Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase

Details

Serval ID
serval:BIB_1E64FD8360EC
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase
Journal
Biophysical Journal
Author(s)
Guthold  M., Zhu  X., Rivetti  C., Yang  G., Thomson  N. H., Kasas  S., Hansma  H. G., Smith  B., Hansma  P. K., Bustamante  C.
ISSN
0006-3495
Publication state
Published
Issued date
10/1999
Peer-reviewed
Oui
Volume
77
Number
4
Pages
2284-2294
Language
english
Notes
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. --- Old month value: Oct
Abstract
The dynamics of nonspecific and specific Escherichia coli RNA polymerase (RNAP)-DNA complexes have been directly observed using scanning force microscopy operating in buffer. To this end, imaging conditions had to be found in which DNA molecules were adsorbed onto mica strongly enough to be imaged, but loosely enough to be able to diffuse on the surface. In sequential images of nonspecific complexes, RNAP was seen to slide along DNA, performing a one-dimensional random walk. Heparin, a substance known to disrupt nonspecific RNAP-DNA interactions, prevented sliding. These observations suggest that diffusion of RNAP along DNA constitutes a mechanism for accelerated promoter location. Sequential images of single, transcribing RNAP molecules were also investigated. Upon addition of 5 microM nucleoside triphosphates to stalled elongation complexes in the liquid chamber, RNAP molecules were seen to processively thread their template at rates of 1.5 nucleotide/s in a direction consistent with the promoter orientation. Transcription assays, performed with radiolabeled, mica-bound transcription complexes, confirmed this rate, which was about three times smaller than the rate of complexes in solution. This assay also showed that the pattern of pause sites and the termination site were affected by the surface. By using the Einstein-Sutherland friction-diffusion relation the loading force experienced by RNAP due to DNA-surface friction is estimated and discussed.
Keywords
Adsorption Aluminum Silicates Buffers Cations, Divalent/pharmacology DNA/genetics/*metabolism DNA-Directed RNA Polymerases/*metabolism Diffusion/drug effects Escherichia coli/*enzymology/genetics Friction Heparin/pharmacology Kinetics Microscopy, Atomic Force Promoter Regions (Genetics)/genetics Protein Binding/drug effects Templates, Genetic Terminator Regions (Genetics)/genetics Transcription, Genetic/drug effects/*genetics
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 15:24
Last modification date
20/08/2019 13:54
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