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Liu M, Miao D, Qin S, Liu H, Bai Y. Mass tags-based mass spectrometric immunoassay and its bioanalysis applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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2
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Shi CX, Li YZ, Liu Q, Chen ZP, Li SS, Yu RQ. Label-free microRNA detection through analyzing the length distribution pattern of the residual fragments of probe DNA produced during exonuclease III assisted signal amplification by mass spectrometry. Talanta 2021; 231:122414. [PMID: 33965054 DOI: 10.1016/j.talanta.2021.122414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/26/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022]
Abstract
Biosensors based on various spectroscopic techniques discriminate the target microRNA (miRNA) from non-target ones with single nucleotide polymorphisms (SNPs) according to the differences in signal intensities which can be caused by other factors besides SNPs. As a result, they are liable to produce false positive results. Herein, we report an attempt to develop a false-positive resistance, sensitive and reliable mass spectrometric platform for miRNA detection. In the proposed platform, the qualitative and quantitative information of the target miRNA was obtained through analyzing mass spectral responses of the multiply charged ions of the residual fragments of the probe DNA produced during exonuclease III assisted signal amplification reaction using an advanced data analysis method. The proposed platform could achieve sensitive and accurate quantitative results for the target miRNA (e.g., miRNA-141) in complex medium with a detection limit of about 1 pM, and unambiguously identify non-target miRNAs with SNPs based on the length distribution patterns of residual fragments of probe DNA. The findings obtained in this study might open an avenue for the design of new miRNA detection methods based on mass spectrometry in combination with various nuclease assisted signal amplification strategies.
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Affiliation(s)
- Cai-Xia Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China; College of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan, 030024, China
| | - Yan-Zi Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China
| | - Qing Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China
| | - Zeng-Ping Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China.
| | - Sha-Sha Li
- College of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan, 030024, China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China
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3
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Zhu YL, Lian YM, Wang JK, Chen ZP, Yu RQ. Highly Sensitive and Specific Mass Spectrometric Platform for miRNA Detection Based on the Multiple-Metal-Nanoparticle Tagging Strategy. Anal Chem 2021; 93:5839-5848. [PMID: 33797890 DOI: 10.1021/acs.analchem.1c00065] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The multiple-metal-nanoparticle tagging strategy has generally been applied to the multiplexed detection of multiple analytes of interest such as microRNAs (miRNAs). Herein, it was used for the first time to improve both the specificity and sensitivity of a novel mass spectroscopic platform for miRNA detection. The mass spectroscopic platform was developed through the integration of the ligation reaction, hybridization chain reaction amplification, multiple-metal-nanoparticle tagging, and inductively coupled plasma mass spectrometry. The high specificity resulted from the adoption of the ligation reaction is further enhanced by the multiple-metal-nanoparticle tagging strategy. The combination of hybridization chain reaction amplification and metal nanoparticle tagging endows the proposed platform with the feature of high sensitivity. The proposed mass spectrometric platform achieved quite satisfactory quantitative results for Let-7a in real-world cell line samples with accuracy comparable to that of the real-time quantitative reverse-transcriptase polymerase chain reaction method. Its limit of detection and limit of quantification for Let-7a were experimentally determined to be about 0.5 and 10 fM, respectively. Furthermore, due to the unique way of utilizing the multiple-metal-nanoparticle tagging strategy, the proposed platform can unambiguously discriminate between the target miRNA and nontarget ones with single-nucleotide polymorphisms based on their response patterns defined by the relative mass spectral intensities among the multiple tagged metal elements and can also provide location information of the mismatched bases. Its unique advantages over conventional miRNA detection methods make the proposed platform a promising and alternative tool in the fields of clinical diagnosis and biomedical research.
