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Wang L, Bu S, Xu S, Huang T, Yang F, Tan Q, Deng M, Xie W, Cai B, Chen J. Double base mismatches mediated catalytic hairpin assembly for enzyme-free single-base mutation detection: integrating signal recognition and amplification in one. Mikrochim Acta 2024; 191:334. [PMID: 38758362 DOI: 10.1007/s00604-024-06366-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 04/14/2024] [Indexed: 05/18/2024]
Abstract
Single nucleotide polymorphism (SNP) biosensors are emerging rapidly for their promising applications in human disease prevention diagnosis, treatment, and prognosis. However, it remains a bottleneck in equipping simple and stable biosensors with the traits of high sensitivity, non-enzyme, and low cost. Double base mismatches mediated chain displacement reactions have attracted fascinating advantages of tailorable thermodynamics stability, non-enzyme, and excellent assembly compliance to involvement in SNP identification. As the base mismatch position and amount in DNA sequence can be artificially adjusted, it provides plenty of selectivity and specificity for exploring perfect biosensors. Herein, a biosensor with double base mismatches mediated catalytic hairpin assembly (CHA) is designed via one base mismatch in the toehold domain and the other base mismatch in the stem sequence of hairpin 1 (H1) by triggering CHA reaction to achieve selective amplification of the mutation target (MT) and fluorescence resonance energy transfer (FRET) effect that is composed of Cy3 and Cy5 terminally attached H1 and hairpin 2 (H2). Depending on the rationally designed base mismatch position and toehold length, the fabricated biosensors show superior SNP detection performance, exhibiting a good linearity with high sensitivity of 6.6 fM detection limit and a broad detection abundance of 1%. The proposed biosensor can be used to detect the KRAS mutation gene in real samples and obtain good recoveries between 106 and 116.99%. Remarkably, these extendible designs of base mismatches can be used for more types of SNP detection, providing flexible adjustment based on base mismatch position and toehold length variations, especially for their thermodynamic model for DNA-strand displacement reactions.
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Affiliation(s)
- Lanyue Wang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Sisi Bu
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Shijie Xu
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Tuo Huang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Fang Yang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Qianglong Tan
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Minxin Deng
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China
| | - Wenlin Xie
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
| | - Bobo Cai
- Zhejiang Hospital, Hangzhou, 310013, China.
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, Hunan, China.
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Zhang Y, Wang L, Ye J, Chen J, Xu S, Bu S, Deng M, Bian L, Zhao X, Zhang C, Weng L, Zhang D. Rationally Designed Dual Base Pair Mismatch Enables Toehold-Mediated Strand Displacement to Efficiently Recognize Single-Nucleotide Polymorphism without Enzymes. Anal Chem 2024; 96:554-563. [PMID: 38112727 DOI: 10.1021/acs.analchem.3c04778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The efficiency of the enzyme-free toehold-mediated strand displacement (TMSD) technique is often insufficient to detect single-nucleotide polymorphism (SNP) that possesses only single base pair mismatch discrimination. Here, we report a novel dual base pair mismatch strategy enabling TMSD biosensing for SNP detection under enzyme-free conditions when coupled with catalytic hairpin assembly (CHA) and fluorescence resonance energy transfer (FRET). The strategy is based on a competitive strand displacement reaction mechanism, affected by the thermodynamic stability originating from rationally designed dual base pair mismatch, for the specific recognition of mutant-type DNA. In particular, enzyme-free nucleic acid circuits, such as CHA, emerge as a powerful method for signal amplification. Eventually, the signal transduction of this proposed biosensor was determined by FRET between streptavidin-coated 605 nm emission quantum dots (605QDs, donor) and Cy5/biotin hybridization (acceptor, from CHA) when incubated with each other. The proposed biosensor displayed high sensitivity to the mutant target (MT) with a detection concentration down to 4.3 fM and led to high discrimination factors for all types of mismatches in multiple sequence contexts. As such, the application of this proposed biosensor to investigate mechanisms of the competitive strand displacement reaction further illustrates the versatility of our dual base pair mismatch strategy, which can be utilized for the creation of a new class of biosensors.
