Stacking with the unnatural DNA base 6-ethynylpyridone

Douglas J. Gibson; Tanja van Mourik

doi:10.1016/j.cplett.2016.12.009

Stacking with the unnatural DNA base 6-ethynylpyridone

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Abstract

It was previously reported that the incorporation of 6-ethynylpyridone (E) into a DNA duplex (replacing T in a T:A base pair) leads to DNA duplexes that are more stable than the T:A-containing duplexes. DFT calculations at the M06-2X/6-31+G(d) and BLYP-D3/6-31+G(d) levels on various base pairs, stacked bases and stacked base pairs in continuum solvation water suggest that the observed increased stability of E:A-containing duplexes is due to the combined effects of stronger base pairing and enhanced stacking of the E:A base pair.

Original language	English
Pages (from-to)	7-13
Number of pages	7
Journal	Chemical Physics Letters
Volume	668
Early online date	8 Dec 2016
DOIs	https://doi.org/10.1016/j.cplett.2016.12.009
Publication status	Published - 16 Jan 2017

Keywords

Unnatural base pair
6-ethynylpyridone
Density functional theory
Stacking
M06-2X
BLYP-D3

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10.1016/j.cplett.2016.12.009

vanMourik_2016_CPL_unnaturalDNA_AAM
© 2016 Elsevier B.V. All rights reserved. This work has been made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at: https://doi.org/10.1016/j.cplett.2016.12.009
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title = "Stacking with the unnatural DNA base 6-ethynylpyridone",

abstract = "It was previously reported that the incorporation of 6-ethynylpyridone (E) into a DNA duplex (replacing T in a T:A base pair) leads to DNA duplexes that are more stable than the T:A-containing duplexes. DFT calculations at the M06-2X/6-31+G(d) and BLYP-D3/6-31+G(d) levels on various base pairs, stacked bases and stacked base pairs in continuum solvation water suggest that the observed increased stability of E:A-containing duplexes is due to the combined effects of stronger base pairing and enhanced stacking of the E:A base pair. ",

keywords = "Unnatural base pair, 6-ethynylpyridone, Density functional theory, Stacking, M06-2X, BLYP-D3",

author = "Gibson, {Douglas J.} and {van Mourik}, Tanja",

note = "The authors are grateful to EaStCHEM for computational support via the EaStCHEM Research Computing Facility.",

year = "2017",

month = jan,

day = "16",

doi = "10.1016/j.cplett.2016.12.009",

language = "English",

volume = "668",

pages = "7--13",

journal = "Chemical Physics Letters",

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T1 - Stacking with the unnatural DNA base 6-ethynylpyridone

AU - Gibson, Douglas J.

AU - van Mourik, Tanja

N1 - The authors are grateful to EaStCHEM for computational support via the EaStCHEM Research Computing Facility.

PY - 2017/1/16

Y1 - 2017/1/16

N2 - It was previously reported that the incorporation of 6-ethynylpyridone (E) into a DNA duplex (replacing T in a T:A base pair) leads to DNA duplexes that are more stable than the T:A-containing duplexes. DFT calculations at the M06-2X/6-31+G(d) and BLYP-D3/6-31+G(d) levels on various base pairs, stacked bases and stacked base pairs in continuum solvation water suggest that the observed increased stability of E:A-containing duplexes is due to the combined effects of stronger base pairing and enhanced stacking of the E:A base pair.

AB - It was previously reported that the incorporation of 6-ethynylpyridone (E) into a DNA duplex (replacing T in a T:A base pair) leads to DNA duplexes that are more stable than the T:A-containing duplexes. DFT calculations at the M06-2X/6-31+G(d) and BLYP-D3/6-31+G(d) levels on various base pairs, stacked bases and stacked base pairs in continuum solvation water suggest that the observed increased stability of E:A-containing duplexes is due to the combined effects of stronger base pairing and enhanced stacking of the E:A base pair.

KW - Unnatural base pair

KW - 6-ethynylpyridone

KW - Density functional theory

KW - Stacking

KW - M06-2X

KW - BLYP-D3

U2 - 10.1016/j.cplett.2016.12.009

DO - 10.1016/j.cplett.2016.12.009

M3 - Article

SN - 0009-2614

VL - 668

SP - 7

EP - 13

JO - Chemical Physics Letters

JF - Chemical Physics Letters

ER -

Stacking with the unnatural DNA base 6-ethynylpyridone

Abstract

Keywords

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