Please use this identifier to cite or link to this item: http://hdl.handle.net/1843/64979
Type: Artigo de Periódico
Title: An asymmetric mesoscopic model for single bulges in RNA
Authors: Erik de Oliveira Martins
Gerald Weber
Abstract: Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.
Subject: Ácido ribonucleico
language: eng
metadata.dc.publisher.country: Brasil
Publisher: Universidade Federal de Minas Gerais
Publisher Initials: UFMG
metadata.dc.publisher.department: ICX - DEPARTAMENTO DE FÍSICA
Rights: Acesso Restrito
metadata.dc.identifier.doi: https://doi.org/10.1063/1.5006948
URI: http://hdl.handle.net/1843/64979
Issue Date: 2017
metadata.dc.url.externa: https://pubs.aip.org/aip/jcp/article/147/15/155102/196704/An-asymmetric-mesoscopic-model-for-single-bulges
metadata.dc.relation.ispartof: The Journal of Chemical Physics
Appears in Collections:Artigo de Periódico

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