Title
Direct observation of one-dimensional diffusion and transcription by Escherichia coli RNA polymerase
Date Issued
01 January 1999
Access level
open access
Resource Type
journal article
Author(s)
Guthold M.
Zhu X.
Rivetti C.
Yang G.
Thomson N.
Kasas S.
Hansma H.
Smith B.
Hansma P.
Universidad de Oregon
Publisher(s)
Biophysical Society
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 μM 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.
Start page
2284
End page
2294
Volume
77
Issue
4
Language
English
OCDE Knowledge area
Ciencia de los polímeros Bioquímica, Biología molecular
Scopus EID
2-s2.0-0032866779
PubMed ID
Source
Biophysical Journal
ISSN of the container
00063495
Sponsor(s)
This work was supported by National Science Foundation Grants MBC 9118482 and BIR 9318945, and National Institutes of Health Grant GM-32543. This work was supported in part by a grant from the Lucille P. Markey Foundation to the Institute of Molecular Biology. Claudio Rivetti was supported in part by an EMBO fellowship and in part by a Human Frontier Science Program (HFSP) long-term fellowship.
Sources of information: Directorio de Producción Científica Scopus