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PMID: 9736691 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 95 ·No. 19 ·1998-09-15 ·Pages 11071-6

Nishinaka T, Shinohara A, Ito Y, Yokoyama S, Shibata T

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.

MeSH Terms
Base Pairing/genetics DNA/chemistry DNA, Bacterial/chemistry DNA, Single-Stranded/chemistry DNA-Binding Proteins/metabolism Deoxyribose/chemistry Escherichia coli/genetics Magnetic Resonance Spectroscopy Models, Molecular Molecular Conformation Nucleic Acid Conformation Rad51 Recombinase Rec A Recombinases/metabolism Recombination, Genetic/genetics Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins
Chemicals
DNA, Bacterial DNA, Single-Stranded DNA-Binding Proteins Saccharomyces cerevisiae Proteins triplex DNA Deoxyribose DNA RAD51 protein, S cerevisiae Rad51 Recombinase Rec A Recombinases
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Nishinaka T
Cellular and Molecular Biology Laboratory, The Institute of Physical and Chemical Research (RIKEN), Saitama 351-0198, Japan.
Shinohara A
Ito Y
Yokoyama S
Shibata T
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.95.19.11071
Published
1998-09-15
Pages
11071-6
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC21597
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.95.19.11071 PMC Full Text View journal details
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