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Murphy ZR, Shields DA, Evrony GD. Serial enrichment of heteroduplex DNA using a MutS-magnetic bead system. Biotechnol J 2023; 18:e2200323. [PMID: 36317440 PMCID: PMC9839629 DOI: 10.1002/biot.202200323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022]
Abstract
Numerous applications in molecular biology and genomics require characterization of mutant DNA molecules present at low levels within a larger sample of non-mutant DNA. This is often achieved either by selectively amplifying mutant DNA, or by sequencing all the DNA followed by computational identification of the mutant DNA. However, selective amplification is challenging for insertions and deletions (indels). Additionally, sequencing all the DNA in a sample may not be cost effective when only the presence of a mutation needs to be ascertained rather than its allelic fraction. The MutS protein evolved to detect DNA heteroduplexes in which the two DNA strands are mismatched. Prior methods have utilized MutS to enrich mutant DNA by hybridizing mutant to non-mutant DNA to create heteroduplexes. However, the purity of heteroduplex DNA these methods achieve is limited because they can only feasibly perform one or two enrichment cycles. We developed a MutS-magnetic bead system that enables rapid serial enrichment cycles. With six cycles, we achieve complete purification of heteroduplex indel DNA originally present at a 5% fraction and over 40-fold enrichment of heteroduplex DNA originally present at a 1% fraction. This system may enable novel approaches for enriching mutant DNA for targeted sequencing.
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Affiliation(s)
- Zachary R. Murphy
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Danielle A. Shields
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Gilad D. Evrony
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
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MutS recognition of mismatches within primed DNA replication intermediates. DNA Repair (Amst) 2022; 119:103392. [PMID: 36095926 DOI: 10.1016/j.dnarep.2022.103392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/24/2022]
Abstract
MutS initiates mismatch repair by recognizing mismatches in newly replicated DNA. Specific interactions between MutS and mismatches within double-stranded DNA promote ADP-ATP exchange and a conformational change into a sliding clamp. Here, we demonstrated that MutS from Pseudomonas aeruginosa associates with primed DNA replication intermediates. The predicted structure of this MutS-DNA complex revealed a new DNA binding site, in which Asn 279 and Arg 272 appeared to directly interact with the 3'-OH terminus of primed DNA. Mutation of these residues resulted in a noticeable defect in the interaction of MutS with primed DNA substrates. Remarkably, MutS interaction with a mismatch within primed DNA induced a compaction of the protein structure and impaired the formation of an ATP-bound sliding clamp. Our findings reveal a novel DNA binding mode, conformational change and intramolecular signaling for MutS recognition of mismatches within primed DNA structures.
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Brovarets' OO, Hovorun DM. Wobble↔Watson-Crick tautomeric transitions in the homo-purine DNA mismatches: a key to the intimate mechanisms of the spontaneous transversions. J Biomol Struct Dyn 2015; 33:2710-5. [PMID: 26237090 DOI: 10.1080/07391102.2015.1077737] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The intrinsic capability of the homo-purine DNA base mispairs to perform wobble↔Watson-Crick/Topal-Fresco tautomeric transitions via the sequential intrapair double proton transfer was discovered for the first time using QM (MP2/DFT) and QTAIM methodologies that are crucial for understanding the microstructural mechanisms of the spontaneous transversions.
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Affiliation(s)
- Ol'ha O Brovarets'
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., 03680 Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., 03022 Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., 03680 Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., 03022 Kyiv , Ukraine
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Rossetti G, Dans PD, Gomez-Pinto I, Ivani I, Gonzalez C, Orozco M. The structural impact of DNA mismatches. Nucleic Acids Res 2015; 43:4309-21. [PMID: 25820425 PMCID: PMC4417165 DOI: 10.1093/nar/gkv254] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 12/17/2014] [Accepted: 03/12/2015] [Indexed: 11/13/2022] Open
Abstract
The structure and dynamics of all the transversion and transition mismatches in three different DNA environments have been characterized by molecular dynamics simulations and NMR spectroscopy. We found that the presence of mismatches produced significant local structural alterations, especially in the case of purine transversions. Mismatched pairs often show promiscuous hydrogen bonding patterns, which interchange among each other in the nanosecond time scale. This therefore defines flexible base pairs, where breathing is frequent, and where distortions in helical parameters are strong, resulting in significant alterations in groove dimension. Even if the DNA structure is plastic enough to absorb the structural impact of the mismatch, local structural changes can be propagated far from the mismatch site, following the expected through-backbone and a previously unknown through-space mechanism. The structural changes related to the presence of mismatches help to understand the different susceptibility of mismatches to the action of repairing proteins.
