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  Predicting B-DNA structure from sequence

Tung, C.-S., Hummer, G., & Soumpasis, D. M.(1995). Predicting B-DNA structure from sequence (LA-UR-95-4181). Los Alamos National Lab. (LANL), Los Alamos, NM (United States).

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Item Permalink: https://hdl.handle.net/21.11116/0000-0009-26E5-A Version Permalink: https://hdl.handle.net/21.11116/0000-000B-91EF-4
Genre: Report

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 Creators:
Tung, Chang-Shun1, Author
Hummer, Gerhard2, Author                 
Soumpasis, D. M.1, Author
Affiliations:
1External Organizations, ou_persistent22              
2Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, ou_persistent22              

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 Abstract: This project developed a reliable method that is capable of predicting B-DNA duplex structure from sequence. From any given sequence, the method predicts a complete double helical structure at the atomic level. Tetramers are used as a basic unit for the study to include the sequence effects from the neighboring base pairs. The equilibrium structures of the 136 distinct Tetramers are deduced from Monte Carlo simulations on a set of reduced coordinates developed at LANL. The prediction methods by this project can be used for searching and defining structural motifs in the functional regions of the genes. We have constructed an atomic modeled structure of a 17 base-pair DNA operator (cro, from phage lambda) with the phosphorus structures solved by x-ray crystallography. With this predicted DNA structure and modeled structures of the alpha-3 helix based on the C- alpha atoms solved by x-ray crystallography, we were able to predict two specific interactions between the cro protein and the DNA (Ser-28 to Gua-14, Lys-32 and Gua-12). These interactions were partially verified by NMR using N-15 labeled DNA operator.

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Language(s): eng - English
 Dates: 1995-12
 Publication Status: Issued
 Pages: 9
 Publishing info: Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
 Table of Contents: -
 Rev. Type: -
 Identifiers: Report Nr.: LA-UR-95-4181
DOI: 10.2172/205116
BibTex Citekey: tung_predicting_1995
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