RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions
1
National Institute of Genetics Mishima, Shizuoka-ken 411-8540, Japan
2
Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
*
Author to whom correspondence should be addressed.
†
Present Address: Veritas Kitayama, 30-1-104 Shimogamo-Minamishiba-cho, Sakyo-ku, Kyoto 606-0841, Japan.
Biomolecules 2021, 11(1), 32; https://doi.org/10.3390/biom11010032
Received: 3 September 2020
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Revised: 24 December 2020
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Accepted: 25 December 2020
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Published: 29 December 2020
(This article belongs to the Special Issue RNA Polymerase and Transcription Mechanism: Forefront of Physicochemical Study)
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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Keywords:
transcriptional regulation; reaction theory; prediction of promoters; one-dimensional diffusion; rate equation; detailed balance; antenna effect; physicochemical techniques
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MDPI and ACS Style
Shimamoto, N.; Imashimizu, M. RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions. Biomolecules 2021, 11, 32. https://doi.org/10.3390/biom11010032
AMA Style
Shimamoto N, Imashimizu M. RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions. Biomolecules. 2021; 11(1):32. https://doi.org/10.3390/biom11010032
Chicago/Turabian StyleShimamoto, Nobuo, and Masahiko Imashimizu. 2021. "RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions" Biomolecules 11, no. 1: 32. https://doi.org/10.3390/biom11010032
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