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Efficient deformation algorithm for plasmid DNA simulations

BACKGROUND: Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformational behavior of DNA molecules. In each iteration these simulation methods rand...

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Autores principales: Raposo, Adriano N, Gomes, Abel JP
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175687/
https://www.ncbi.nlm.nih.gov/pubmed/25225011
http://dx.doi.org/10.1186/1471-2105-15-301
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author Raposo, Adriano N
Gomes, Abel JP
author_facet Raposo, Adriano N
Gomes, Abel JP
author_sort Raposo, Adriano N
collection PubMed
description BACKGROUND: Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformational behavior of DNA molecules. In each iteration these simulation methods randomly generate a new trial conformation, which is either accepted or rejected according to a criterion based on energy calculations and stochastic rules. These simulation trials are generated using a method based on crankshaft motion that, apart from some slight improvements, has remained the same for many years. RESULTS: In this paper, we present a new algorithm for the deformation of plasmid DNA molecules for Monte Carlo simulations. The move underlying our algorithm preserves the size and connectivity of straight-line segments of the plasmid DNA skeleton. We also present the results of three experiments comparing our deformation move with the standard and biased crankshaft moves in terms of acceptance ratio of the trials, energy and temperature evolution, and average displacement of the molecule. Our algorithm can also be used as a generic geometric algorithm for the deformation of regular polygons or polylines that preserves the connections and lengths of their segments. CONCLUSION: Compared with both crankshaft moves, our move generates simulation trials with higher acceptance ratios and smoother deformations, making it suitable for real-time visualization of plasmid DNA coiling. For that purpose, we have adopted a DNA assembly algorithm that uses nucleotides as building blocks.
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spelling pubmed-41756872014-09-27 Efficient deformation algorithm for plasmid DNA simulations Raposo, Adriano N Gomes, Abel JP BMC Bioinformatics Methodology Article BACKGROUND: Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformational behavior of DNA molecules. In each iteration these simulation methods randomly generate a new trial conformation, which is either accepted or rejected according to a criterion based on energy calculations and stochastic rules. These simulation trials are generated using a method based on crankshaft motion that, apart from some slight improvements, has remained the same for many years. RESULTS: In this paper, we present a new algorithm for the deformation of plasmid DNA molecules for Monte Carlo simulations. The move underlying our algorithm preserves the size and connectivity of straight-line segments of the plasmid DNA skeleton. We also present the results of three experiments comparing our deformation move with the standard and biased crankshaft moves in terms of acceptance ratio of the trials, energy and temperature evolution, and average displacement of the molecule. Our algorithm can also be used as a generic geometric algorithm for the deformation of regular polygons or polylines that preserves the connections and lengths of their segments. CONCLUSION: Compared with both crankshaft moves, our move generates simulation trials with higher acceptance ratios and smoother deformations, making it suitable for real-time visualization of plasmid DNA coiling. For that purpose, we have adopted a DNA assembly algorithm that uses nucleotides as building blocks. BioMed Central 2014-09-15 /pmc/articles/PMC4175687/ /pubmed/25225011 http://dx.doi.org/10.1186/1471-2105-15-301 Text en © Raposo and Gomes; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Raposo, Adriano N
Gomes, Abel JP
Efficient deformation algorithm for plasmid DNA simulations
title Efficient deformation algorithm for plasmid DNA simulations
title_full Efficient deformation algorithm for plasmid DNA simulations
title_fullStr Efficient deformation algorithm for plasmid DNA simulations
title_full_unstemmed Efficient deformation algorithm for plasmid DNA simulations
title_short Efficient deformation algorithm for plasmid DNA simulations
title_sort efficient deformation algorithm for plasmid dna simulations
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175687/
https://www.ncbi.nlm.nih.gov/pubmed/25225011
http://dx.doi.org/10.1186/1471-2105-15-301
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