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Affiliation(s)
- Giulia Rossetti
- Joint BSC-CRG-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain Computational Biophysics, German Research School for Simulation Sciences (Joint venture of RWTH Aachen University and Forschungszentrum Jülich, Germany), D-52425 Jülich, Germany and Institute for Advanced Simulation IAS-5, Computational Biomedicine, Forschungszentrum Jülich, D-52425 Jülich, Germany Juelich Supercomputing Center (JSC), Forschungszentrum Jülich, Jülich, Germany
| | - Pablo D Dans
- Joint BSC-CRG-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Irene Gomez-Pinto
- Joint BSC-CRG-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, Madrid 28006, Spain
| | - Ivan Ivani
- Joint BSC-CRG-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Carlos Gonzalez
- Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, Madrid 28006, Spain
| | - Modesto Orozco
- Joint BSC-CRG-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac, 10, Barcelona 08028, Spain Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, Barcelona 08028, Spain
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5
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Impact of a mutator phenotype on motility and cell adherence in Salmonella Heidelberg. Vet Microbiol 2012; 159:99-106. [DOI: 10.1016/j.vetmic.2012.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 03/13/2012] [Accepted: 03/16/2012] [Indexed: 02/04/2023]
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The C-terminal domain is sufficient for endonuclease activity of Neisseria gonorrhoeae MutL. Biochem J 2009; 423:265-77. [PMID: 19656086 DOI: 10.1042/bj20090626] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The mutL gene of Neisseria gonorrhoeae has been cloned and the gene product purified. We have found that the homodimeric N. gonorrhoeae MutL (NgoL) protein displays an endonuclease activity that incises covalently closed circular DNA in the presence of Mn(2+), Mg(2+) or Ca(2+) ions, unlike human MutLalpha which shows endonuclease activity only in the presence of Mn(2+). We report in the present paper that the C-terminal domain of N. gonorrhoeae MutL (NgoL-CTD) consisting of amino acids 460-658 exhibits Mn(2+)-dependent endonuclease activity. Sedimentation velocity, sedimentation equilibrium and dynamic light scattering experiments show NgoL-CTD to be a dimer. The probable endonucleolytic active site is localized to a metal-binding motif, DMHAX2EX4E, and the nicking endonuclease activity is dependent on the integrity of this motif. By in vitro comparison of wild-type and a mutant NgoL-CTD protein, we show that the latter protein exhibits highly reduced endonuclease activity. We therefore suggest that the mode of excision initiation in DNA mismatch repair may be different in organisms that lack MutH protein, but have MutL proteins that harbour the D[M/Q]HAX2EX4E motif.
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Le Gall S, Desbordes L, Gracieux P, Saffroy S, Bousarghin L, Bonnaure-Mallet M, Jolivet-Gougeon A. Distribution of mutation frequencies among Salmonella enterica isolates from animal and human sources and genetic characterization of a Salmonella Heidelberg hypermutator. Vet Microbiol 2009; 137:306-12. [DOI: 10.1016/j.vetmic.2009.01.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 01/08/2009] [Accepted: 01/12/2009] [Indexed: 01/11/2023]
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Lopez-Crapez E, Malinge JM, Gatchitch F, Casano L, Langlois T, Pugnière M, Roquet F, Mathis G, Bazin H. A homogeneous resonance energy transfer-based assay to monitor MutS/DNA interactions. Anal Biochem 2008; 383:301-6. [PMID: 18824153 DOI: 10.1016/j.ab.2008.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2008] [Revised: 08/29/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
Probing the interactions of the DNA mismatch repair protein MutS with altered and damaged DNA is of great interest both for the understanding of the mismatch repair system function and for the development of tools to detect mutations. Here we describe a homogeneous time-resolved fluorescence (HTRF) assay to study the interactions of Escherichia coli MutS protein with various DNA substrates. First, we designed an indirect HTRF assay on a microtiter plate format and demonstrated its general applicability through the analysis of the interactions between MutS and mismatched DNA or DNA containing the most common lesion of the anticancer drug cisplatin. Then we directly labeled MutS with the long-lived fluorescent donor molecule europium tris-bipyridine cryptate ([TBP(Eu(3+))]) and demonstrated by electrophoretic mobility shift assay that this chemically labeled protein retained DNA mismatch binding property. Consequently, we used [TBP(Eu(3+))]-MutS to develop a faster and simpler semidirect HTRF assay.
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Affiliation(s)
- Evelyne Lopez-Crapez
- Department of Oncobiology, Cancer Research Center, CRLC Val d'Aurelle-Paul Lamarque, 34298 Montpellier Cedex 5, France.
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