Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions

In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the m...

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Main Authors: C. Ngaojampa, P. Nimmanpipug, L. D. Yu, S. Anuntalabhochai, V. S. Lee
Format: Journal
Published: 2018
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http://cmuir.cmu.ac.th/jspui/handle/6653943832/50356
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Institution: Chiang Mai University
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spelling th-cmuir.6653943832-503562018-09-04T04:30:35Z Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions C. Ngaojampa P. Nimmanpipug L. D. Yu S. Anuntalabhochai V. S. Lee Physics and Astronomy In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation. © 2010 Elsevier B.V. All rights reserved. 2018-09-04T04:30:35Z 2018-09-04T04:30:35Z 2011-02-15 Journal 0168583X 2-s2.0-79251532379 10.1016/j.nimb.2010.12.069 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=79251532379&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/50356
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
topic Physics and Astronomy
spellingShingle Physics and Astronomy
C. Ngaojampa
P. Nimmanpipug
L. D. Yu
S. Anuntalabhochai
V. S. Lee
Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions
description In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation. © 2010 Elsevier B.V. All rights reserved.
format Journal
author C. Ngaojampa
P. Nimmanpipug
L. D. Yu
S. Anuntalabhochai
V. S. Lee
author_facet C. Ngaojampa
P. Nimmanpipug
L. D. Yu
S. Anuntalabhochai
V. S. Lee
author_sort C. Ngaojampa
title Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions
title_short Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions
title_full Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions
title_fullStr Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions
title_full_unstemmed Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions
title_sort combined quantum-mechanics/molecular-mechanics dynamics simulation of a-dna double strands irradiated by ultra-low-energy carbon ions
publishDate 2018
url https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=79251532379&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/50356
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