Ovarian Cancer Diagnosis and Treatment. Technol Cancer Res Treat 2022; 21:15330338221114497. [PMID: 36062718 PMCID: PMC9446467 DOI: 10.1177/15330338221114497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cancer is a public health problem that threatens human health. Due to the lack of
specific and rapid diagnosis and treatment methods, the 5-year survival rate of
patients has not been effectively improved in the past 10 years. Abnormal gene
expression is closely related to the occurrence and development of cancer.
Cancer diagnosis and treatment methods based on genetic testing have received
extensive attention in recent years. It is essential to explore specific and
rapid cancer genetic testing methods. Taking ovarian cancer as an example, we
reviewed the progress of specific and rapid nucleic acid detection methods
related to cancer risk assessment, low-abundance mutation detection, and
methylation detection, to provide new strategies and ideas for related
research.
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Affiliation(s)
- Kejun Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Shuangshuang Cheng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, 12403Huazhong University of Science and Technology, Wuhan, China
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3
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Tang X, Chen X, Liao Y, Yan B, Hu H, Ming Z, Liu L, Li L, Mao Z, Xiao X. Self-Internal-Reference Probe System for Control-Free Quantification of Mutation Abundance. Anal Chem 2021; 93:13274-13283. [PMID: 34546716 DOI: 10.1021/acs.analchem.1c02877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene mutations are important biomarkers for the diagnosis, classification, monitoring, and prognosis evaluation of cancers and genetic diseases. Both personalized cancer treatment and noninvasive prenatal testing require methods to accurately determine the abundance of mutation. At present, the widely adopted and convenient methods for measuring mutation abundance are mainly based on relative quantification, which requires negative samples and strict control of the analyte amounts. The development of DNA-probe-based methods that can determine the mutation abundance without negative samples nor control of analyte amount is highly preferred. The key to solving this bottleneck lies in whether the probe's response to mutation abundance can be completely independent of the number of targeted DNA strands. Herein, we propose the design of a self-internal-reference probe system. We established a theoretical model of this system and used the model to guide the design of probes. In this model, we provided quantitative corrections to the test results from the internal reference, thereby eliminating the influence of substrate amount. Therefore, the purification and quantification processes toward polymerase chain reaction (PCR) amplicons can be omitted. We applied this system to analyze unquantified PCR products aimed at cancer mutation detection and noninvasive prenatal testing.
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Affiliation(s)
- Xiaofeng Tang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Xin Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Yangwei Liao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Bei Yan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Hao Hu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Zhihao Ming
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Liquan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
| | - Longjie Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China.,School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, P. R. China
| | - Zenghui Mao
- Center of Reproductive Medicine, Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, Changsha 410007, P. R. China
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P. R. China
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4
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Zhang Z, Hu Y, Yuan W, Hu M, Deng Y, Xiao X, Wu T. Endonuclease IV-Regulated DNAzyme Motor for Universal Single-nucleotide Variation Discrimination. Anal Chem 2021; 93:9939-9948. [PMID: 34235928 DOI: 10.1021/acs.analchem.1c02230] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-nucleotide variation (SNV) detection plays significant roles in disease diagnosis and treatment. Generally, auxiliary probe, restricted design rules, complicated detection system, and repeated experimental parameter optimization are needed to obtain satisfactory tradeoff between sensitivity and selectivity for SNV discrimination, especially when different mutant sites need to be distinguished. To overcome these limitations, we developed a universal, straightforward, and relatively cheap SNV discrimination strategy, which simultaneously possessed high sensitivity and selectivity. The excellent performance of this strategy was ascribed to the SNV discrimination property of endonuclease IV (Endo IV) and the different hydrolysis behavior between free deoxyribozyme (DNAzyme) and the trapped DNAzyme to the substrates modified on gold nanoparticles (AuNPs). When Endo IV recognized the mutant-type target (MT), free DNAzyme was released from the probe, and the DNAzyme motor was activated with the help of cofactor Mn2+ to generate an amplified fluorescence signal. On the contrary, the wild-type target (WT) could not effectively trigger the DNAzyme motor. Moreover, for different SNV types, the corresponding probe could be designed by simply changing the sequence hybridized with the target and retaining the DNAzyme sequence. Thus, the fluorescence signal generation system does not need to change for different SNV targets. Five clinical-related SNVs were determined with the limit of detection (LOD) ranging from 0.01 to 0.05%, which exhibited competitive sensitivity over existing SNV detection methods. This strategy provided another insight into the properties of Endo IV and DNAzyme, expanded the applications of DNAzyme motor, and has great potential to be used for precision medicine.
