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Conformational and electronic effects on the formation of anti cyclobutane pyrimidine dimers in G-quadruplex structures

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Conformational and electronic effects on the formation of anti cyclobutane pyrimidine dimers in G-quadruplex structures

Content Provider	Royal Society of Chemistry (RSC)
Author	Matsika, Spiridoula Lee, Wook
Copyright Year	2017
Abstract	Cyclobutane pyrimidine dimers (CPDs) are the most commonly formed photochemical products when nucleic acids interact with UV radiation. In duplex DNA, the relative inflexible structure allows for only the cis, syn CPD isomer to be formed. G-quadruplex structures, however, have loops that are more flexible and allow for different orientations of the bases to interact. As a result, the highly unusual formation of an anti CPD has been observed in these structures. Due to the close proximity between two opposing loops containing the TTA sequence in two G-quadruplex structures (called “form-3” and “basket”), a high yield of anti CPD formation was expected in these structures. However, while significant yields of anti CPDs are observed in form-3, the anti CPD is hardly observed in the basket structure. To account for this inconsistency, we examine the process of anti CPD formation in form-3 and basket structures using simulations at the atomistic level. Here, we consider the conformational effect using MD simulations, which show whether the formation of the anti CPD is structurally feasible. Quantum mechanical/molecular mechanical (QM/MM) calculations of excited states are also used to consider the electronic effect by an adjacent guanine base which can quench the formation of the anti CPD through charge transfer (CT). Our results are in qualitative agreement with the experimental results, predicting a significant yield of the anti CPD in the form-3 structure and a negligible yield in the basket structure, while they also predict the formation of the cis, syn CPD between two opposing loops in form-3. Most importantly, our simulation results show that the yields of the anti CPD in the G-quadruplex are affected significantly by both conformational and electronic effects.
Starting Page	3325
Ending Page	3336
Page Count	12
File Format	HTM / HTML PDF
ISSN	14639076
Volume Number	19
Issue Number	4
Journal	Physical Chemistry Chemical Physics
DOI	10.1039/c6cp05604k
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	TTA CPD Interaction DNA G-quadruplex Basket Cyclobutane Guanine Pyrimidine dimer Photochemistry Isomer
Content Type	Text
Resource Type	Article
Subject	Physics and Astronomy Physical and Theoretical Chemistry

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