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Zhang C, Li Z, Liu J, Liu C, Zhang H, Lee WG, Yao C, Guo H, Xu F. Synthetic Gene Circuit-Based Assay with Multilevel Switch Enables Background-Free and Absolute Quantification of Circulating Tumor DNA. RESEARCH (WASHINGTON, D.C.) 2023; 6:0217. [PMID: 37789988 PMCID: PMC10543738 DOI: 10.34133/research.0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 10/05/2023]
Abstract
Circulating tumor DNA (ctDNA) detection has found widespread applications in tumor diagnostics and treatment, where the key is to obtain accurate quantification of ctDNA. However, this remains challenging due to the issue of background noise associated with existing assays. In this work, we developed a synthetic gene circuit-based assay with multilevel switch (termed CATCH) for background-free and absolute quantification of ctDNA. The multilevel switch combining a small transcription activating RNA and a toehold switch was designed to simultaneously regulate transcription and translation processes in gene circuit to eliminate background noise. Moreover, such a multilevel switch-based gene circuit was integrated with a Cas9 nickase H840A (Cas9n) recognizer and a molecular beacon reporter to form CATCH for ctDNA detection. The CATCH can be implemented in one-pot reaction at 35 °C with virtually no background noise, and achieve robust absolute quantification of ctDNA when integrated with a digital chip (i.e., digital CATCH). Finally, we validated the clinical capability of CATCH by detecting drug-resistant ctDNA mutations from the plasma of 76 non-small cell lung cancer (NSCLC) patients, showing satisfying clinical sensitivity and specificity. We envision that the simple and robust CATCH would be a powerful tool for next-generation ctDNA detection.
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Affiliation(s)
- Chao Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
- TFX Group-Xi'an Jiaotong University Institute of Life Health, Xi'an 710049, P.R. China
| | - Jie Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Chang Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Haoqing Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
| | - Won Gu Lee
- Department of Mechanical Engineering,
Kyung Hee University, Yongin 17104, Republic of Korea
| | - Chunyan Yao
- Department of Transfusion Medicine, Southwest Hospital,
Third Military Medical University (Army Medical University), Chongqing 400038, P.R. China
| | - Hui Guo
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P.R. China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education,
School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, P.R. China
- Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi’an 710049, P.R. China
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2
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Sun Y, Zheng X, Wang H, Yan M, Chen Z, Yang Q, Shao Y. Research advances of SERS analysis method based on silent region molecules for food safety detection. Mikrochim Acta 2023; 190:387. [PMID: 37700165 DOI: 10.1007/s00604-023-05968-9] [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: 06/22/2023] [Accepted: 08/27/2023] [Indexed: 09/14/2023]
Abstract
Food safety is a critical issue that is closely related to people's health and safety. As a simple, rapid, and sensitive detection technique, surface-enhanced Raman scattering (SERS) technology has significant potential for food safety detection. Recently, researchers have shown a growing interest in utilizing silent region molecules for SERS analysis. These molecules exhibit significant Raman scattering peaks in the cellular Raman silent region between 1800 and 2800 cm-1 avoiding overlapping with the SERS spectrum of biological matrices in the range 600-1800 cm-1, which could effectively circumvent matrix effects and improve the SERS accuracy. In this review, the application of silent region molecules-based SERS analytical technique for food safety detection is introduced, detection strategies including label-free detection and labeled detection are discussed, and recent applications of SERS analysis technology based on molecules containing alkyne and nitrile groups, as well as Prussian blue (PB) in the detection of pesticides, mycotoxins, metal ions, and foodborne pathogens are highlighted. This review aims to draw the attention to the silent region molecules-based SERS analytical technique and to provide theoretical support for its further applications in food safety detection.
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Affiliation(s)
- Yuhang Sun
- School of Bioengineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, Shandong, People's Republic of China
- Institution of Quality Standard and Testing Technology for Agro-Products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xinxin Zheng
- School of Bioengineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, Shandong, People's Republic of China
| | - Hao Wang
- School of Bioengineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, Shandong, People's Republic of China
- Institution of Quality Standard and Testing Technology for Agro-Products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Mengmeng Yan
- Institution of Quality Standard and Testing Technology for Agro-Products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Zilei Chen
- Institution of Quality Standard and Testing Technology for Agro-Products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Qinzheng Yang
- School of Bioengineering, State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353, Shandong, People's Republic of China.
| | - Yong Shao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing, 100081, China.