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Affiliation(s)
- Yan-Li Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Yan-Mei Lian
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Ji-Kai Wang
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy & Pharmacology, University of South China, Hengyang 421001, P. R. China
| | - Zeng-Ping Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
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4
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Kang N, Lee JM, Jeon A, Oh HB, Moon B. Design and synthesis of new mass tags for matrix-free laser desorption ionization mass spectrometry (LDI-MS) based on 6,11-dihydrothiochromeno[4,3-b]indole. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.07.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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5
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Topolyan AP, Strizhevskaya DA, Belyaeva MA, Brylev VA, Ustinov AV, Formanovsky AA, Korshun VA. A triphenylcyclopropenylium mass tag: synthesis and application to ultrasensitive LC/MS analysis of amines. Analyst 2016; 141:3289-95. [DOI: 10.1039/c5an02642c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Thiol adducts of triphenylcyclopropenylium undergo efficient heterolytic dissociation in electrospray (ESI) or laser desorption ionization (LDI) mass spectrometry giving rise to a prominent signal of an aromatic C3Ph3+ cation.
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Affiliation(s)
- Artyom P. Topolyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
| | | | - Maria A. Belyaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
| | - Vladimir A. Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
- Lumiprobe Corp
- Hallandale Beach
| | | | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry
- 117997 Moscow
- Russia
- Gause Institute of New Antibiotics
- 119021 Moscow
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6
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Lorey M, Adler B, Yan H, Soliymani R, Ekström S, Yli-Kauhaluoma J, Laurell T, Baumann M. Mass-Tag Enhanced Immuno-Laser Desorption/Ionization Mass Spectrometry for Sensitive Detection of Intact Protein Antigens. Anal Chem 2015; 87:5255-62. [DOI: 10.1021/acs.analchem.5b00304] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Martina Lorey
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
- Institute
of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FI-00014, Finland
- Unit
of Systems Toxicology, Finnish Institute of Occupational Health, Topeliuksenkatu 41 b, FI-00250 Helsinki, Finland
| | - Belinda Adler
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Hong Yan
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Rabah Soliymani
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
| | - Simon Ekström
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Jari Yli-Kauhaluoma
- Division
of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 University of Helsinki, Finland
| | - Thomas Laurell
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
- Department
of Biomedical Engineering, Dongguk University, 202 Science Building Phildong 3ga. Joong-Gu Seoul, Republic of Korea
| | - Marc Baumann
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
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7
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Huang Y, Zhu J, Li G, Chen Z, Jiang JH, Shen GL, Yu RQ. Electrochemical detection of point mutation based on surface hybridization assay conjugated allele-specific polymerase chainreaction. Biosens Bioelectron 2013; 42:526-31. [DOI: 10.1016/j.bios.2012.10.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/23/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022]
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8
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Dai C, Cazares LH, Wang L, Chu Y, Wang SL, Troyer DA, Semmes OJ, Drake RR, Wang B. Using boronolectin in MALDI-MS imaging for the histological analysis of cancer tissue expressing the sialyl Lewis X antigen. Chem Commun (Camb) 2011; 47:10338-40. [PMID: 21853197 DOI: 10.1039/c1cc11814e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Certain carbohydrate-based biomarkers are known to correlate with cancer formation and progression. By targeting sialyl Lewis X, we have developed the first boronolectin-MS tag conjugate, which allows for MALDI-based imaging of cancer based on its cell surface carbohydrate.
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Affiliation(s)
- Chaofeng Dai
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302-4098, USA
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9
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Electrochemical biosensors for detection of point mutation based on surface ligation reaction and oligonucleotides modified gold nanoparticles. Anal Chim Acta 2011; 688:163-7. [PMID: 21334481 DOI: 10.1016/j.aca.2011.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 12/21/2010] [Accepted: 01/04/2011] [Indexed: 11/23/2022]
Abstract
An electrochemical method for point mutation detection based on surface ligation reaction and oligonucleotides (ODNs) modified gold nanoparticles (AuNPs) was demonstrated. Point mutation identification was achieved using Escherichia coli DNA ligase. This system for point mutation detection relied on a sandwich assay comprising capture ODN immobilized on Au electrodes, target ODN and ligation ODN. Because of the sequence-specific surface reactions of E. coli DNA ligase, the ligation ODN covalently linked to the capture ODN only in the presence of a perfectly complementary target ODN. The presence of ligation products on Au electrode was detected using chronocoulometry through hybridization with reporter ODN modified AuNPs. The use of AuNPs improved the sensitivity of chronocoulometry in this approach, a detection limit of 0.9 pM complementary ODN was obtained. For single base mismatched ODN (smODN), a negligible signal was observed. Even if the concentration ratio of complementary ODN to smODN was decreased to 1:1000, a detectable signal was observed. This work may provide a specific, sensitive and cost-efficient approach for point mutant detection.