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Affiliation(s)
- Yunshan Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lanyue Wang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Jing Ye
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Shijie Xu
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Sisi Bu
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Minxin Deng
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan, China
| | - Lina Bian
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
| | - Xiaoyu Zhao
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, P. R. China
| | - Chunlong Zhang
- Research Center for Intelligent Robotics, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lin Weng
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311121, China
| | - Diming Zhang
- Research Center for Intelligent Sensing Systems, Zhejiang Laboratory, Hangzhou 311121, China
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Wang ZK, Yuan ZX, Qian C, Liu XW. Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution. Anal Chem 2023; 95:18398-18406. [PMID: 38055795 DOI: 10.1021/acs.analchem.3c03316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.
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Affiliation(s)
- Zhao-Kun Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zhen-Xuan Yuan
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Chen Qian
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xian-Wei Liu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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Bozan M, Popp D, Kallies R, da Rocha UN, Klähn S, Bühler K. Whole-genome sequence of the filamentous diazotrophic cyanobacterium Tolypothrix sp. PCC 7712 and its comparison with non-diazotrophic Tolypothrix sp. PCC 7601. Front Microbiol 2022; 13:1042437. [PMID: 36425037 PMCID: PMC9679502 DOI: 10.3389/fmicb.2022.1042437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/11/2022] [Indexed: 03/14/2024] Open
Abstract
Cyanobacteria are highly promising microorganisms in forthcoming biotechnologies. Besides the systematic development of molecular tools for genetic engineering, the design of chassis strains and novel reactor concepts are in focus. The latter includes capillary biofilm reactors (CBR), which offer a high surface area-to-volume ratio and very high cell densities. In this context, Tolypothrix sp. PCC 7712 was found to be highly suited for this reactor system due to maximal surface coverage, extraordinarily strong biofilm attachment, and high biomass formation. Here, we provide the genome sequence of Tolypothrix sp. PCC 7712 to potentially allow targeted strain engineering. Surprisingly, it was almost identical to an available incomplete genome draft of Tolypothrix sp. PCC 7601. Thus, we completely sequenced this strain as well and compared it in detail to strain PCC 7712. Comparative genome analysis revealed 257 and 80 unique protein-coding sequences for strains PCC 7601 and PCC 7712, respectively. Clustering genomes based on average nucleotide identity (ANI) and 16S rRNA homology showed 99.98% similarity and only minor distance, respectively, between the two strains in contrast to 21 other cyanobacterial genomes. Despite these high similarities, both strains differ in the ability to fix atmospheric nitrogen and show specific sequence variations, which are discussed in the paper.
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Affiliation(s)
- Mahir Bozan
- Department of Solar Materials, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Denny Popp
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Stephan Klähn
- Department of Solar Materials, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Katja Bühler
- Department of Solar Materials, Helmholtz-Centre for Environmental Research (UFZ), Leipzig, Germany
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Buitrago Acosta MC, Montúfar R, Guyot R, Mariac C, Tranbarger TJ, Restrepo S, Couvreur TLP. Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:1540-1544. [PMID: 36046105 PMCID: PMC9423826 DOI: 10.1080/23802359.2022.2109437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bactris gasipaes var. gasipaes (Arecaceae, Palmae) is an economically and socially important plant species for populations across tropical South and Central America. It has been domesticated from its wild variety, B. gasipaes var. chichagui, since pre-Columbian times. In this study, we sequenced the plastome of the cultivated variety, B. gasipaes Kunth var. gasipaes and compared it with the published plastome of the wild variety. The chloroplast sequence obtained was 156,580 bp. The cultivated chloroplast sequence was conserved compared to the wild type sequence with 99.8% of nucleotide identity. We did, however, identify multiple Single Nucleotide Variants (SNVs), insertions, microsatellites and a resolved region of missing nucleotides. A SNV in one of the core barcode markers (matK) was detected between the wild and cultivated accessions. Phylogenetic analysis was carried out across the Arecaceae family and compared to previous reports, resulting in an identical topology. This study is a step forward in understanding the genome evolution of this species.
