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DNA base stacking involving adenine and 2-aminopurine

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vanMourik_2015_SC_DNABase_CCBY.pdf (2.328Mb)
Date
02/2016
Author
van Mourik, Tanja
Hogan, Simon William Leslie
Keywords
Stacking
2-aminopurine
Adenine
Density functional theory
DNA bases
QD Chemistry
NDAS
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Abstract
The potential energy surfaces of stacked structures consisting of adenine (A) and 2-aminopurine (2AP) have been investigated in the gas phase. Both face-to-back (the double ring system of one base exactly on top of that of the other one) and face-to-face (one base flipped by 180°) A/A, 2AP/2AP and A/2AP stacks were considered. Minima and transition states were optimised at the counterpoise-corrected M06-2X/6-31+G(d) level of theory. For each type of stack, between five and nine minima were located, usually connected by low barriers of 1-2 kcal/mol. This shows the large conformational flexibility of these stacked base pairs. The double-ring system in A and 2AP affords multiple minima with similar twist angles, making the potential energy surface of stacks comprising of purine bases more complex than those of pyrimidine stacks. The locations of the stationary points on the potential energy surface differ for the three different systems; thus, the replacement of A by 2AP in a base stack changes its potential energy landscape.
Citation
van Mourik , T & Hogan , S W L 2016 , ' DNA base stacking involving adenine and 2-aminopurine ' , Structural Chemistry , vol. 27 , no. 1 , pp. 145-168 . https://doi.org/10.1007/s11224-015-0708-3
Publication
Structural Chemistry
Status
Peer reviewed
DOI
https://doi.org/10.1007/s11224-015-0708-3
ISSN
1040-0400
Type
Journal article
Rights
Copyright 2015 the Authors. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://crea tivecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
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  • University of St Andrews Research
URI
http://hdl.handle.net/10023/8230

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