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Sarangi MK, Zvoda V, Holte MN, Becker NA, Peters JP, Maher LJ, Ansari A. Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A. Nucleic Acids Res 2019; 47:2871-2883. [PMID: 30698746 PMCID: PMC6451137 DOI: 10.1093/nar/gkz022] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 01/17/2023] Open
Abstract
The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60°. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18-base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6A-bound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45°C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35°C. Microseconds-resolved laser temperature-jump perturbation of the yNhp6a–DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 μs−1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein.
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Affiliation(s)
- Manas Kumar Sarangi
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Viktoriya Zvoda
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Molly Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Nicole A Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Justin P Peters
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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2
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Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res 2019; 46:1741-1755. [PMID: 29267885 PMCID: PMC5829579 DOI: 10.1093/nar/gkx1215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
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Affiliation(s)
- Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serguei V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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3
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Ishino S, Nishi Y, Oda S, Uemori T, Sagara T, Takatsu N, Yamagami T, Shirai T, Ishino Y. Identification of a mismatch-specific endonuclease in hyperthermophilic Archaea. Nucleic Acids Res 2016; 44:2977-86. [PMID: 27001046 PMCID: PMC4838380 DOI: 10.1093/nar/gkw153] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/29/2016] [Indexed: 12/17/2022] Open
Abstract
The common mismatch repair system processed by MutS and MutL and their homologs was identified in Bacteria and Eukarya. However, no evidence of a functional MutS/L homolog has been reported for archaeal organisms, and it is not known whether the mismatch repair system is conserved in Archaea. Here, we describe an endonuclease that cleaves double-stranded DNA containing a mismatched base pair, from the hyperthermophilic archaeon Pyrococcus furiosus The corresponding gene revealed that the activity originates from PF0012, and we named this enzyme Endonuclease MS (EndoMS) as the mismatch-specific Endonuclease. The sequence similarity suggested that EndoMS is the ortholog of NucS isolated from Pyrococcus abyssi, published previously. Biochemical characterizations of the EndoMS homolog from Thermococcus kodakarensis clearly showed that EndoMS specifically cleaves both strands of double-stranded DNA into 5'-protruding forms, with the mismatched base pair in the central position. EndoMS cleaves G/T, G/G, T/T, T/C and A/G mismatches, with a more preference for G/T, G/G and T/T, but has very little or no effect on C/C, A/C and A/A mismatches. The discovery of this endonuclease suggests the existence of a novel mismatch repair process, initiated by the double-strand break generated by the EndoMS endonuclease, in Archaea and some Bacteria.
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Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Yuki Nishi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Soichiro Oda
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Takashi Uemori
- Takara Bio Inc., Nojihigashi 7-4-38, Kusatsu, Shiga 525-0058, Japan
| | - Takehiro Sagara
- Takara Bio Inc., Nojihigashi 7-4-38, Kusatsu, Shiga 525-0058, Japan
| | - Nariaki Takatsu
- Takara Bio Inc., Nojihigashi 7-4-38, Kusatsu, Shiga 525-0058, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
| | - Tsuyoshi Shirai
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Fukuoka 812-8581, Japan
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4
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Monakhova M, Ryazanova A, Hentschel A, Viryasov M, Oretskaya T, Friedhoff P, Kubareva E. Chromatographic isolation of the functionally active MutS protein covalently linked to deoxyribonucleic acid. J Chromatogr A 2015; 1389:19-27. [PMID: 25746757 DOI: 10.1016/j.chroma.2015.02.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/10/2015] [Accepted: 02/16/2015] [Indexed: 12/11/2022]
Abstract
DNA metabolism is based on formation of different DNA-protein complexes which can adopt various conformations. To characterize functioning of such complexes, one needs a solution-based technique which allows fixing a complex in a certain transient conformation. The crosslinking approach is a popular tool for such studies. However, it is under debate if the protein components retain their natural activities in the resulting crosslinked complexes. In the present work we demonstrate the possibility of obtaining pure DNA conjugate with functionally active protein using as example MutS protein from Escherichia coli mismatch repair system. A conjugate of a chemically modified mismatch-containing DNA duplex with MutS is fixed by thiol-disulfide exchange reaction. To perform a reliable test of the protein activity in the conjugate, such conjugate must be thoroughly separated from the uncrosslinked protein and DNA prior to the test. In the present work, we employ anion exchange chromatography for this purpose for the first time and demonstrate this technique to be optimal for the conjugate purification. The activity test is a FRET-based detection of DNA unbending. We show experimentally that MutS in the conjugate retains its ability to unbend DNA in response to ATP addition and find out for the first time that the DNA unbending rate increases with increasing ATP concentration. Since the crosslinked complexes contain active MutS protein, they can be used in further experiments to investigate MutS interactions with other proteins of the mismatch repair system.
