Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level

We present a comparison between atomistic and coarse grain models for DNA developed in our group, which we introduce here with the name SIRAH. Molecular dynamics of DNA fragments performed using implicit and explicit solvation approaches show good agreement in structural and dynamical features with...

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Detalles Bibliográficos
Autores principales: Dans, P.D., Darré, L., Machado, M.R., Zeida, A., Brandner, A.F., Pantano, S.
Formato: SER
Materias:
counterions
flexibility
Molecular dynamics
narrowing
nucleic acids
simulations
WT4
Counterions
DNA
Ionic strength
Nucleic acids
Solvation
Bioinformatics
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_03029743_v8213LNBI_n_p71_Dans
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
Descripción
Sumario:We present a comparison between atomistic and coarse grain models for DNA developed in our group, which we introduce here with the name SIRAH. Molecular dynamics of DNA fragments performed using implicit and explicit solvation approaches show good agreement in structural and dynamical features with published state of the art atomistic simulations of double stranded DNA (using Amber and Charmm force fields). The study of the multi-microsecond timescale results in counterion condensation on DNA, in coincidence with high-resolution X-ray crystals. This result indicates that our model for solvation is able to correctly reproduce ionic strength effects, which are very difficult to capture by CG schemes. © 2013 Springer International Publishing.

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