title: Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA.
abstract: We perform single-molecule spatial tracking measurements of a DNA repair protein, the C-terminal domain of Ada (C-Ada) from Escherichia coli, moving on DNA extended by flow. The trajectories of single proteins labeled with a fluorophore are constructed. We analyze single-protein dwell times on DNA for different flow rates and conclude that sliding (with essentially no hopping) is the mechanism of C-Ada motion along stretched DNA. We also analyze the trajectory results with a drift-diffusion Langevin equation approach to elucidate the influence of flow on the protein motion; systematic variation of the flow enables one to estimate the microscopic friction. We integrate the step-size probability distribution to obtain a version of the fluctuation theorem that articulates the relation between the entropy production and consumption under the adjustable drag (i.e., bias) from the flow. This expression allows validation of the Langevin equation description of the motion. Comparison of the rate of sliding with recent computer simulations of DNA repair suggests that C-Ada could conduct its repair function while moving at near the one-dimensional diffusion limit.
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Yihan
authors.initials: Y
authors.lastname: Lin
authors.forename: Tong
authors.initials: T
authors.lastname: Zhao
authors.forename: Xing
authors.initials: X
authors.lastname: Jian
authors.forename: Zishaan
authors.initials: Z
authors.lastname: Farooqui
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Qu
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.forename: Aaron R
authors.initials: AR
authors.lastname: Dinner
authors.forename: Norbert F
authors.initials: NF
authors.lastname: Scherer
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D004260:DNA Repair / Q000502:physiology; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000737:chemistry*; D017276:Friction; D007700:Kinetics; D016014:Linear Models; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D019853:O(6)-Methylguanine-DNA Methyltransferase / Q000737:chemistry*; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D029968:Escherichia coli Proteins; D014157:Transcription Factors; D004247:DNA; C045675:Ada protein, E coli; D019853:O(6)-Methylguanine-DNA Methyltransferase