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Affiliation(s)
- Mayya Monakhova
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Alexandra Ryazanova
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Andreas Hentschel
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Mikhail Viryasov
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
| | - Tatiana Oretskaya
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Elena Kubareva
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
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5
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Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor. J Chem Phys 2014; 139:121927. [PMID: 24089739 DOI: 10.1063/1.4818596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteins that recognize and bind to specific sites on DNA often distort the DNA at these sites. The rates at which these DNA distortions occur are considered to be important in the ability of these proteins to discriminate between specific and nonspecific sites. These rates have proven difficult to measure for most protein-DNA complexes in part because of the difficulty in separating the kinetics of unimolecular conformational rearrangements (DNA bending and kinking) from the kinetics of bimolecular complex association and dissociation. A notable exception is the Integration Host Factor (IHF), a eubacterial architectural protein involved in chromosomal compaction and DNA recombination, which binds with subnanomolar affinity to specific DNA sites and bends them into sharp U-turns. The unimolecular DNA bending kinetics has been resolved using both stopped-flow and laser temperature-jump perturbation. Here we expand our investigation by presenting a global analysis of the ionic strength dependence of specific binding affinity and relaxation kinetics of an IHF-DNA complex. This analysis enables us to obtain each of the underlying elementary rates (DNA bending/unbending and protein-DNA association/dissociation), and their ionic strength dependence, even under conditions where the two processes are coupled. Our analysis indicates interesting differences in the ionic strength dependence of the bi- versus unimolecular steps. At moderate [KCl] (100-500 mM), nearly all the ionic strength dependence to the overall equilibrium binding affinity appears in the bimolecular association/dissociation of an initial, presumably weakly bent, encounter complex, with a slope SK(bi) ≈ 8 describing the loglog-dependence of the equilibrium constant to form this complex on [KCl]. In contrast, the unimolecular equilibrium constant to form the fully wrapped specific complex from the initial complex is nearly independent of [KCl], with SK(uni) < 0.5. This result is counterintuitive because there are at least twice as many ionic protein-DNA contacts in the fully wrapped complex than in the weakly bent intermediate. The following picture emerges from this analysis: in the bimolecular step, the observed [KCl]-dependence is consistent with the number of DNA counterions expected to be released when IHF binds nonspecifically to DNA whereas in the unimolecular reorganization step, the weak [KCl]-dependence suggests that two effects cancel one another. On one hand, formation of additional protein-DNA contacts in the fully wrapped complex releases bound counterions into bulk solution, which is entropically favored by decreasing [salt]. On the other hand, formation of the fully wrapped complex also releases tightly bound water molecules, which is osmotically favored by increasing [salt]. More generally, our global analysis strategy is applicable to other protein-DNA complexes, and opens up the possibility of measuring DNA bending rates in complexes where the unimolecular and bimolecular steps are not easily separable.
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Affiliation(s)
- Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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6
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Groothuizen FS, Fish A, Petoukhov MV, Reumer A, Manelyte L, Winterwerp HHK, Marinus MG, Lebbink JHG, Svergun DI, Friedhoff P, Sixma TK. Using stable MutS dimers and tetramers to quantitatively analyze DNA mismatch recognition and sliding clamp formation. Nucleic Acids Res 2013; 41:8166-81. [PMID: 23821665 PMCID: PMC3783165 DOI: 10.1093/nar/gkt582] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The process of DNA mismatch repair is initiated when MutS recognizes mismatched DNA bases and starts the repair cascade. The Escherichia coli MutS protein exists in an equilibrium between dimers and tetramers, which has compromised biophysical analysis. To uncouple these states, we have generated stable dimers and tetramers, respectively. These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-length protein by X-ray crystallography and small angle X-ray scattering. Our structural data reveal that the tetramerization domains are flexible with respect to the body of the protein, resulting in mostly extended structures. Tetrameric MutS has a slow dissociation from DNA, which can be due to occasional bending over and binding DNA in its two binding sites. In contrast, the dimer dissociation is faster, primarily dependent on a combination of the type of mismatch and the flanking sequence. In the presence of ATP, we could distinguish two kinetic groups: DNA sequences where MutS forms sliding clamps and those where sliding clamps are not formed efficiently. Interestingly, this inability to undergo a conformational change rather than mismatch affinity is correlated with mismatch repair.
