DNA sequence alignment by microhomology sampling during homologous recombination

Zhi Qi, Sy Redding, Ja Yil Lee, Bryan Gibb, Youngho Kwon, Hengyao Niu, William A. Gaines, Patrick Sung, Eric C. Greene

Research output: Contribution to journalArticlepeer-review

139 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)856-869
Number of pages14
Issue number5
StatePublished - Feb 26 2015
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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