Mechanics and Single-Molecule Interrogation of DNA Recombination

Annu Rev Biochem. 2016 Jun 2;85:193-226. doi: 10.1146/annurev-biochem-060614-034352. Epub 2016 Apr 18.


The repair of DNA by homologous recombination is an essential, efficient, and high-fidelity process that mends DNA lesions formed during cellular metabolism; these lesions include double-stranded DNA breaks, daughter-strand gaps, and DNA cross-links. Genetic defects in the homologous recombination pathway undermine genomic integrity and cause the accumulation of gross chromosomal abnormalities-including rearrangements, deletions, and aneuploidy-that contribute to cancer formation. Recombination proceeds through the formation of joint DNA molecules-homologously paired but metastable DNA intermediates that are processed by several alternative subpathways-making recombination a versatile and robust mechanism to repair damaged chromosomes. Modern biophysical methods make it possible to visualize, probe, and manipulate the individual molecules participating in the intermediate steps of recombination, revealing new details about the mechanics of genetic recombination. We review and discuss the individual stages of homologous recombination, focusing on common pathways in bacteria, yeast, and humans, and place particular emphasis on the molecular mechanisms illuminated by single-molecule methods.

Keywords: BRCA2; DNA repair; RecA/RAD51; helicase; microscopy; visual biochemistry.

Publication types

  • Review

MeSH terms

  • Chromosome Aberrations
  • DNA / genetics*
  • DNA / metabolism
  • DNA Damage
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Endodeoxyribonucleases / genetics
  • Endodeoxyribonucleases / metabolism
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Exodeoxyribonuclease V / genetics
  • Exodeoxyribonuclease V / metabolism
  • Exodeoxyribonucleases / genetics
  • Exodeoxyribonucleases / metabolism
  • Gene Expression Regulation
  • Genomic Instability
  • Humans
  • Rad52 DNA Repair and Recombination Protein / genetics
  • Rad52 DNA Repair and Recombination Protein / metabolism
  • RecQ Helicases / genetics
  • RecQ Helicases / metabolism
  • Recombination, Genetic*
  • Recombinational DNA Repair*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Single Molecule Imaging


  • DNA-Binding Proteins
  • RAD50 protein, S cerevisiae
  • Rad52 DNA Repair and Recombination Protein
  • Saccharomyces cerevisiae Proteins
  • DNA
  • Endodeoxyribonucleases
  • Exodeoxyribonucleases
  • MRE11 protein, S cerevisiae
  • Exodeoxyribonuclease V
  • RecQ protein, E coli
  • RecQ Helicases