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Affiliation(s)
- Flora S Groothuizen
- Division of Biochemistry and CancerGenomiCs.nl, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands, European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany, Institute for Biochemistry, Justus Liebig University, Heinrich-Buff Ring 58, D-35392, Giessen, Germany, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA, Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, the Netherlands and Department of Radiation Oncology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, the Netherlands
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7
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Abstract
The mismatch repair (MMR) system detects non-Watson-Crick base pairs and strand misalignments arising during DNA replication and mediates their removal by catalyzing excision of the mispair-containing tract of nascent DNA and its error-free resynthesis. In this way, MMR improves the fidelity of replication by several orders of magnitude. It also addresses mispairs and strand misalignments arising during recombination and prevents synapses between nonidentical DNA sequences. Unsurprisingly, MMR malfunction brings about genomic instability that leads to cancer in mammals. But MMR proteins have recently been implicated also in other processes of DNA metabolism, such as DNA damage signaling, antibody diversification, and repair of interstrand cross-links and oxidative DNA damage, in which their functions remain to be elucidated. This article reviews the progress in our understanding of the mechanism of replication error repair made during the past decade.
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Affiliation(s)
- Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland.
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8
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Abstract
DNA mismatch repair (MMR) corrects replication errors in newly synthesized DNA. It also has an antirecombination action on heteroduplexes that contain similar but not identical sequences. This review focuses on the genetics and development of MMR and not on the latest biochemical mechanisms. The main focus is on MMR in Escherichia coli, but examples from Streptococcuspneumoniae and Bacillussubtilis have also been included. In most organisms, only MutS (detects mismatches) and MutL (an endonuclease) and a single exonucleaseare present. How this system discriminates between newlysynthesized and parental DNA strands is not clear. In E. coli and its relatives, however, Dam methylation is an integral part of MMR and is the basis for strand discrimination. A dedicated site-specific endonuclease, MutH, is present, andMutL has no endonuclease activity; four exonucleases can participate in MMR. Although it might seem that the accumulated wealth of genetic and biochemical data has given us a detailed picture of the mechanism of MMR in E. coli, the existence of three competing models to explain the initiation phase indicates the complexity of the system. The mechanism of the antirecombination action of MMR is largely unknown, but only MutS and MutL appear to be necessary. A primary site of action appears to be on RecA, although subsequent steps of the recombination process can also be inhibited. In this review, the genetics of Very Short Patch (VSP) repair of T/G mismatches arising from deamination of 5-methylcytosineresidues is also discussed.
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9
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Mapping the Transition State for DNA Bending by IHF. J Mol Biol 2012; 418:300-15. [DOI: 10.1016/j.jmb.2012.02.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 02/14/2012] [Accepted: 02/17/2012] [Indexed: 01/01/2023]
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Tashiro Y, Katabami A, Saito K, Umeno D. A system for the rapid determination of the mutation spectrum in Escherichia coli. ANAL SCI 2012; 28:95-101. [PMID: 22322800 DOI: 10.2116/analsci.28.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The first step toward elucidating the mutagenic effects of chemicals and pathways is to determine the specificity of the mutations generated spontaneously or in response to treatment with mutagens. We constructed a set of plasmid-encoded probes for the specific detection of each type of base substitution mutation. Using these probes, we were able to quickly determine both the mutation rate and the specificity of the mutations caused by different types of mutagens and mutagenic conditions. We also developed a PCR-based method to rapidly and robustly determine the mutation spectrum in response to various mutagenic samples in parallel. This system allows one to not only analyze the mutation specificity of various chemicals, but also to search for novel genetic elements that promote the specific mutation events.
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Affiliation(s)
- Yohei Tashiro
- Department of Applied Chemistry and Biotechnology, Chiba University, 1-33 Yayoi, Inage, Chiba 263–8522, Japan
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11
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Hombauer H, Campbell CS, Smith CE, Desai A, Kolodner RD. Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates. Cell 2012; 147:1040-53. [PMID: 22118461 DOI: 10.1016/j.cell.2011.10.025] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/22/2011] [Accepted: 10/07/2011] [Indexed: 11/17/2022]
Abstract
DNA mismatch repair (MMR) increases replication fidelity by eliminating mispaired bases resulting from replication errors. In Saccharomyces cerevisiae, mispairs are primarily detected by the Msh2-Msh6 complex and corrected following recruitment of the Mlh1-Pms1 complex. Here, we visualized functional fluorescent versions of Msh2-Msh6 and Mlh1-Pms1 in living cells. We found that the Msh2-Msh6 complex is an S phase component of replication centers independent of mispaired bases; this localized pool accounted for 10%-15% of MMR in wild-type cells but was essential for MMR in the absence of Exo1. Unexpectedly, Mlh1-Pms1 formed nuclear foci that, although dependent on Msh2-Msh6 for formation, rarely colocalized with Msh2-Msh6 replication-associated foci. Mlh1-Pms1 foci increased when the number of mispaired bases was increased; in contrast, Msh2-Msh6 foci were unaffected. These findings suggest the presence of replication machinery-coupled and -independent pathways for mispair recognition by Msh2-Msh6, which direct formation of superstoichiometric Mlh1-Pms1 foci that represent sites of active MMR.
