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Zhang Y, Xu S, Luo M, Chen J, Wang L, Yang F, Ye J, Liu J, He B, Weng L, Li S, Zhang D. Hairpin-Empowered Invasive Reaction Combined with Catalytic Hairpin Assembly Cascade Amplification for the Specific Detection of Single-Nucleotide Polymorphisms. Anal Chem 2024; 96:10283-10293. [PMID: 38864304 DOI: 10.1021/acs.analchem.4c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Single-nucleotide polymorphism (SNP) is widely used in the study of disease-related genes and in the genetic study of animal and plant strains. Therefore, SNP detection is crucial for biomedical diagnosis and treatment as well as for molecular design breeding of animals and plants. In this regard, this article describes a novel technique for detecting SNP using flap endonuclease 1 (FEN 1) as a specific recognition element and catalytic hairpin assembly (CHA) cascade reaction as a signal amplification strategy. The mutant target (MT) was hybridized with a biotin-modified upstream probe and hairpin-type downstream probe (DP) to form a specific three-base overlapping structure. Then, FEN 1 was employed for three-base overlapping structure-specific recognition, namely, the precise SNP site identification and the 5' flap of DP dissociation. After dissociation, the hybridized probes were magnetically separated by a streptavidin-biotin complex. Especially, the ability to establish such a hairpin-type DP provided a powerful tool that could be used to hide the cut sequence (CS) and avoid false-positive signals. The cleaved CS initiated the CHA reaction and allowed superior fluorescence signal generation. Owing to the high specificity of FEN 1 for single base recognition, only the MT could be distinguished from the wild-type target and mismatched DNA. Owing to the dual signal amplification, as low as 0.36 fM MT and 1% mutation abundance from the mixtures could be detected, respectively. Furthermore, it could accurately identify SNPs from human cancer cells, as well as soybean leaf genome extracts. This strategy paves the way for the development of more precise and sensitive tools for diagnosing early onset diseases as well as molecular design breeding tools.
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Affiliation(s)
- Yunshan Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shijie Xu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Ma Luo
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Lanyue Wang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Fang Yang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Jing Ye
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jichong Liu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Bingxiao He
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lin Weng
- Research Center for Intelligent Computing Platforms, Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Diming Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
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4
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McGinn S, Bauer D, Brefort T, Dong L, El-Sagheer A, Elsharawy A, Evans G, Falk-Sörqvist E, Forster M, Fredriksson S, Freeman P, Freitag C, Fritzsche J, Gibson S, Gullberg M, Gut M, Heath S, Heath-Brun I, Heron AJ, Hohlbein J, Ke R, Lancaster O, Le Reste L, Maglia G, Marie R, Mauger F, Mertes F, Mignardi M, Moens L, Oostmeijer J, Out R, Pedersen JN, Persson F, Picaud V, Rotem D, Schracke N, Sengenes J, Stähler PF, Stade B, Stoddart D, Teng X, Veal CD, Zahra N, Bayley H, Beier M, Brown T, Dekker C, Ekström B, Flyvbjerg H, Franke A, Guenther S, Kapanidis AN, Kaye J, Kristensen A, Lehrach H, Mangion J, Sauer S, Schyns E, Tost J, van Helvoort JMLM, van der Zaag PJ, Tegenfeldt JO, Brookes AJ, Mir K, Nilsson M, Willcocks JP, Gut IG. New technologies for DNA analysis--a review of the READNA Project. N Biotechnol 2015; 33:311-30. [PMID: 26514324 DOI: 10.1016/j.nbt.2015.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/17/2015] [Indexed: 01/09/2023]
Abstract
The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.
