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Völker J, Gindikin V, Klump HH, Plum GE, Breslauer KJ. Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states. J Am Chem Soc 2012; 134:6033-44. [PMID: 22397401 PMCID: PMC3318849 DOI: 10.1021/ja3010896] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Indexed: 11/30/2022]
Abstract
DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.
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Affiliation(s)
- Jens Völker
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Vera Gindikin
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
| | - Horst H. Klump
- Department
of Molecular and
Cell Biology, University of Cape Town,
Private Bag, Rondebosch 7800, South Africa
| | - G. Eric Plum
- IBET Inc., 1507 Chambers
Road, Suite 301, Columbus, Ohio 43212, United States
| | - Kenneth J. Breslauer
- Department
of Chemistry and
Chemical Biology, Rutgers, The State University of New
Jersey, 610 Taylor Road, Piscataway, New Jersey 08854,
United States
- The Cancer Institute
of New Jersey, New Brunswick, New Jersey 08901, United
States
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Cristóvão M, Sisamakis E, Hingorani MM, Marx AD, Jung CP, Rothwell PJ, Seidel CAM, Friedhoff P. Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA. Nucleic Acids Res 2012; 40:5448-64. [PMID: 22367846 PMCID: PMC3384296 DOI: 10.1093/nar/gks138] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mismatch repair (MMR) corrects replication errors such as mismatched bases and loops in DNA. The evolutionarily conserved dimeric MMR protein MutS recognizes mismatches by stacking a phenylalanine of one subunit against one base of the mismatched pair. In all crystal structures of G:T mismatch-bound MutS, phenylalanine is stacked against thymine. To explore whether these structures reflect directional mismatch recognition by MutS, we monitored the orientation of Escherichia coli MutS binding to mismatches by FRET and anisotropy with steady state, pre-steady state and single-molecule multiparameter fluorescence measurements in a solution. The results confirm that specifically bound MutS bends DNA at the mismatch. We found additional MutS–mismatch complexes with distinct conformations that may have functional relevance in MMR. The analysis of individual binding events reveal significant bias in MutS orientation on asymmetric mismatches (G:T versus T:G, A:C versus C:A), but not on symmetric mismatches (G:G). When MutS is blocked from binding a mismatch in the preferred orientation by positioning asymmetric mismatches near the ends of linear DNA substrates, its ability to authorize subsequent steps of MMR, such as MutH endonuclease activation, is almost abolished. These findings shed light on prerequisites for MutS interactions with other MMR proteins for repairing the appropriate DNA strand.
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Affiliation(s)
- Michele Cristóvão
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Evangelos Sisamakis
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Manju M. Hingorani
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Andreas D. Marx
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Caroline P. Jung
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
| | - Paul J. Rothwell
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
| | - Claus A. M. Seidel
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
| | - Peter Friedhoff
- Institute for Biochemistry, FB 08, Justus Liebig University, Heinrich-Buff Ring 58, D-35392 Giessen, Germany, Department of Cell Biology and Genetics, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands, Molecular Physical Chemistry, Heinrich-Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany, Department of Applied Physics, Experimental Biomolecular Physics, Royal Institute of Technology, SE-106 91 Stockholm, Sweden and Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, CT 06459, USA
- *To whom correspondence should be addressed. Tel: +49 641 9935407; Fax: +49 641 9935409;
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