Cargando…
Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene
[Image: see text] The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalize...
Autores principales: | , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
|
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465685/ https://www.ncbi.nlm.nih.gov/pubmed/36036695 http://dx.doi.org/10.1021/acs.jpcb.2c04327 |
_version_ | 1784787854117830656 |
---|---|
author | Panczyk, Tomasz Nieszporek, Jolanta Nieszporek, Krzysztof |
author_facet | Panczyk, Tomasz Nieszporek, Jolanta Nieszporek, Krzysztof |
author_sort | Panczyk, Tomasz |
collection | PubMed |
description | [Image: see text] The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3′ and 5′ ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3′ and 5′ ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure. |
format | Online Article Text |
id | pubmed-9465685 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-94656852022-09-13 Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene Panczyk, Tomasz Nieszporek, Jolanta Nieszporek, Krzysztof J Phys Chem B [Image: see text] The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3′ and 5′ ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3′ and 5′ ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure. American Chemical Society 2022-08-29 2022-09-08 /pmc/articles/PMC9465685/ /pubmed/36036695 http://dx.doi.org/10.1021/acs.jpcb.2c04327 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Panczyk, Tomasz Nieszporek, Jolanta Nieszporek, Krzysztof Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene |
title | Molecular Dynamics
Simulations of Interactions between
Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized
Graphene |
title_full | Molecular Dynamics
Simulations of Interactions between
Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized
Graphene |
title_fullStr | Molecular Dynamics
Simulations of Interactions between
Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized
Graphene |
title_full_unstemmed | Molecular Dynamics
Simulations of Interactions between
Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized
Graphene |
title_short | Molecular Dynamics
Simulations of Interactions between
Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized
Graphene |
title_sort | molecular dynamics
simulations of interactions between
human telomeric i-motif deoxyribonucleic acid and functionalized
graphene |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9465685/ https://www.ncbi.nlm.nih.gov/pubmed/36036695 http://dx.doi.org/10.1021/acs.jpcb.2c04327 |
work_keys_str_mv | AT panczyktomasz moleculardynamicssimulationsofinteractionsbetweenhumantelomericimotifdeoxyribonucleicacidandfunctionalizedgraphene AT nieszporekjolanta moleculardynamicssimulationsofinteractionsbetweenhumantelomericimotifdeoxyribonucleicacidandfunctionalizedgraphene AT nieszporekkrzysztof moleculardynamicssimulationsofinteractionsbetweenhumantelomericimotifdeoxyribonucleicacidandfunctionalizedgraphene |