Please use this identifier to cite or link to this item: http://hdl.handle.net/1843/65617
Type: Artigo de Periódico
Title: Evaluating hydrogen bonds and base stacking of single, tandem and terminal GU mismatches in RNA with a mesoscopic model
Authors: Tauanne Dias Amarante
Gerald Weber
Abstract: Guanine−Uracil (GU) mismatches are crucial to the stability of the RNA double helix and need to be considered in RNA folding algorithms for numerous biotechnological applications. Yet despite its importance, many aspects of GU base pairs are still poorly understood. There is also a lack of parametrization which prevents it to be considered in mesoscopic models. Here, we adapted the mesoscopic Peyrard–Bishop model to deal with context-dependent hydrogen bonds of GU mismatches and calculated the model parameters related to hydrogen bonding and base stacking from available experimental melting temperatures. The context-dependence causes a proliferation of parameters which made the problem computationally very demanding. We were able to overcome this problem by systematically regrouping the parameters during the minimization procedure. Our results not only provide the much needed parametrization but also answer several questions about the general properties of GU base pairs, as they can be associated straightforwardly to hydrogen bonding and base stacking. In particular, we found a very small Morse potential for tandem 5′-GU-3′, which confirms a single hydrogen bond for this configuration, answering a long-standing question over conflicting experimental findings. Terminal GU base pairs are known to increase the duplex stability, but it is not clear why. Our results suggest that the increased terminal stability is mostly due to stronger hydrogen bonding.
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/10.1021/acs.jcim.5b00571
URI: http://hdl.handle.net/1843/65617
Issue Date: 2016
metadata.dc.url.externa: https://pubs.acs.org/doi/10.1021/acs.jcim.5b00571
metadata.dc.relation.ispartof: Journal of Chemical Information and Modeling
Appears in Collections:Artigo de Periódico

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