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Affiliation(s)
- Steven McGinn
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - David Bauer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas Brefort
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Liqin Dong
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Afaf El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Abdou Elsharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany; Faculty of Sciences, Division of Biochemistry, Chemistry Department, Damietta University, New Damietta City, Egypt
| | - Geraint Evans
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Elin Falk-Sörqvist
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | | | - Peter Freeman
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Camilla Freitag
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department of Applied Physics, Chalmers University of Technology, Kemivägen 10, 412 96 Göteborg, Sweden
| | - Spencer Gibson
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Mats Gullberg
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Simon Heath
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Isabelle Heath-Brun
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrew J Heron
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Johannes Hohlbein
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Rongqin Ke
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Owen Lancaster
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Ludovic Le Reste
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Giovanni Maglia
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Rodolphe Marie
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Florence Mauger
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Florian Mertes
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Marco Mignardi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Lotte Moens
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | | | - Ruud Out
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | | | - Fredrik Persson
- Department of Physics, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Vincent Picaud
- CEA-Saclay, Bât DIGITEO 565 - Pt Courrier 192, 91191 Gif-sur-Yvette Cedex, France
| | - Dvir Rotem
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Nadine Schracke
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Jennifer Sengenes
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | - Peer F Stähler
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - David Stoddart
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Xia Teng
- FlexGen BV, Galileiweg 8, 2333 BD Leiden, The Netherlands
| | - Colin D Veal
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Nathalie Zahra
- University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, England, UK
| | - Markus Beier
- Comprehensive Biomarker Center GmbH, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
| | - Tom Brown
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK; Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Rd, Oxford OX1 3TA, UK
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Björn Ekström
- Olink AB, Dag Hammarskjölds väg 52A, 752 37 Uppsala, Sweden
| | - Henrik Flyvbjerg
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University (CAU), Am Botanischen Garten 11, D-24118 Kiel, Germany
| | - Simone Guenther
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, Parks Road, Oxford OX1 3PU, UK
| | - Jane Kaye
- HeLEX - Centre for Health, Law and Emerging Technologies, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Anders Kristensen
- DTU Nanotech, Oerstedsplads Building 345 East, 2800, Kongens Lyngby, Denmark
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Jonathan Mangion
- Thermo Fisher Scientific Frankfurter Straße 129B, 64293 Darmstadt, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Emile Schyns
- PHOTONIS France S.A.S. Avenue Roger Roncier, 19100 Brive B.P. 520, 19106 BRIVE Cedex, France
| | - Jörg Tost
- CEA - Centre National de Génotypage, 2, rue Gaston Cremieux, 91057 Evry Cedex, France
| | | | - Pieter J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE Eindhoven, The Netherlands
| | - Jonas O Tegenfeldt
- Division of Solid State Physics and NanoLund, Lund University, Box 118, 22100 Lund, Sweden
| | | | - Kalim Mir
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, Se-171 21 Solna, Sweden; Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - James P Willcocks
- Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, UK
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, C/Baldiri Reixac 7, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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16
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Mauger F, Bauer K, Calloway CD, Semhoun J, Nishimoto T, Myers TW, Gelfand DH, Gut IG. DNA sequencing by MALDI-TOF MS using alkali cleavage of RNA/DNA chimeras. Nucleic Acids Res 2007; 35:e62. [PMID: 17426131 PMCID: PMC1885642 DOI: 10.1093/nar/gkm056] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Approaches developed for sequencing DNA with detection by mass spectrometry use strategies that deviate from the Sanger-type methods. Procedures demonstrated so far used the sequence specificity of RNA endonucleases, as unfortunately equivalent enzymes for DNA do not exist and therefore require transcription of DNA into RNA prior to fragmentation. We have developed a novel, rapid and accurate concept for DNA sequencing using mass spectrometry and RNA/DNA chimeras and applied it to sequence mitochondrial DNA. Our method is based on the preparation of a chimeric RNA/DNA with a DNA polymerase that also incorporates ribonucleotides. Sequencing is carried out with one ribonucleotide (ATP, CTP or GTP) and the other three nucleotides in their deoxyribo-form. The product is treated with alkali, which cleaves 3' of all ribonucleotides to form a terminal 3' phosphate. Conditions have been streamlined so that molecular, biological and alkali cleavage conditions are compatible with matrix-assisted laser desorption/ionization time-of-flight (MALDI) mass spectrometric analysis. Fragment analysis by MALDI MS provides a sequence-specific fingerprint, which allows the identification of differences between a reference and another sequence. Due to the mass profile, the position and kind of the mutation can be assigned. These differences between signatures are indicative of known, unidentified, rare and private mutations. This novel DNA sequencing protocol was applied to sequence the hypervariable region 1 (HV1) of mitochondrial DNA in 22 individuals.
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Affiliation(s)
- Florence Mauger
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - Keith Bauer
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - Cassandra D. Calloway
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - Jérémy Semhoun
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - Tetsuya Nishimoto
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - Thomas W. Myers
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - David H. Gelfand
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
| | - Ivo G. Gut
- Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA
- *To whom correspondence should be addressed +33 160 87 84 00+33 160 87 83 83
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