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Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site. / Dulin, David; Vilfan, Igor D.; Berghuis, Bojk A.; Poranen, Minna M.; Depken, Martin; Dekker, Nynke H.

In: Nucleic Acids Research, Vol. 43, No. 21, 2015, p. 10421-10429.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Dulin, D, Vilfan, ID, Berghuis, BA, Poranen, MM, Depken, M & Dekker, NH 2015, 'Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site' Nucleic Acids Research, vol. 43, no. 21, pp. 10421-10429. https://doi.org/10.1093/nar/gkv1098

APA

Vancouver

Author

Dulin, David ; Vilfan, Igor D. ; Berghuis, Bojk A. ; Poranen, Minna M. ; Depken, Martin ; Dekker, Nynke H. / Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site. In: Nucleic Acids Research. 2015 ; Vol. 43, No. 21. pp. 10421-10429.

BibTeX

@article{4df172d66083432cb46e8d307b55cea7,
title = "Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site",
abstract = "Transcription in RNA viruses is highly dynamic, with a variety of pauses interrupting nucleotide addition by RNA-dependent RNA polymerase (RdRp). For example, rare but lengthy pauses (>20 s) have been linked to backtracking for viral single-subunit RdRps. However, while such backtracking has been well characterized for multi-subunit RNA polymerases (RNAPs) from bacteria and yeast, little is known about the details of viral RdRp backtracking and its biological roles. Using high-throughput magnetic tweezers, we quantify the backtracking by RdRp from the double-stranded (ds) RNA bacteriophage φ6, a model system for RdRps. We characterize the probability of entering long backtracks as a function of force and propose a model in which the bias toward backtracking is determined by the base paring at the dsRNA fork.We further discover that extensive backtracking provides access to a new 3′-end that allows for the de novo initiation of a second RdRp. This previously unidentified behavior provides a new mechanism for rapid RNA synthesis using coupled RdRps and hints at a possible regulatory pathway for gene expression during viral RNA transcription.",
author = "David Dulin and Vilfan, {Igor D.} and Berghuis, {Bojk A.} and Poranen, {Minna M.} and Martin Depken and Dekker, {Nynke H.}",
year = "2015",
doi = "10.1093/nar/gkv1098",
language = "English",
volume = "43",
pages = "10421--10429",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "21",

}

RIS

TY - JOUR

T1 - Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site

AU - Dulin, David

AU - Vilfan, Igor D.

AU - Berghuis, Bojk A.

AU - Poranen, Minna M.

AU - Depken, Martin

AU - Dekker, Nynke H.

PY - 2015

Y1 - 2015

N2 - Transcription in RNA viruses is highly dynamic, with a variety of pauses interrupting nucleotide addition by RNA-dependent RNA polymerase (RdRp). For example, rare but lengthy pauses (>20 s) have been linked to backtracking for viral single-subunit RdRps. However, while such backtracking has been well characterized for multi-subunit RNA polymerases (RNAPs) from bacteria and yeast, little is known about the details of viral RdRp backtracking and its biological roles. Using high-throughput magnetic tweezers, we quantify the backtracking by RdRp from the double-stranded (ds) RNA bacteriophage φ6, a model system for RdRps. We characterize the probability of entering long backtracks as a function of force and propose a model in which the bias toward backtracking is determined by the base paring at the dsRNA fork.We further discover that extensive backtracking provides access to a new 3′-end that allows for the de novo initiation of a second RdRp. This previously unidentified behavior provides a new mechanism for rapid RNA synthesis using coupled RdRps and hints at a possible regulatory pathway for gene expression during viral RNA transcription.

AB - Transcription in RNA viruses is highly dynamic, with a variety of pauses interrupting nucleotide addition by RNA-dependent RNA polymerase (RdRp). For example, rare but lengthy pauses (>20 s) have been linked to backtracking for viral single-subunit RdRps. However, while such backtracking has been well characterized for multi-subunit RNA polymerases (RNAPs) from bacteria and yeast, little is known about the details of viral RdRp backtracking and its biological roles. Using high-throughput magnetic tweezers, we quantify the backtracking by RdRp from the double-stranded (ds) RNA bacteriophage φ6, a model system for RdRps. We characterize the probability of entering long backtracks as a function of force and propose a model in which the bias toward backtracking is determined by the base paring at the dsRNA fork.We further discover that extensive backtracking provides access to a new 3′-end that allows for the de novo initiation of a second RdRp. This previously unidentified behavior provides a new mechanism for rapid RNA synthesis using coupled RdRps and hints at a possible regulatory pathway for gene expression during viral RNA transcription.

UR - http://www.scopus.com/inward/record.url?scp=84983786069&partnerID=8YFLogxK

U2 - 10.1093/nar/gkv1098

DO - 10.1093/nar/gkv1098

M3 - Article

VL - 43

SP - 10421

EP - 10429

JO - Nucleic Acids Research

T2 - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 21

ER -

ID: 8846571