Knowledge-Based Prediction of DNA Atomic Structure from Nucleic Sequence

Marcos J. Araú;zo-Bravo (marara@bse.kyutech.ac.jp)
Akinori Sarai (sarai@bse.kyutech.ac.jp)

Department of Biosciences and Bioinformatics, Kyushu Institute of Technology, 1-1 Kawazu, Iizuka, Fukuoka 820-8502, Japan


Abstract

A simple knowledge-based method for DNA atomic structure prediction from nucleic sequence is presented. We used free B-DNA crystal structures to estimate the distribution of trinucleotide base pairs and tetranucleotide base-pair steps conformational coordinates. We used these distributions as a basis to predict the 3D position of the non-hydrogen atoms of the nucleic bases of any arbitrary DNA sequence of any length. The only constraint imposed was that the structure is a B-DNA one with Watson-Crick complementary base pairs. The method was tested on not seen DNA structures with sequence lengths varying from 6bp to 12bp. The obtained predictions have RMSE around 0.5Å for the translational conformational coordinates, and around 5° for the rotational. For the estimation of the nucleic base non-hydrogen atom coordinates the RMSE is around 1.1Å. The knowledge-based method outperformed a technique based on genetic algorithms in the prediction of B-DNA structures.

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Japanese Society for Bioinformatics