title: Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics.
abstract: DNA is the carrier of genetic information and, as such, is at the center of most essential cellular processes. To regulate its physiological function, specific proteins and motor enzymes constantly change conformational states with well-controlled dynamics. Twenty-five years ago, Schafer, Gelles, Sheetz, and Landick employed the tethered particle motion (TPM) technique for the first time to study transcription by RNA polymerase at the single-molecule level. TPM has since then remained one of the simplest, most affordable, and yet incisive single-molecule techniques available. It is an in vitro technique which allows investigation of DNA-protein interactions that change the effective length of a DNA tether. In this chapter, we will describe a recent strategy to multiplex TPM which substantially increases the throughput of TPM experiments, as well as a simulation to estimate the time resolution of experiments, such as transcriptional elongation assays, in which lengthy time averaging of the signal is impossible due to continual change of the DNA tether length. These improvements allow efficient study of several DNA-protein systems, including transcriptionally active DNA-RNA polymerase I complexes and DNA-gyrase complexes.
authors.affiliation: Emory University, Atlanta, GA, United States.
authors.forename: S
authors.initials: S
authors.lastname: Ucuncuoglu
authors.affiliation: University of Alabama at Birmingham, Birmingham, AL, United States.
authors.forename: D A
authors.initials: DA
authors.lastname: Schneider
authors.affiliation: Emory University, Atlanta, GA, United States.
authors.forename: E R
authors.initials: ER
authors.lastname: Weeks
authors.affiliation: Emory University, Atlanta, GA, United States.
authors.forename: D
authors.initials: D
authors.lastname: Dunlap
authors.affiliation: Emory University, Atlanta, GA, United States. Electronic address: lfinzi@emory.edu.
authors.forename: L
authors.initials: L
authors.lastname: Finzi
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics; D027081:DNA Gyrase / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology; D009038:Motion; D009690:Nucleic Acid Conformation; D012318:RNA Polymerase I / Q000737:chemistry* / Q000235:genetics; D000072760:Single Molecule Imaging / Q000379:methods*
chemical_list: D004247:DNA; D012318:RNA Polymerase I; D027081:DNA Gyrase
keywords: Gyrase; RNA polymerase I; Simulated diffusion; Single molecule; Tethered particle motion