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Affiliation(s)
| | - Rommel Montúfar
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Romain Guyot
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Cedric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | | | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Thomas L. P. Couvreur
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
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Xiong Y, Tang H. A Sensitive PCR-Based Method for Somatic Mutations Enrichment and Screening. Cancer Manag Res 2021; 13:8099-8107. [PMID: 34737638 PMCID: PMC8558320 DOI: 10.2147/cmar.s335679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/11/2021] [Indexed: 11/23/2022] Open
Abstract
Background EGFR and KRAS are the most frequently mutated genes in lung cancers, occurring in about 60% of all cases. Mutation genes assay has emerged as a promising blood-based biomarker for monitoring cancer dynamics noninvasively. However, detection can be challenging in patients where plasma often contains low levels of tumor-derived DNA fragments. Methods We have developed a nuclease-based enrichment assay for detecting mutant alleles. The procedure is based on Surveyor endonuclease cleaves mismatched DNA molecules, and these DNA fragments were enriched for mutation screening. We screened lung cancer specimens for mutations in exons 18 and 21 of EGFR, and the majority of activating mutations in lung cancer occur in codons 12 (G12X) and 13 (G13X) of exon 2 of the KRAS gene. The method screened all mutant genes with the same pair primers and three relevant TaqMan probes. Results The method can effectively remove wild-type sequences and enrich mutation DNA, and the sensitivity detectable mutant allele frequencies (MAF) achieved 0.001%. The method increases the sensitivity and efficiency of mutation DNA for cancers screening. This highlights the importance of complex DNA variation like mutations in exon 21 of EGFR and exon 2 of the KRAS gene detected by the same probe. Conclusion We developed a simple and sensitive methodology for mutation gene screening. The method is a cost-effective and sensitive method for mutation DNA enrichment and detection.
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Affiliation(s)
- Yaming Xiong
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Hailing Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
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Liu ZJ, Yang LY, Wei QX, Ye CL, Xu XW, Zhong GX, Zheng YJ, Chen JY, Lin XH, Liu AL. A novel ligase chain reaction-based electrochemical biosensing strategy for highly sensitive point mutation detection from human whole blood. Talanta 2020; 216:120966. [PMID: 32456905 DOI: 10.1016/j.talanta.2020.120966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 01/15/2023]
Abstract
Challenged by the detection of trace amounts of mutants and disturbance from endogenous substances in clinical samples, herein, we present a novel electrochemical biosensor based on ligase chain reaction (eLCR) via the thermostable ligase with high mutation recognizing ability. The lengthened double-stranded DNAs exponentially generated via LCR were uniformly distributed on a bovine serum albumin-modified gold electrode, in which the phosphate buffer was tactfully added to remove adsorbed uninterested-probes, and thereafter the amperometry current was collected for the specific binding of streptavidin-poly-HRP and subsequent catalysis in the 3, 3', 5, 5'-tetramethylbenzidine substrate that contained hydrogen peroxide. It found that, under optimized conditions, the proposed biosensor exhibited a high selectivity of mutant targets from the 104-fold excess of co-existent wild targets within a detection limit of 0.5 fM. Impressively, without the involvement of pre-PCR, the homozygous mutants were specifically distinguished from the wild genotype of CYP2C19*2 allele in human whole blood samples. Therefore, the proposed eLCR, due to its advantages in simple primer design, operational ease and ease of miniaturization, has demonstrated its considerable potential for point-of-care testing in the diagnosis of point mutation-related diseases and personalized medicine.
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Affiliation(s)
- Zhou-Jie Liu
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Liang-Yong Yang
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Qing-Xia Wei
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Chen-Liu Ye
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiong-Wei Xu
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Guang-Xian Zhong
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China
| | - Yan-Jie Zheng
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- Department of Pharmacy, Central Laboratory, Fujian Provincial Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, China.
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China.
| | - Ai-Lin Liu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China.
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