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3
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Multifunctional Hybrid Nanozymes for Magnetic Enrichment and Bioelectrocatalytic Sensing of Circulating Tumor RNA during Minimal Residual Disease Monitoring. Catalysts 2023. [DOI: 10.3390/catal13010178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Iron oxide nanozymes are a form of nanomaterial with both superparamagnetic and enzyme-mimicking properties. Ongoing research efforts have been made to create multifunctional iron oxide hybrid nanozymes with auxiliary properties through biomolecular modifications. Such iron oxide hybrid nanozymes can be useful for rapid and cost-effective analysis of circulating tumor nucleic acids (ctNAs) in patient liquid biopsies during minimal residual disease (MRD) monitoring of cancer recurrence. Herein, the use of streptavidin-modified iron oxide hybrid nanozymes is reported for magnetic enrichment and bioelectrocatalytic sensing of three prostate cancer (PCa) ctRNA biomarkers with high detection specificity and sensitivity (10 copies) over an ultrabroad dynamic range (five orders of magnitude). Furthermore, the feasibility of ctRNA analysis for pre- and post-cancer treatment MRD monitoring is demonstrated using PCa urinary liquid biopsy samples.
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4
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Wang J, Koo KM, Trau M. Tetraplex Immunophenotyping of Cell Surface Proteomes via Synthesized Plasmonic Nanotags and Portable Raman Spectroscopy. Anal Chem 2022; 94:14906-14916. [PMID: 36256869 DOI: 10.1021/acs.analchem.2c02262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiplex immunophenotyping of cell surface proteomes is useful for cell characterization as well as providing valuable information on a patient's physiological or pathological state. Current methods for multiplex immunophenotyping of cell surface proteomes still have associated technical pitfalls in terms of limited multiplexing capability, challenging result interpretation, and large equipment footprint limited to use in a laboratory setting. Herein, we presented a portable surface-enhanced Raman spectroscopy (SERS) assay for multiplex cell surface immunophenotyping. We synthesized and functionalized customizable SERS nanotags for cell labeling and subsequent signal measurement using a portable Raman spectrometer. We extensively evaluated and validated the analytical assay performance of the portable SERS immunophenotyping assay in two different cellular models (red blood cells and breast cancer cells). In terms of analytical specificity, the cell surface immunophenotyping of both red blood cells and breast cancer cells correlated well with flow cytometry. The portable SERS immunophenotyping assay also has comparable analytical repeatability to flow cytometry, with coefficient of variation values of 21.89-23.33% and 6.88-17.32% for detecting red blood cells and breast cancer cells, respectively. The analytical detection limits were 77 cells/mL for red blood cells and 1-17 cells/mL for breast cancer cells. As an alternative to flow cytometry, the portable SERS immunophenotyping assay demonstrated excellent analytical assay performance and possessed advantages such as quick sample-to-result turnaround time, multiplexing capability, and small equipment footprint.
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Affiliation(s)
- Jing Wang
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350007, P. R. China.,Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kevin M Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Sinnamon Park, QLD 4073, Australia.,The University of Queensland Centre for Clinical Research (UQCCR), Herston, QLD 4029, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Velaga R, Koo KM, Mainwaring PN. Harnessing gene fusion-derived neoantigens for 'cold' breast and prostate tumor immunotherapy. Immunotherapy 2022; 14:1165-1179. [PMID: 36043380 DOI: 10.2217/imt-2022-0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Breast and prostate cancers are generally considered immunologically 'cold' tumors due to multiple mechanisms rendering them unresponsive to immune checkpoint blockade therapies. With little success in garnering positive outcomes in modern immunotherapeutic clinical trials, it is prudent to re-examine the role of immunogenic neoantigens in these cold tumors. Gene fusions are driver mutations in hormone-driven cancers that can result in alternative mutation-specific neoantigens to promote immunotherapy sensitivity. This review focuses on 1) gene fusion formation mechanisms in neoantigen generation; 2) gene fusion neoantigens in cancer immunotherapeutic strategies and associated clinical trials; and 3) challenges and opportunities in computational and liquid biopsy technologies. This review is anticipated to initiate further research into gene fusion neoantigens of cold tumors for further experimental validation.
