Knowledge-based prediction of DNA atomic structure from nucleic sequence.

Marcos J Araúzo-Bravo; Akinori Sarai

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PubMed · 16901085

Knowledge-based prediction of DNA atomic structure from nucleic sequence.

Marcos J Araúzo-Bravo·Akinori Sarai

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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 0.5 A for the translational conformational coordinates, and around 5 degrees for the rotational. For the estimation of the nucleic base non-hydrogen atom coordinates the RMSE is around 1.1 A. The knowledge-based method outperformed a technique based on genetic algorithms in the prediction of B-DNA structures.

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Base Sequence Crystallography, X-Ray DNA Nucleic Acid Conformation Journal Article Research Support, Non-U.S. Gov't

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Marcos J Araúzo-Bravo, Akinori Sarai. 2005. Knowledge-based prediction of DNA atomic structure from nucleic sequence.. https://pubmed.ncbi.nlm.nih.gov/16901085/

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