The hidden physical codes for modulating the prokaryotic transcription initiation

Yong-chun Zuo and Qian-zhong Li

Physica A: Statistical Mechanics and its Applications, 2010, vol. 389, issue 19, 4217-4223

Abstract: Promoters contain specific DNA sequences and response regulatory elements, which are close to the adjacent gene’s transcription start site (TSS). And they largely controls the biological activation of the gene. Accurate transcription initiation is an essential step in the elucidation of gene regulation and understanding of the life-cycles. Although many studies have been made in this area, the mechanism of transcriptional regulation is still obscure. In this study, the six physical structural variables based on molecular dynamics (MD) simulations, three rotational descriptors and three translational descriptors, are first introduced to analyze the core promoter regions of the E. coli K12 genome. The specific structural patterns in the promoter region show that this suite of DNA geometric flexibility parameters originating from the three-dimensional structure can describe the transcription initiation of the prokaryotic genome well. Further, the prediction results by using these hidden physical codes also demonstrate that the DNA structural properties are helpful for increasing the in silico prediction of prokaryotic promoters.

Keywords: E. coli K12 promoter; DNA geometric flexibility; Structural parameters; Transcription initiation regulation; Promoter recognition (search for similar items in EconPapers)
Date: 2010
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S0378437110004644
Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:389:y:2010:i:19:p:4217-4223

DOI: 10.1016/j.physa.2010.05.034

Access Statistics for this article

Physica A: Statistical Mechanics and its Applications is currently edited by K. A. Dawson, J. O. Indekeu, H.E. Stanley and C. Tsallis

More articles in Physica A: Statistical Mechanics and its Applications from Elsevier
Bibliographic data for series maintained by Catherine Liu ().