title: Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: a model for homology search in homologous genetic recombination.
abstract: Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions are essential for homologous genetic recombination in various organisms. From NMR studies, we previously reported a novel deoxyribose-base stacking interaction between adjacent residues on the extended single-stranded DNA bound to RecA protein. In this study, we found that the same DNA structure was induced by the binding to Saccharomyces cerevisiae Rad51 protein, indicating that the unique DNA structure induced by the binding to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of this structure, we have formulated the structure of duplex DNA within filaments formed by RecA protein and its homologs. Two types of molecular structures are presented. One is the duplex structure that has the N-type sugar pucker. Its helical pitch is approximately 95 A (18.6 bp/turn), corresponding to that of an active, or ATP-form of the RecA filament. The other is one that has the S-type sugar pucker. Its helical pitch is approximately 64 A (12.5 bp/turn), corresponding to that of an inactive, or ADP-form of the RecA filament. During this modeling, we found that the interconversion of sugar puckers between the N-type and the S-type rotates bases horizontally, while maintaining the deoxyribose-base stacking interaction. We propose that this base rotation enables base pair switching between double-stranded DNA and single-stranded DNA to take place, facilitating homologous pairing and strand exchange. A possible mechanism for strand exchange involving DNA rotation also is discussed.
authors.affiliation: Cellular and Molecular Biology Laboratory, The Institute of Physical and Chemical Research (RIKEN), Saitama 351-0198, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Nishinaka
authors.forename: A
authors.initials: A
authors.lastname: Shinohara
authors.forename: Y
authors.initials: Y
authors.lastname: Ito
authors.forename: S
authors.initials: S
authors.lastname: Yokoyama
authors.forename: T
authors.initials: T
authors.lastname: Shibata
mesh_terms: D020029:Base Pairing / Q000235:genetics; D004247:DNA / Q000737:chemistry; D004269:DNA, Bacterial / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000378:metabolism; D003855:Deoxyribose / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D051135:Rad51 Recombinase; D011938:Rec A Recombinases / Q000378:metabolism*; D011995:Recombination, Genetic / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins
chemical_list: D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; C051802:triplex DNA; D003855:Deoxyribose; D004247:DNA; C495151:RAD51 protein, S cerevisiae; D051135:Rad51 Recombinase; D011938:Rec A Recombinases