Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study

G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is k...

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Main Authors: Phan, Anh Tuân, Voityuk, Alexander A., Lech, Christopher Jacques, Maria-Elisabeth, Maria-Elisabeth
Other Authors: School of Physical and Mathematical Sciences
Format: Article
Language:English
Published: 2015
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Online Access:https://hdl.handle.net/10356/98114
http://hdl.handle.net/10220/38528
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-981142023-02-28T19:40:48Z Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study Phan, Anh Tuân Voityuk, Alexander A. Lech, Christopher Jacques Maria-Elisabeth, Maria-Elisabeth School of Physical and Mathematical Sciences DRNTU::Science::Chemistry::Physical chemistry::Molecular structure and bonding G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K+ ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads. Accepted version 2015-08-27T06:11:18Z 2019-12-06T19:50:44Z 2015-08-27T06:11:18Z 2019-12-06T19:50:44Z 2015 2015 Journal Article Lech, C. J., Phan, A. T., Michel-Beyerle, M. E., & Voityuk, A. A. (2015). Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study. The Journal of Physical Chemistry B, 119(9), 3697-3705. https://hdl.handle.net/10356/98114 http://hdl.handle.net/10220/38528 10.1021/jp512767j en The journal of physical chemistry B © 2015 American Chemical Society. This is the author created version of a work that has been peer reviewed and accepted for publication by The Journal of Physical Chemistry B, American Chemical Society. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [http://dx.doi.org/10.1021/jp512767j]. 28 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Science::Chemistry::Physical chemistry::Molecular structure and bonding
spellingShingle DRNTU::Science::Chemistry::Physical chemistry::Molecular structure and bonding
Phan, Anh Tuân
Voityuk, Alexander A.
Lech, Christopher Jacques
Maria-Elisabeth, Maria-Elisabeth
Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study
description G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K+ ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads.
author2 School of Physical and Mathematical Sciences
author_facet School of Physical and Mathematical Sciences
Phan, Anh Tuân
Voityuk, Alexander A.
Lech, Christopher Jacques
Maria-Elisabeth, Maria-Elisabeth
format Article
author Phan, Anh Tuân
Voityuk, Alexander A.
Lech, Christopher Jacques
Maria-Elisabeth, Maria-Elisabeth
author_sort Phan, Anh Tuân
title Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study
title_short Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study
title_full Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study
title_fullStr Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study
title_full_unstemmed Influence of base stacking geometry on the nature of excited states in G-quadruplexes : a time-dependent DFT study
title_sort influence of base stacking geometry on the nature of excited states in g-quadruplexes : a time-dependent dft study
publishDate 2015
url https://hdl.handle.net/10356/98114
http://hdl.handle.net/10220/38528
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