Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model

Biophysical Journal
Martin Zacharias

Abstract

A number of trinucleotide sequences in DNA can form compact and stable hairpin loops that may have significance for DNA replication and transcription. The conformational analysis of these motifs is important for an understanding of the function and design of nucleic acid structures. Extensive conformational searches have been performed on three experimentally known trinucleotide hairpin loops (AGC, AAA, and GCA) closed by a four-base-pair stem. An implicit solvation model based on the generalized Born method has been employed during energy minimization and conformational search. In addition, energy-minimized conformers were evaluated using a finite-difference Poisson-Boltzmann approach. For all three loop sequences, conformations close to experiment were found as lowest-energy structures among several thousand alternative energy minima. The inclusion of reaction-field contributions was found to be important for a realistic conformer ranking. Most generated hairpin loop structures within approximately 5 kcal x mol(-1) of the lowest-energy structure have a similar topology. Structures within approximately 10 kcal x mol(-1) could be classified into about five structural families representing distinct arrangements of loop nucleotid...Continue Reading

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Citations

Oct 17, 2002·Journal of Molecular Recognition : JMR·L F Pineda De Castro, M Zacharias
Jul 5, 2011·Nucleic Acids Research·Srinivasaraghavan Kannan, Martin Zacharias
Nov 18, 2003·Proceedings of the National Academy of Sciences of the United States of America·Hugh Nymeyer, Angel E García
Jul 31, 2007·Biophysical Journal·Srinivasaraghavan Kannan, Martin Zacharias
Jun 28, 2003·Biophysical Journal·Gilberto Villescas-Diaz, Martin Zacharias
Jul 30, 2016·RNA Biology·Kristina SzameitUlrich Hahn
Apr 17, 2002·Journal of Molecular Biology·Eric J SorinVijay S Pande
Feb 11, 2010·Physical Chemistry Chemical Physics : PCCP·Srinivasaraghavan Kannan, Martin Zacharias
Feb 27, 2020·Current Topics in Medicinal Chemistry·Nathanael K ProctorJ Phillip Bowen
Oct 12, 2004·Journal of Biomolecular Structure & Dynamics·G Villescas-Diaz, M Zacharias
Jan 12, 2021·Chembiochem : a European Journal of Chemical Biology·Charles-Alexandre MattelaerEveline Lescrinier
May 19, 2021·Journal of Chemical Theory and Computation·Charles-Alexandre MattelaerEveline Lescrinier

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