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Affiliation(s)
- Ravi Velaga
- Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Kevin M Koo
- XING Technologies Pty Ltd, Brisbane, QLD 4073, Australia.,The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD 4029, Australia
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6
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Koo KM, Trau M. Molecular locker probe enrichment of gene fusion variants from matched patient liquid biopsy specimens for magneto-bioelectrocatalytic nanosensing. NANOSCALE 2022; 14:4225-4233. [PMID: 35234786 DOI: 10.1039/d1nr07845c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The accurate and sensitive analysis of recurrent gene fusion mutant variants in circulating tumor nucleic acids (NAs) of patient liquid biopsy samples is crucial for realizing clinical potential for cancer screening, diagnostics, and therapeutics. Gene fusion analysis is especially challenging in patient liquid biopsy samples because of trace biotarget levels in high non-target background of highly similar native and variant NA sequences. Herein, we describe accurate analysis of three prostate cancer gene fusion mutant variants in matched plasma and urine specimens from real cancer patients and healthy controls (n = 80) by (i) direct locker probe enrichment of multiple gene fusion mutant variants without tedious upstream sample processing; (ii) magneto-bioelectrocatalytic cycling readout using both NA-intercalating and freely diffusive redox probes for superior signal enhancement. For each mutant variant, an ultrabroad dynamic range (10-105 copies) was achieved with enhanced 10 copies (zmol) detection limit. With the combination of locker probe enrichment and magneto-bioelectrocatalytic cycling readout for NA mutant variant analysis, the potential of non-invasive liquid biopsies may be exploited for the benefit of cancer patients.
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Affiliation(s)
- Kevin M Koo
- The University of Queensland Centre for Clinical Research (UQCCR), QLD 4029, Australia.
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, QLD 4073, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia
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7
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Wang Y, Fang Y, Zhu Y, Bi S, Liu Y, Ju H. Single cell multi-miRNAs quantification with hydrogel microbeads for liver cancer cell subtypes discrimination. Chem Sci 2022; 13:2062-2070. [PMID: 35308856 PMCID: PMC8848760 DOI: 10.1039/d1sc05304c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022] Open
Abstract
The simultaneous quantification of multi-miRNAs in single cells reveals cellular heterogeneity, and benefits the subtypes discrimination of cancer cells . Though micro-droplet techniques enable successful single cell encapsulation, the isolated and restricted reaction space of microdroplets causes cross-reactions and inaccuracy for simultaneous multi-miRNAs quantification. Herein, we develop a hydrogel microbead based strategy for the simultaneous sensitive quantification of miRNA-21, 122 and 222 in single cells. Single cells are encapsulated and undergo cytolysis in hydrogel microbeads. The three target miRNAs are retained in the microbead by pre-immobilized capture probes, and activate rolling circle amplification (RCA) reactions. The RCA products are hybridized with corresponding dye labelled DNA reporters, and the respective fluorescence intensities are recorded for multi-miRNA quantification. The porous structure of the hydrogel microbeads allows the free diffusion of reactants and easy removal of unreacted DNA strands, which effectively avoids nonspecific cross-reactions. Clear differentiation of cellular heterogeneity and subpopulation discrimination are achieved for three kinds of liver cancer cells and one normal liver cell. A single cell multi-miRNAs quantification strategy is reported. Single cells are encapsulated and undergo cytolysis in hydrogel microbeads, then the quantitative analysis of three miRNAs is used to achieve sub-populations discrimination for liver cells.![]()
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Affiliation(s)
- Yingfei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 PR China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 PR China
| | - Yu Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 PR China
| | - Shiyi Bi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 PR China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 PR China.,Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210023 China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210023 PR China
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8
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Wu L, Dias A, Diéguez L. Surface enhanced Raman spectroscopy for tumor nucleic acid: Towards cancer diagnosis and precision medicine. Biosens Bioelectron 2022; 204:114075. [DOI: 10.1016/j.bios.2022.114075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/13/2022] [Accepted: 02/02/2022] [Indexed: 11/25/2022]
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9
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Zhu D, Li A, Di Y, Wang Z, Shi J, Ni X, Wang Y. Interference-free SERS nanoprobes for labeling and imaging of MT1-MMP in breast cancer cells. NANOTECHNOLOGY 2021; 33:115702. [PMID: 34874311 DOI: 10.1088/1361-6528/ac4065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/06/2021] [Indexed: 06/13/2023]
Abstract
The expression of membrane type-1 matrix metalloproteinase (MT1-MMP) in cancer cells is critical for understanding the development, invasion and metastasis of cancers. In this study, we devised an interference-free surface-enhanced Raman scattering (SERS) nanoprobe with high selectivity and specificity for MT1-MMP. The nanoprobe was comprised of silver core-silica shell nanoparticle with a Raman reporter tag (4-mercaptobenzonitrile) embedded in the interface. Moreover, the nitrile group in 4-mercaptobenzonitrile shows a unique characteristic peak in the Raman-silent region (1800-2800 cm-1), which eliminates spectral overlapping or background interference in the Raman fingerprint region (500-1800 cm-1). After surface modification with a targeting peptide, the nanoprobe allowed visualization and evaluation of MT1-MMP in breast cancer cells via SERS spectrometry. This interference-free, peptide-functionalized SERS nanoprobe is supposed to be conducive to early diagnosis and invasive assessment of cancer in clinical settings.
