Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

Hannah L. Klein, Kenny K.H. Ang, Michelle R. Arkin, Emily C. Beckwitt, Yi Hsuan Chang, Jun Fan, Youngho Kwon, Michael J. Morten, Sucheta Mukherjee, Oliver J. Pambos, Hafez El Sayyed, Elizabeth S. Thrall, João P. Vieira-Da-Rocha, Quan Wang, Shuang Wang, Hsin Yi Yeh, Julie S. Biteen, Peter Chi, Wolf Dietrich Heyer, Achillefs N. KapanidisJoseph J. Loparo, Terence R. Strick, Patrick Sung, Bennett Van Houten, Hengyao Niu, Eli Rothenberg

Research output: Contribution to journalReview articlepeer-review

9 Scopus citations


Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

Original languageEnglish (US)
Pages (from-to)65-101
Number of pages37
JournalMicrobial Cell
Issue number1
StatePublished - Jan 2019


  • Chromatin dynamics
  • Chromosome rearrangements
  • Crossovers
  • DNA breaks
  • DNA helicases
  • DNA repair centers
  • DNA repair synthesis
  • DNA resection
  • DSBs
  • Double strand break repair
  • Endonuclease protection assay
  • FRET
  • Fluorescent proteins
  • Genome instability
  • Gross chromosome rearrangements
  • Homologous recombination
  • Mismatch repair
  • Nonhomologous end joining
  • Nucleotide excision repair
  • PALM
  • Photoactivated fluorescent proteins
  • Recombinase filament assembly
  • Single-molecule
  • Single-particle tracking
  • Structure-selective endonucleases
  • Super resolution
  • Synthesis-dependent strand annealing
  • Transcription coupled repair

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Applied Microbiology and Biotechnology
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Molecular Biology
  • Genetics
  • Cell Biology
  • Virology


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