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Influence of secondary structure on recovery from pauses during early stages of RNA transcription

Klopper, A. V. and Bois, J. S. and Grill, S. W. (2010) Influence of secondary structure on recovery from pauses during early stages of RNA transcription. Physical Review E, 81 (3). Art. No. 030904. ISSN 1539-3755. https://resolver.caltech.edu/CaltechAUTHORS:20200415-091356287

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Abstract

The initial stages of transcription by RNA polymerase are frequently marked by pausing and stalling events. These events have been linked to an inactive backtracked state in which the polymerase diffuses along the template DNA. We investigate theoretically the influence of RNA secondary structure in confining this diffusion. The effective confinement length peaks at transcript lengths commensurate with early stalling. This finite-size effect accounts for slow progress at the beginning of transcription, which we illustrate via stochastic hopping models for backtracking polymerases.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1103/physreve.81.030904DOIArticle
ORCID:
AuthorORCID
Bois, J. S.0000-0001-7137-8746
Grill, S. W.0000-0002-2290-5826
Additional Information:© 2010 The American Physical Society. Received 31 March 2009; revised manuscript received 29 October 2009; published 18 March 2010. The authors wish to thank A. Carlsson, M. Depken, E. Galburt, F. Jülicher, B. Lindner, K. Neugebauer, D. Ó Maoiléidigh, and J. Parrondo for insightful discussion. J.S.B. acknowledges the Human Frontier Science Program for funding.
Funders:
Funding AgencyGrant Number
Human Frontier Science ProgramUNSPECIFIED
Issue or Number:3
Classification Code:PACS number(s): 87.14.gn, 87.14.ej, 87.15.bd, 87.15.Cc
Record Number:CaltechAUTHORS:20200415-091356287
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200415-091356287
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:102549
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:15 Apr 2020 16:18
Last Modified:15 Apr 2020 16:18

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