Klein, Hannah L.Hannah L.KleinAng, Kenny K. H.Kenny K. H.AngArkin, Michelle R.Michelle R.ArkinBeckwitt, Emily C.Emily C.BeckwittChang, Yi-HsuanYi-HsuanChangFan, JunJunFanKwon, YounghoYounghoKwonMorten, Michael J.Michael J.MortenMukherjee, SuchetaSuchetaMukherjeePambos, Oliver J.Oliver J.PambosSayyed, Hafez ElHafez ElSayyedThrall, Elizabeth S.Elizabeth S.ThrallVieira-Da-Rocha, João P.João P.Vieira-Da-RochaWang, QuanQuanWangWang, ShuangShuangWangYeh, Hsin-YiHsin-YiYehBiteen, Julie S.Julie S.BiteenHUNG-YUAN CHIHeyer, Wolf-DietrichWolf-DietrichHeyerKapanidis, Achillefs N.Achillefs N.KapanidisLoparo, Joseph J.Joseph J.LoparoStrick, Terence R.Terence R.StrickSung, PatrickPatrickSungVan Houten, BennettBennettVan HoutenNiu, HengyaoHengyaoNiuRothenberg, EliEliRothenberg2019-12-262019-12-2620192311-263823112638https://scholars.lib.ntu.edu.tw/handle/123456789/440633https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062960597&doi=10.15698%2fmic2019.01.665&partnerID=40&md5=a8b1b8ce71dac486f9aa775053493db4Genomes 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. © 2019 Klein et al.Chromatin dynamics; Chromosome rearrangements; Crossovers; DNA breaks; DNA helicases; DNA repair centers; DNA repair synthesis; DNA resection; Double strand break repair; DSBs; Endonuclease protection assay; Fluorescent proteins; FRET; 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[SDGs]SDG3agarose; DNA helicase; endonuclease; helicase; oligonucleotide; pif1 helicase; Rad51 protein; recombinase; single stranded DNA; streptavidin; translesion polymerase; unclassified drug; bacterial cell; biochemical analysis; biotinylation; bleaching; cellular distribution; chemical labeling; complex formation; DNA end joining repair; DNA recombination; DNA repair; DNA synthesis; dwell time; enzyme assay; fluorescence imaging; fluorescence resonance energy transfer; gene mutation; genetic manipulation; homologous recombination; hybridization; in vitro study; live cell imaging; mismatch repair; nonhuman; protein analysis; protein DNA interaction; quantitative analysis; regulatory mechanism; Review; single cell analysis; single molecule imagingreview10.15698/mic2019.01.6652-s2.0-85062960597