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Affiliation(s)
- Dan Zhu
- Jiangsu Key Laboratory on Opto-electronic Technology, School of Computer and Electronic Information/School of Artificial Intelligence, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China
| | - Anran Li
- Jiangsu Key Laboratory on Opto-electronic Technology, School of Computer and Electronic Information/School of Artificial Intelligence, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China
| | - Yunsong Di
- Jiangsu Key Laboratory on Opto-electronic Technology, School of Computer and Electronic Information/School of Artificial Intelligence, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China
| | - Zhuyuan Wang
- Advanced Photonics Center, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, Jiangsu, People's Republic of China
| | - Jingzhan Shi
- Jiangsu Key Laboratory on Opto-electronic Technology, School of Computer and Electronic Information/School of Artificial Intelligence, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China
| | - Xiaoqi Ni
- Jiangsu Key Laboratory on Opto-electronic Technology, School of Computer and Electronic Information/School of Artificial Intelligence, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China
| | - Yiping Wang
- Jiangsu Key Laboratory on Opto-electronic Technology, School of Computer and Electronic Information/School of Artificial Intelligence, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China
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Lu X, Hu C, Jia D, Fan W, Ren W, Liu C. Amplification-Free and Mix-and-Read Analysis of Multiplexed MicroRNAs on a Single Plasmonic Microbead. NANO LETTERS 2021; 21:6718-6724. [PMID: 34324345 DOI: 10.1021/acs.nanolett.1c02473] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, a single microbead covered with a plasmonic layer is employed as the microreactor for the multiplexed miRNA analysis without nucleic acid amplification. On the plasmonic layer, the S9.6 antibody is adopted as the universal module for binding DNA/miRNA duplexes regardless of the sequence. Meanwhile, there is also a SERS reporter gold nanoparticle (GNP) pool, in which each group of GNPs is labeled with both a Raman coding molecule and a DNA probe for recognizing a given miRNA of interest. The target miRNAs will lead to the specific capture of the corresponding SERS reporter GNPs onto the plasmonic layer, which will enormously enhance the target miRNA-induced SERS signals. Finally, the enhanced SERS signals concentrated on the microbead will be mapped out by a confocal Raman microscope. The proposed method achieves the high-precision sensing of sub-pM target miRNA in a simple mix-and-read format and possesses multiplexed assay capability.
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Affiliation(s)
- Xiaohui Lu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an, Shaanxi Province 710119, P. R. China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, Shaanxi Province 710119, P. R. China
- School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Chen Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an, Shaanxi Province 710119, P. R. China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, Shaanxi Province 710119, P. R. China
- School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Dailu Jia
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an, Shaanxi Province 710119, P. R. China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, Shaanxi Province 710119, P. R. China
- School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an, Shaanxi Province 710119, P. R. China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, Shaanxi Province 710119, P. R. China
- School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an, Shaanxi Province 710119, P. R. China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, Shaanxi Province 710119, P. R. China
- School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Xi'an, Shaanxi Province 710119, P. R. China
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Xi'an, Shaanxi Province 710119, P. R. China
- School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi Province 710119, P. R. China
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11
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Luo G, Zhang J, Yang M, He H, Huang Z. Selenium atom on phosphate enhances specificity and sensitivity of DNA polymerization and detection. J Mater Chem B 2021; 9:5636-5644. [PMID: 34196647 DOI: 10.1039/d1tb00428j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA polymerization is of high specificity in vivo. However, its specificity is much lower in vitro, which limits advanced applications of DNA polymerization in ultrasensitive nucleic acid detection. Herein, we report a unique mechanism of single selenium-atom modified dNTP (dNTPαSe) to enhance polymerization specificity. We have found that both dNTPαSe (approximately 660 fold) and Se-DNA (approximately 2.8 fold) have lower binding affinity to DNA polymerase than canonical ones, and the Se-DNA duplex has much lower melting-temperature (Tm) than the corresponding canonical DNA duplex. The reduced affinity and Tm can destabilize the substrate-primer-template-enzyme assembly, thereby largely slowing down the mismatch of DNA polymerization and enhancing the amplification specificity and in turn detection sensitivity. Furthermore, the Se-strategy enables us to develop the selenium enhanced specific isothermal amplification (SEA) for nucleic acid detection with high specificity and sensitivity (up to detection of single-digit copies), allowing convenient detection of clinical HPV and COVID-19 viruses in the low-copy number. Clearly, we have discovered the exciting mechanism for enhancing DNA polymerization accuracy, amplification specificity and detection sensitivity by SEA, up to two orders of magnitude higher.
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Affiliation(s)
- Guangcheng Luo
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China. and Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jun Zhang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Mei Yang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Hongfei He
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China.
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China. and SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, China
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