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Chen L, Yang W, Li D, Ma Y, Chen L, You S, Liu S. Poly cytosine (C)/poly adenine (A) modified probe for signal "on-off-on" assay of single-base mismatched dsDNA by a competitive mechanism. Anal Chim Acta 2023; 1239:340705. [PMID: 36628713 DOI: 10.1016/j.aca.2022.340705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
Direct discrimination of single-base mismatched dsDNA by a simple method or strategy would provide enormous opportunities for applications in the fields of life sciences and disease diagnosis. Herein, the peroxidase-mimicking activity of a metal-organic framework nanoprobe (MOF) was well exploited for the direct discrimination of single-base mismatched dsDNA based on a competition-induced signal on-off-on mechanism. The single-base mismatched dsDNA related with FecB gene (usually guanine (G)/thymine (T) mismatch) and MIL-88B-NH2 were used as target and MOF model, respectively. Firstly, polyA/polyC were loosely adsorbed onto the MOFs via the weak interaction to block the peroxidase activity of MOF, inducing the signal transition from on to off. Unexpectedly, the single-base mismatched (GT) dsDNA could reverse the signal response of MOF probe from off to on. But it could not occur for other nonspecific mismatches, such as CT and TT-mismatched dsDNA. A synergistic interaction mechanism between multiple GT mismatches and polyA/polyC was attempted to explain the competitive dissociation of polyA/polyC from MOF for the recovery of peroxidase activity. With it, a wide linear detection ranges from 10-9 M-10-5 M of GT mismatched dsDNA and a low detection limit of 0.247 nM could be achieved, even in the real samples. The effect of mismatched base number or position was also studied. Such a simple, rapid, cost-effective, and one-step mixing and checking method for single-base mismatched dsDNA discrimination eliminates the complex sample pretreatment, special DNA probe design, exclusive amplification or signal readout means. It thus offers a simple and effective route for direct discrimination of mismatched dsDNA and might hold a huge potential for the applications in gene analysis, disease diagnosis, and elementary research in life sciences.
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Affiliation(s)
- Lihua Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Wenjie Yang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Dong Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Yunkang Ma
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Lili Chen
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Shuang You
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Key Laboratory of Ecochemical Engineering, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, PR China.
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Xia J, Xu T, Qing J, Wang L, Tang J. Detection of Single Nucleotide Polymorphisms by Fluorescence Embedded Dye SYBR Green I Based on Graphene Oxide. Front Chem 2021; 9:631959. [PMID: 33869140 PMCID: PMC8044317 DOI: 10.3389/fchem.2021.631959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/11/2021] [Indexed: 11/28/2022] Open
Abstract
The detection of single nucleotide polymorphisms (SNPs) is of great significance in the early diagnosis of diseases and the rational use of drugs. Thus, a novel biosensor based on the quenching effect of fluorescence-embedded SYBR Green I (SG) dye and graphene oxide (GO) was introduced in this study. The probe DNA forms a double helix structure with perfectly complementary DNA (pcDNA) and 15 single-base mismatch DNA (smDNA) respectively. SG is highly intercalated with perfectly complementary dsDNA (pc-dsDNA) and exhibits strong fluorescence emission. Single-base mismatch dsDNA (SNPs) has a loose double-stranded structure and exhibits poor SG intercalation and low fluorescence sensing. At this time, the sensor still showed poor SNP discrimination. GO has a strong effect on single-stranded DNA (ssDNA), which can reduce the fluorescence response of probe DNA and eliminate background interference. And competitively combined with ssDNA in SNPs, quenching the fluorescence of SG/SNP, while the fluorescence value of pc-dsDNA was retained, increasing the signal-to-noise ratio. At this time, the sensor has obtained excellent SNP resolution. Different SNPs detect different intensities of fluorescence in the near-infrared region to evaluate the sensor's identification of SNPs. The experimental parameters such as incubation time, incubation temperature and salt concentration were optimized. Under optimal conditions, 1 nM DNA with 0–10 nM linear range and differentiate 5% SNP were achieved. The detection method does not require labeling, is low cost, simple in operation, exhibits high SNP discrimination and can be distinguished by SNP at room temperature.
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Affiliation(s)
- Jiaoyun Xia
- School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha, China
| | - Tong Xu
- School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha, China
| | - Jing Qing
- School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha, China
| | - Lihua Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Junlong Tang
- School of Physics and Electronic Science, Changsha University of Science and Technology, Changsha, China
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