title: Atomic force microscopy captures the initiation of methyl-directed DNA mismatch repair.
abstract: In Escherichia coli, errors in newly-replicated DNA, such as the incorporation of a nucleotide with a mis-paired base or an accidental insertion or deletion of nucleotides, are corrected by a methyl-directed mismatch repair (MMR) pathway. While the enzymology of MMR has long been established, many fundamental aspects of its mechanisms remain elusive, such as the structures, compositions, and orientations of complexes of MutS, MutL, and MutH as they initiate repair. Using atomic force microscopy, we--for the first time--record the structures and locations of individual complexes of MutS, MutL and MutH bound to DNA molecules during the initial stages of mismatch repair. This technique reveals a number of striking and unexpected structures, such as the growth and disassembly of large multimeric complexes at mismatched sites, complexes of MutS and MutL anchoring latent MutH onto hemi-methylated d(GATC) sites or bound themselves at nicks in the DNA, and complexes directly bridging mismatched and hemi-methylated d(GATC) sites by looping the DNA. The observations from these single-molecule studies provide new opportunities to resolve some of the long-standing controversies in the field and underscore the dynamic heterogeneity and versatility of MutSLH complexes in the repair process.
authors.affiliation: Department of Mechanical Engineering and Materials Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham NC 27708, USA. Electronic address: eric.josephs@duke.edu.
authors.forename: Eric A
authors.initials: EA
authors.lastname: Josephs
authors.affiliation: Department of Mechanical Engineering and Materials Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham NC 27708, USA.
authors.forename: Tianli
authors.initials: T
authors.lastname: Zheng
authors.affiliation: Department of Mechanical Engineering and Materials Science, Edmund T. Pratt, Jr. School of Engineering, Duke University, Durham NC 27708, USA. Electronic address: pemar@duke.edu.
authors.forename: Piotr E
authors.initials: PE
authors.lastname: Marszalek
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism / Q000648:ultrastructure*; D053843:DNA Mismatch Repair; D045643:DNA Repair Enzymes / Q000378:metabolism / Q000648:ultrastructure*; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure; D004268:DNA-Binding Proteins / Q000378:metabolism / Q000648:ultrastructure*; D004706:Endodeoxyribonucleases / Q000378:metabolism / Q000648:ultrastructure*; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism / Q000648:ultrastructure*; D018625:Microscopy, Atomic Force / Q000379:methods; D057054:Molecular Imaging / Q000379:methods; D000070956:MutL Proteins; D051719:MutS DNA Mismatch-Binding Protein / Q000378:metabolism / Q000648:ultrastructure*; D009692:Nucleic Acid Heteroduplexes / Q000648:ultrastructure
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C074770:MutL protein, E coli; D009692:Nucleic Acid Heteroduplexes; D004706:Endodeoxyribonucleases; C059682:methyl-directed mismatch repair protein, E coli; D000251:Adenosine Triphosphatases; D000070956:MutL Proteins; D051719:MutS DNA Mismatch-Binding Protein; D045643:DNA Repair Enzymes
keywords: Atomic force microscopy; DNA looping; Methyl-directed DNA mismatch repair; MutH; MutL; MutS