title: State transition analysis of spontaneous branch migration of the Holliday junction by photon-based single-molecule fluorescence resonance energy transfer.
abstract: Branch migration of Holliday junction (HJ) DNA in solution is a spontaneous conformational change between multiple discrete states. We applied single-molecule fluorescence resonance energy transfer (smFRET) measurement to three-state branch migration. The photon-based variational Bayes-hidden Markov model (VB-HMM) method was applied to fluorescence signals to reproduce the state transition trajectories and evaluate the transition parameters, such as transition rate. The upper limit of time resolution suggested in simulation was nearly achieved for the state dynamics with relatively small FRET changes, and the distinctions in the populations of different states were successfully retrieved. We also discuss the suitability of the HJ as a standard sample for smFRET dynamics measurements and data analysis.
authors.affiliation: Cellular Informatics Laboratory, RIKEN, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Okamoto
authors.affiliation: Cellular Informatics Laboratory, RIKEN, Japan. Electronic address: sako@riken.jp.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Sako
mesh_terms: D045566:DNA, Cruciform / Q000737:chemistry*; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D007700:Kinetics; D017785:Photons
chemical_list: D045566:DNA, Cruciform
keywords: Conformational dynamics; FRET; Hidden Markov model; Single photon counting; Single-molecule measurement; Variational Bayes