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RNA polymerase is a powerful torsional motor.

作者信息

Ma Jie, Wang Michelle D

机构信息

Department of Physics; Laboratory of Atomic and Solid State Physics; Cornell University; Ithaca, NY USA; Howard Hughes Medical Institute; Cornell University; Ithaca, NY USA.

出版信息

Cell Cycle. 2014;13(3):337-8. doi: 10.4161/cc.27508. Epub 2013 Dec 13.

DOI:10.4161/cc.27508

PMID:24335432

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3956522/

Abstract

摘要

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RNA polymerase is a powerful torsional motor.

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The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template.

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Transient and dynamic DNA supercoiling potently stimulates the promoter in .

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Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies.

Cell. 1989 Jan 13;56(1):111-8. doi: 10.1016/0092-8674(89)90989-6.

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本文引用的文献

Transcription under torsion.

Science. 2013 Jun 28;340(6140):1580-3. doi: 10.1126/science.1235441.

Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics.

Phys Rev Lett. 2013 Apr 26;110(17):178103. doi: 10.1103/PhysRevLett.110.178103. Epub 2013 Apr 25.

Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors.

Phys Rev Lett. 2011 Sep 2;107(10):108102. doi: 10.1103/PhysRevLett.107.108102. Epub 2011 Sep 1.

The functional response of upstream DNA to dynamic supercoiling in vivo.

Nat Struct Mol Biol. 2008 Feb;15(2):146-54. doi: 10.1038/nsmb.1372. Epub 2008 Jan 13.

Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection.

Nat Methods. 2007 Mar;4(3):223-5. doi: 10.1038/nmeth1013. Epub 2007 Feb 25.

Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching.

Science. 2006 Nov 17;314(5802):1139-43. doi: 10.1126/science.1131398.

Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase.

Nature. 2001 Jan 4;409(6816):113-5. doi: 10.1038/35051126.

Supercoiling of the DNA template during transcription.

Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024-7. doi: 10.1073/pnas.84.20.7024.

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RNA polymerase is a powerful torsional motor.

Cell Cycle. 2014;13(3):337-8. doi: 10.4161/cc.27508. Epub 2013 Dec 13.

Transcription under torsion.

Science. 2013 Jun 28;340(6140):1580-3. doi: 10.1126/science.1235441.

Interplay between DNA supercoiling and transcription elongation.

Transcription. 2014;5(3):e28636. doi: 10.4161/trns.28636.

The Role of Supercoiling in the Motor Activity of RNA Polymerases.

Methods Mol Biol. 2018;1805:215-232. doi: 10.1007/978-1-4939-8556-2_11.

In vitro transcription initiation from three different Escherichia coli promoters. Effect of supercoiling.

Eur J Biochem. 1985 Apr 15;148(2):293-8. doi: 10.1111/j.1432-1033.1985.tb08838.x.

The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template.

EMBO J. 1992 Feb;11(2):667-72. doi: 10.1002/j.1460-2075.1992.tb05098.x.

Transient and dynamic DNA supercoiling potently stimulates the promoter in .

J Biol Chem. 2017 Sep 1;292(35):14566-14575. doi: 10.1074/jbc.M117.794628. Epub 2017 Jul 10.

Structural coupling between RNA polymerase composition and DNA supercoiling in coordinating transcription: a global role for the omega subunit?

mBio. 2011 Aug 2;2(4). doi: 10.1128/mBio.00034-11. Print 2011.

Dependence of transcription-coupled DNA supercoiling on promoter strength in Escherichia coli topoisomerase I deficient strains.

Gene. 2013 Feb 10;514(2):82-90. doi: 10.1016/j.gene.2012.11.011. Epub 2012 Nov 29.

Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies.

Cell. 1989 Jan 13;56(1):111-8. doi: 10.1016/0092-8674(89)90989-6.

引用本文的文献

Torsion is a Dynamic Regulator of DNA Replication Stalling and Reactivation.

bioRxiv. 2024 Oct 17:2024.10.14.618227. doi: 10.1101/2024.10.14.618227.

Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations.

Mol Microbiol. 2023 Jan;119(1):19-28. doi: 10.1111/mmi.15014. Epub 2022 Dec 30.

Two-phase dynamics of DNA supercoiling based on DNA polymer physics.

Biophys J. 2022 Feb 15;121(4):658-669. doi: 10.1016/j.bpj.2022.01.001. Epub 2022 Jan 10.

Torsional Stiffness of Extended and Plectonemic DNA.

Phys Rev Lett. 2021 Jul 9;127(2):028101. doi: 10.1103/PhysRevLett.127.028101.

DNA supercoiling and transcription in bacteria: a two-way street.

BMC Mol Cell Biol. 2019 Jul 18;20(1):26. doi: 10.1186/s12860-019-0211-6.

Transcription factor regulation of RNA polymerase's torque generation capacity.

Proc Natl Acad Sci U S A. 2019 Feb 12;116(7):2583-2588. doi: 10.1073/pnas.1807031116. Epub 2019 Jan 11.

Efficient CRISPR/Cas9-based genome editing and its application to conditional genetic analysis in Marchantia polymorpha.

PLoS One. 2018 Oct 31;13(10):e0205117. doi: 10.1371/journal.pone.0205117. eCollection 2018.

Transient and dynamic DNA supercoiling potently stimulates the promoter in .

J Biol Chem. 2017 Sep 1;292(35):14566-14575. doi: 10.1074/jbc.M117.794628. Epub 2017 Jul 10.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression.

Biophys Rev. 2016 Sep;8(3):209-220. doi: 10.1007/s12551-016-0205-y. Epub 2016 Jun 16.

DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression.

Biophys Rev. 2016 Nov;8(Suppl 1):89-100. doi: 10.1007/s12551-016-0238-2. Epub 2016 Nov 14.

本文引用的文献

Transcription under torsion.

Science. 2013 Jun 28;340(6140):1580-3. doi: 10.1126/science.1235441.

Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics.

Phys Rev Lett. 2013 Apr 26;110(17):178103. doi: 10.1103/PhysRevLett.110.178103. Epub 2013 Apr 25.

Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors.

Phys Rev Lett. 2011 Sep 2;107(10):108102. doi: 10.1103/PhysRevLett.107.108102. Epub 2011 Sep 1.

The functional response of upstream DNA to dynamic supercoiling in vivo.

Nat Struct Mol Biol. 2008 Feb;15(2):146-54. doi: 10.1038/nsmb.1372. Epub 2008 Jan 13.

Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection.

Nat Methods. 2007 Mar;4(3):223-5. doi: 10.1038/nmeth1013. Epub 2007 Feb 25.

Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching.

Science. 2006 Nov 17;314(5802):1139-43. doi: 10.1126/science.1131398.

Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase.

Nature. 2001 Jan 4;409(6816):113-5. doi: 10.1038/35051126.

Supercoiling of the DNA template during transcription.

Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024-7. doi: 10.1073/pnas.84.20.7024.

RNA polymerase is a powerful torsional motor.

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