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Affiliation(s)
- Hans Hombauer
- Ludwig Institute for Cancer Research, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0669, USA
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12
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Heinze RJ, Sekerina S, Winkler I, Biertümpfel C, Oretskaya TS, Kubareva E, Friedhoff P. Covalently trapping MutS on DNA to study DNA mismatch recognition and signaling. MOLECULAR BIOSYSTEMS 2012; 8:1861-4. [DOI: 10.1039/c2mb25086a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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Nakano SI, Kanzaki T, Nakano M, Miyoshi D, Sugimoto N. Measurements of the binding of a large protein using a substrate density-controlled DNA chip. Anal Chem 2011; 83:6368-72. [PMID: 21774522 DOI: 10.1021/ac201312d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DNA chip that immobilizes DNA oligonucleotides on a solid plate surface is used for many diagnostic applications. For maximizing the detection sensitivity and accuracy, it is important to control the DNA density on a chip surface and establish a convenient method for optimizing the density. Here, the binding of DNA mismatch-binding protein MutS to the DNA substrate on the chip was investigated, which can be applied for high-throughput single-nucleotide polymorphism analysis in a genome. We prepared the DNA chips where the DNA substrate density was changed simply by using a mixed DNA solution. The binding of MutS was significantly influenced by the amount of DNA substrate on the chip as a consequence of steric crowding, and the moderate density that gave the distance between the DNA substrates greater than the size of the protein was appropriate to obtain accurate kinetic parameters. The substrate density-controlled DNA chip prepared using the mixed DNA solution has distinctive advantages for maximizing the detection capability and kinetic analysis of the binding of MutS and probably also other large proteins.
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Affiliation(s)
- Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Chuo-ku, Kobe, Japan.
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14
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Atomic force microscopy captures MutS tetramers initiating DNA mismatch repair. EMBO J 2011; 30:2881-93. [PMID: 21666597 DOI: 10.1038/emboj.2011.180] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 05/10/2011] [Indexed: 11/09/2022] Open
Abstract
In spite of extensive research, the mechanism by which MutS initiates DNA mismatch repair (MMR) remains controversial. We use atomic force microscopy (AFM) to capture how MutS orchestrates the first step of E. coli MMR. AFM images captured two types of MutS/DNA complexes: single-site binding and loop binding. In most of the DNA loops imaged, two closely associated MutS dimers formed a tetrameric complex in which one of the MutS dimers was located at or near the mismatch. Surprisingly, in the presence of ATP, one MutS dimer remained at or near the mismatch site and the other, while maintaining contact with the first dimer, relocated on the DNA by reeling in DNA, thereby producing expanding DNA loops. Our results indicate that MutS tetramers composed of two non-equivalent MutS dimers drive E. coli MMR, and these new observations now reconcile the apparent contradictions of previous 'sliding' and 'bending/looping' models of interaction between mismatch and strand signal.
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15
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Sass LE, Lanyi C, Weninger K, Erie DA. Single-molecule FRET TACKLE reveals highly dynamic mismatched DNA-MutS complexes. Biochemistry 2010; 49:3174-90. [PMID: 20180598 DOI: 10.1021/bi901871u] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first step in DNA mismatch repair (MMR) is the recognition of DNA mismatches or nucleotide insertions/deletions (IDLs) by MutS and MutS homologues. To investigate the conformational properties of MutS-mismatch complexes, we used single-molecule fluorescence resonance energy transfer (smFRET) to examine the dynamics of MutS-induced DNA bending at a GT mismatch. The FRET measurements reveal that the MutS-GT mismatch recognition complex is highly dynamic, undergoing conformational transitions between many states with different degrees of DNA bending. Due to the complexity of the data, we developed an analysis approach, called FRET TACKLE, in which we combine direct analysis of FRET transitions with examination of kinetic lifetimes to identify all of the conformational states and characterize the kinetics of the binding and conformational equilibria. The data reveal that MutS-GT complexes can reside in six different conformations, which have lifetimes that differ by as much as 20-fold and exhibit rates of interconversion that vary by 2 orders of magnitude. To gain further insight into the dynamic properties of GT-MutS complexes and to bolster the validity of our analysis, we complemented our experimental data with Monte Carlo simulations. Taken together, our results suggest that the dynamics of the MutS-mismatch complex could govern the efficiency of repair of different DNA mismatches. Finally, in addition to revealing these important biological implications of MutS-DNA interactions, this FRET TACKLE method will enable the analysis of the complex dynamics of other biological systems.
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Affiliation(s)
- Lauryn E Sass
- Department of Chemistry, University of North Carolina, Chapel Hill,North Carolina 27599, USA
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