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10
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Birikh KR, Bernad PL, Shmanai VV, Malakhov AD, Shchepinov MS, Korshun VA. SNP detection using trityl mass tags. Methods Mol Biol 2009; 578:345-61. [PMID: 19768604 DOI: 10.1007/978-1-60327-411-1_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
A new method suitable for single nucleotide polymorphism (SNP) detection using differential oligonucleotide probe extension has been developed. Sulfur-linked laser-cleavable trityl labels are implemented in this protocol. The method is based on mass spectrometry and utilizes a single surface for affinity purification of extended probes and matrix-independent desorption-ionization of the cleavable labels. The usefulness of this method for SNP genotyping is demonstrated.
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Affiliation(s)
- Klara R Birikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya, Moscow, Russia
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11
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[Microchip electrophoresis coupled with multiplex allele-specific am-plification for typing multiple single nucleotide polymorphisms (SNPs) simultaneously]. YI CHUAN = HEREDITAS 2009; 31:219-24. [PMID: 19273432 DOI: 10.3724/sp.j.1005.2009.00219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A new method of DNA adapter ligation-mediated allele-specific amplification (ALM-ASA) was developed for typing multiple single nucleotide polymorphisms (SNPs) on the platform of microchip electrophoresis. Using seven SNPs of 794C>T, 1274C>T, 2143T>C, 2766T>del, 3298G>A, 5200G>A, and 5277C>T in the interleukin 1B (IL1B) gene as a target object, a long DNA fragment containing the seven SNPs of interest was pre-amplified to enhance the specificity. The pre-amplified DNA fragment was digested by a restriction endonuclease to form sticky ends; and then the adapter was ligated to either end of the digested fragment. Using the adapter-ligated fragments as templates, a 7-plex allele-specific amplification was performed by 7 allele-specific primers and a universal primer in one tube. The allele-specific products amplified were separated by chip electrophoresis and the types of SNPs were easily discriminated by the product sizes. The seven SNPs in IL1B gene in 48 healthy Chinese were successfully typed by microchip electrophoresis and the results coincided with those by PCR-restriction fragment length polymorphism and sequencing method. The method established was accurate and can be used to type multiple SNPs simultaneously. In combination with microchip electrophoresis for readout, ALM-ASA assay can be used for fast SNP detection with a small amount of sample. Using self-prepared gel matrix and reused chips for analysis, the SNP can be typed at an ultra low cost.
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12
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Huang Y, Zhang YL, Xu X, Jiang JH, Shen GL, Yu RQ. Highly Specific and Sensitive Electrochemical Genotyping via Gap Ligation Reaction and Surface Hybridization Detection. J Am Chem Soc 2009; 131:2478-80. [DOI: 10.1021/ja808700d] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yong Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Yan-Li Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Xiangmin Xu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Guo-Li Shen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P.R. China, Department of Medical Genetics, School of Basic Medical Sciences, South Medical University, Guangzhou 510515, P.R. China
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13
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Weisbrod SH, Marx A. Novel strategies for the site-specific covalent labelling of nucleic acids. Chem Commun (Camb) 2008:5675-85. [PMID: 19009049 DOI: 10.1039/b809528k] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.
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Affiliation(s)
- Samuel H Weisbrod
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457, Konstanz, Germany
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14
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Ustinov AV, Shmanai VV, Patel K, Stepanova IA, Prokhorenko IA, Astakhova IV, Malakhov AD, Skorobogatyi MV, Bernad PL, Khan S, Shahgholi M, Southern EM, Korshun VA, Shchepinov MS. Reactive trityl derivatives: stabilised carbocation mass-tags for life sciences applications. Org Biomol Chem 2008; 6:4593-608. [DOI: 10.1039/b810600b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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