title: Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking.
abstract: RNA polymerase (RNAP) transcribes DNA discontinuously, with periods of rapid nucleotide addition punctuated by frequent pauses. We investigated the mechanism of transcription by measuring the effect of both hindering and assisting forces on the translocation of single Escherichia coli transcription elongation complexes, using an optical trapping apparatus that allows for the detection of pauses as short as one second. We found that the vast majority of pauses are brief (1-6 s at 21 degrees C, 1 mM NTPs), and that the probability of pausing at any particular position on a DNA template is low and fairly constant. Neither the probability nor the duration of these ubiquitous pauses was affected by hindering or assisting loads, establishing that they do not result from the backtracking of RNAP along the DNA template. We propose instead that they are caused by a structural rearrangement within the enzyme.
authors: Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.
authors: Keir C
authors: KC
authors: Neuman
authors: Elio A
authors: EA
authors: Abbondanzieri
authors: Robert
authors: R
authors: Landick
authors: Jeff
authors: J
authors: Gelles
authors: Steven M
authors: SM
authors: Block
mesh_terms: D004269:DNA, Bacterial / Q000096:biosynthesis / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D007700:Kinetics; D008954:Models, Biological; D011336:Probability; D011485:Protein Binding; D011487:Protein Conformation; D013698:Templates, Genetic; D013997:Time Factors; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D012321:DNA-Directed RNA Polymerases