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

Biomolecules

Masahiko Imashimizu¹  Nobuo Shimamoto² 

[1] Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;National Institute of Genetics Mishima, Shizuoka-ken 411-8540, Japan;

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

DOI  :  10.3390/biom11010032

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown