Prediction of replication origins by calculating DNA structural properties

Wei Chen; Pengmian Feng; Hao Lin

doi:10.1016/j.febslet.2012.02.034

Prediction of replication origins by calculating DNA structural properties

FEBS Lett. 2012 Mar 23;586(6):934-8. doi: 10.1016/j.febslet.2012.02.034. Epub 2012 Feb 28.

Authors

Wei Chen¹, Pengmian Feng, Hao Lin

Affiliation

¹ Department of Physics, School of Sciences, Hebei United University, Tangshan, China. chenwei_imu@yahoo.com.cn

PMID: 22449982
DOI: 10.1016/j.febslet.2012.02.034

Abstract

In this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the Saccharomyces cerevisiae genome. We found that both DNA bendability and cleavage intensity in core replication regions were significantly lower than in the linker regions. By using these two DNA structural characteristics, we developed a computational model for ORI prediction and evaluated the model in a benchmark dataset. The predictive performance of the jackknife cross-validation indicates that DNA bendability and cleavage intensity have the ability to describe core replication regions and our model is effective in ORI prediction.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA / chemistry*
DNA / genetics
DNA / metabolism
DNA Replication*
Databases, Nucleic Acid
Models, Genetic*
Nucleic Acid Conformation*
Replication Origin*
Saccharomyces cerevisiae / genetics

Substances

DNA