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Affiliation(s)
- Zhen Zhang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuqiang Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenqian Yuan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuhan Deng
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xianjin Xiao
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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5
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Liu C, Liu Y, Zhu E, Zhang Q, Wei X, Wang B. Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement. Nucleic Acids Res 2020; 48:10691-10701. [PMID: 33045746 PMCID: PMC7641751 DOI: 10.1093/nar/gkaa835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 01/19/2023] Open
Abstract
Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.
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Affiliation(s)
- Chanjuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Enqiang Zhu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
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Chen X, Liu N, Liu L, Chen W, Chen N, Lin M, Xu J, Zhou X, Wang H, Zhao M, Xiao X. Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization. Nat Commun 2019; 10:4675. [PMID: 31611572 PMCID: PMC6791858 DOI: 10.1038/s41467-019-12593-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022] Open
Abstract
Sensitive and specific DNA hybridization is essential for nucleic acid chemistry. Competitive composition of probe and blocker has been the most adopted probe design for its relatively high sensitivity and specificity. However, the sensitivity and specificity were inversely correlated over the length and concentration of the blocker strand, making the optimization process cumbersome. Herein, we construct a theoretical model for competitive DNA hybridization, which disclose that both the thermodynamics and kinetics contribute to the inverse correlation. Guided by this, we invent the 4-way Strand Exchange LEd Competitive DNA Testing (SELECT) system, which breaks up the inverse correlation. Using SELECT, we identified 16 hot-pot mutations in human genome under uniform conditions, without optimization at all. The specificities were all above 140. As a demonstration of the clinical practicability, we develop probe systems that detect mutations in human genomic DNA extracted from ovarian cancer patients with a detection limit of 0.1%. Optimisation of nucleic acid probes and blocker strands can be laborious. Here the authors construct a theoretical model of competitive DNA hybridisation to design DNA probes for optimisation-free mutation detection.
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Affiliation(s)
- Xin Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Na Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Liquan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Wei Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China
| | - Na Chen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Meng Lin
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Jiaju Xu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Xing Zhou
- Department of Obstetrics and Gynaecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, PR China
| | - Hongbo Wang
- Department of Obstetrics and Gynaecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, PR China.
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, PR China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China. .,Department of Obstetrics and Gynaecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, PR China.
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7
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Yu W, Li J, Zuo C, Tao Y, Bai S, Li J, Zhang Z, Xie G. Specific discrimination and universal signal amplification for RNA detection by coupling toehold exchange with RCA through nucleolytic conversion of a structure-switched hairpin probe. Anal Chim Acta 2019; 1068:96-103. [PMID: 31072482 DOI: 10.1016/j.aca.2019.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 12/27/2022]
Abstract
Herein, we combined toehold exchange with ligation-free rolling circle amplification (RCA) by programming nucleolytic conversion of hairpin probe into sensors, allowed for both high specific recognition and universal signal amplification for RNA detection. The rational engineered HP ensured highly specific recognition based on toehold exchange and allowed the pre-formed circular template for RCA to be shared for different RNAs detection. Generally, detecting different RNA requires different circular template for signal amplification. In this paper, the circular template for RCA was independent of the sequences of the target, so the signal amplification system was an universal one for different RNAs detection. Taking miRNA let-7d as a model target, this method showed a wide linear range from 1 fM to 1 nM with a detection limit of 0.46 fM and exhibited a remarkable selectivity even in distinguishing homologous miRNAs with 1-nt or 2-nt difference. To evaluate the potential of the method, it was applied to analysis the let-7d concentration in human serum, total RNA, and cell lysates. In conclusion, we believe this method exhibits potential for both specific discrimination and universal signal amplification for RNA analysis in complex matrices.
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Affiliation(s)
- Wen Yu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Juqiong Li
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Chen Zuo
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yiyi Tao
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Shulian Bai
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Junlong Li
- Department of Laboratory Medicine, The Affiliated University City Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhang Zhang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
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8
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Fluorometric detection of silver(I) using cytosine-Ag(I)-cytosine pair formation, DNA assembly and the AND logic operation of a multiple-component DNAzyme. Mikrochim Acta 2019; 186:522. [DOI: 10.1007/s00604-019-3615-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/14/2019] [Indexed: 02/07/2023]
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9
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Preparation of graphene oxide quantum dots from waste toner, and their application to a fluorometric DNA hybridization assay. Mikrochim Acta 2019; 186:483. [DOI: 10.1007/s00604-019-3539-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 05/22/2019] [Indexed: 01/19/2023]
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