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Molecular interactions between their components can be observed at the single-molecule level and quantified using colocalization single-molecule spectroscopy, in which individual labeled molecules are seen transiently associating with a surface-tethered partner, or other total internal reflection fluorescence microscopy approaches in which the interactions elicit changes in fluorescence in the labeled surface-tethered partner. When multiple interacting partners can form ternary, quaternary and higher order complexes, the types of spatial and temporal organization of these complexes can be deduced from the order of appearance and reorganization of the components. Time evolution of complex architectures can be followed by changes in the fluorescence behavior in multiple channels. Here, we describe the kinetic event resolving algorithm (KERA), a software tool for organizing and sorting the discretized fluorescent trajectories from a range of single-molecule experiments. KERA organizes the data in groups by transition patterns, and displays exhaustive dwell time data for each interaction sequence. Enumerating and quantifying sequences of molecular interactions provides important information regarding the underlying mechanism of the assembly, dynamics and architecture of the macromolecular complexes. We demonstrate KERA\u2019s utility by analyzing conformational dynamics of two DNA binding proteins: replication protein A and xeroderma pigmentosum complementation group D helicase.<\/jats:p>","DOI":"10.1093\/nar\/gkab087","type":"journal-article","created":{"date-parts":[[2021,2,24]],"date-time":"2021-02-24T07:22:34Z","timestamp":1614151354000},"page":"e53-e53","source":"Crossref","is-referenced-by-count":13,"title":["KERA: analysis tool for multi-process, multi-state single-molecule data"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6315-9778","authenticated-orcid":false,"given":"Joseph","family":"Tibbs","sequence":"first","affiliation":[{"name":"Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2889-1039","authenticated-orcid":false,"given":"Mohamed","family":"Ghoneim","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0608-3284","authenticated-orcid":false,"given":"Colleen C","family":"Caldwell","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Troy","family":"Buzynski","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wayne","family":"Bowie","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elizabeth\u00a0M","family":"Boehm","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M\u00a0Todd","family":"Washington","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00a0M\u00a0Ali","family":"Tabei","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7375-8037","authenticated-orcid":false,"given":"Maria","family":"Spies","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,2,28]]},"reference":[{"key":"2021052017403244000_B1","article-title":"Making choices: DNA replication fork recovery mechanisms","author":"Kondratick","year":"2020","journal-title":"Semin. Cell Dev. Biol."},{"key":"2021052017403244000_B2","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1080\/10409238.2020.1811630","article-title":"An updated perspective on the polymerase division of labor during eukaryotic DNA replication","volume":"55","author":"Guilliam","year":"2020","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"key":"2021052017403244000_B3","doi-asserted-by":"crossref","first-page":"402","DOI":"10.3390\/cancers12020402","article-title":"Physiological and pathological roles of RAD52 at DNA replication forks","volume":"12","author":"Malacaria","year":"2020","journal-title":"Cancers"},{"key":"2021052017403244000_B4","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1080\/10409230802341296","article-title":"SSB as an organizer\/mobilizer of genome maintenance complexes","volume":"43","author":"Shereda","year":"2008","journal-title":"Crit. Rev. Biochem. Mol. 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