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Cell. 2015 Feb 26;160(5):856-869. doi: 10.1016/j.cell.2015.01.029. Epub 2015 Feb 12.

DNA sequence alignment by microhomology sampling during homologous recombination.

Author information

1
Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.
2
Department of Chemistry, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA.
3
Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
4
Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, 650 West 168(th) Street, New York, NY 10032, USA. Electronic address: ecg2108@columbia.edu.

Abstract

Homologous recombination (HR) mediates the exchange of genetic information between sister or homologous chromatids. During HR, members of the RecA/Rad51 family of recombinases must somehow search through vast quantities of DNA sequence to align and pair single-strand DNA (ssDNA) with a homologous double-strand DNA (dsDNA) template. Here, we use single-molecule imaging to visualize Rad51 as it aligns and pairs homologous DNA sequences in real time. We show that Rad51 uses a length-based recognition mechanism while interrogating dsDNA, enabling robust kinetic selection of 8-nucleotide (nt) tracts of microhomology, which kinetically confines the search to sites with a high probability of being a homologous target. Successful pairing with a ninth nucleotide coincides with an additional reduction in binding free energy, and subsequent strand exchange occurs in precise 3-nt steps, reflecting the base triplet organization of the presynaptic complex. These findings provide crucial new insights into the physical and evolutionary underpinnings of DNA recombination.

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PMID:
25684365
PMCID:
PMC4344887
DOI:
10.1016/j.cell.2015.01.029
[Indexed for MEDLINE]
Free PMC Article

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