RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions

The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate...
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Autor*in:	Nobuo Shimamoto [verfasserIn] Masahiko Imashimizu [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2020

Schlagwörter:	transcriptional regulation reaction theory prediction of promoters one-dimensional diffusion rate equation detailed balance

Übergeordnetes Werk:	In: Biomolecules - MDPI AG, 2013, 11(2020), 1, p 32
Übergeordnetes Werk:	volume:11 ; year:2020 ; number:1, p 32

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/biom11010032

Katalog-ID:	DOAJ034151419

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spelling	10.3390/biom11010032 doi (DE-627)DOAJ034151419 (DE-599)DOAJbf642e8256d447379dd21e37377faebb DE-627 ger DE-627 rakwb eng QR1-502 Nobuo Shimamoto verfasserin aut RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate equations are commonly used to describe reactions involved in transcription, but they tend to be used unaware of the timescales of relevant physical processes. In this review, we discuss the limitation of rate equation for describing three-dimensional diffusion and one-dimensional diffusion along DNA. We then introduce the chemical ratchet mechanism recently proposed for explaining the antenna effect, an enhancement of the binding affinity to a specific site on longer DNA, which deviates from a thermodynamic rule. We show that chemical ratchet cannot be described with a single set of rate equations but alternative sets of rate equations that temporally switch no faster than the binding reaction. transcriptional regulation reaction theory prediction of promoters one-dimensional diffusion rate equation detailed balance Microbiology Masahiko Imashimizu verfasserin aut In Biomolecules MDPI AG, 2013 11(2020), 1, p 32 (DE-627)735688915 (DE-600)2701262-1 2218273X nnns volume:11 year:2020 number:1, p 32 https://doi.org/10.3390/biom11010032 kostenfrei https://doaj.org/article/bf642e8256d447379dd21e37377faebb kostenfrei https://www.mdpi.com/2218-273X/11/1/32 kostenfrei https://doaj.org/toc/2218-273X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2020 1, p 32
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allfieldsSound	10.3390/biom11010032 doi (DE-627)DOAJ034151419 (DE-599)DOAJbf642e8256d447379dd21e37377faebb DE-627 ger DE-627 rakwb eng QR1-502 Nobuo Shimamoto verfasserin aut RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions 2020 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate equations are commonly used to describe reactions involved in transcription, but they tend to be used unaware of the timescales of relevant physical processes. In this review, we discuss the limitation of rate equation for describing three-dimensional diffusion and one-dimensional diffusion along DNA. We then introduce the chemical ratchet mechanism recently proposed for explaining the antenna effect, an enhancement of the binding affinity to a specific site on longer DNA, which deviates from a thermodynamic rule. We show that chemical ratchet cannot be described with a single set of rate equations but alternative sets of rate equations that temporally switch no faster than the binding reaction. transcriptional regulation reaction theory prediction of promoters one-dimensional diffusion rate equation detailed balance Microbiology Masahiko Imashimizu verfasserin aut In Biomolecules MDPI AG, 2013 11(2020), 1, p 32 (DE-627)735688915 (DE-600)2701262-1 2218273X nnns volume:11 year:2020 number:1, p 32 https://doi.org/10.3390/biom11010032 kostenfrei https://doaj.org/article/bf642e8256d447379dd21e37377faebb kostenfrei https://www.mdpi.com/2218-273X/11/1/32 kostenfrei https://doaj.org/toc/2218-273X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2020 1, p 32
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author	Nobuo Shimamoto
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topic_title	QR1-502 RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions transcriptional regulation reaction theory prediction of promoters one-dimensional diffusion rate equation detailed balance
topic	misc QR1-502 misc transcriptional regulation misc reaction theory misc prediction of promoters misc one-dimensional diffusion misc rate equation misc detailed balance misc Microbiology
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title_auth	RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions
abstract	The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate equations are commonly used to describe reactions involved in transcription, but they tend to be used unaware of the timescales of relevant physical processes. In this review, we discuss the limitation of rate equation for describing three-dimensional diffusion and one-dimensional diffusion along DNA. We then introduce the chemical ratchet mechanism recently proposed for explaining the antenna effect, an enhancement of the binding affinity to a specific site on longer DNA, which deviates from a thermodynamic rule. We show that chemical ratchet cannot be described with a single set of rate equations but alternative sets of rate equations that temporally switch no faster than the binding reaction.
abstractGer	The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate equations are commonly used to describe reactions involved in transcription, but they tend to be used unaware of the timescales of relevant physical processes. In this review, we discuss the limitation of rate equation for describing three-dimensional diffusion and one-dimensional diffusion along DNA. We then introduce the chemical ratchet mechanism recently proposed for explaining the antenna effect, an enhancement of the binding affinity to a specific site on longer DNA, which deviates from a thermodynamic rule. We show that chemical ratchet cannot be described with a single set of rate equations but alternative sets of rate equations that temporally switch no faster than the binding reaction.
abstract_unstemmed	The study of transcription and its regulation is an interdisciplinary field that is closely connected with genetics, structural biology, and reaction theory. Among these, although less attention has been paid to reaction theory, it is becoming increasingly useful for research on transcription. Rate equations are commonly used to describe reactions involved in transcription, but they tend to be used unaware of the timescales of relevant physical processes. In this review, we discuss the limitation of rate equation for describing three-dimensional diffusion and one-dimensional diffusion along DNA. We then introduce the chemical ratchet mechanism recently proposed for explaining the antenna effect, an enhancement of the binding affinity to a specific site on longer DNA, which deviates from a thermodynamic rule. We show that chemical ratchet cannot be described with a single set of rate equations but alternative sets of rate equations that temporally switch no faster than the binding reaction.
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title_short	RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions
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RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions

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