TY - JOUR
T1 - Thermodynamic Stability of DNA Duplexes Comprising the Simplest T → du Substitutions
AU - Carr, Carolyn E.
AU - Khutsishvili, Irine
AU - Gold, Barry
AU - Marky, Luis A.
N1 - Funding Information:
*E-mail: [email protected]. Telephone: (402) 559-4628. Fax: (402) 559-9543. ORCID Carolyn E. Carr: 0000-0002-9688-6015 Barry Gold: 0000-0002-2610-978X Luis A. Marky: 0000-0001-5572-7707 Present Addresses †I.K.: Institute of Physics, Javakhishvili State University, 0186 Tbilisi, Georgia. ‡B.G.: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261. Funding This work was supported by National Science Foundation Grant MCB-1122029. Notes The authors declare no competing financial interest.
Publisher Copyright:
© Copyright 2018 American Chemical Society.
PY - 2018/10/2
Y1 - 2018/10/2
N2 - Members of the uracil-DNA glycosylase (UDG) enzyme family recognize and bind uracil, sequestering it within the binding site pocket and catalyzing the cleavage of the base from the deoxyribose, leaving an abasic site. The recognition and binding are passive and rely on innate dynamic motions of DNA wherein base pairs undergo thermally induced breakage and conformational fluctuations. Once the uracil breaks from its base pair, it can be recognized and bound by the enzyme, which then alters its conformation for sequestration and catalysis. Our results suggest that the thymine to uracil substitution, which differs only by a single methyl group, causes a destabilization of the duplex thermodynamics, which would lead to an increase in the population of the extrahelical state and increase the probability of uracil being recognized and excised from DNA by UDG. This destabilization is dependent on the identity of the nearest-neighbor base-pair stacks; a G·C nearest neighbor leads to thermal and enthalpic destabilization that is weaker that that seen with two A·T neighbors. In addition, uracil substitution yields a nearest-neighbor increase in the counterion uptake of the duplexes but decreases the level of immobilization of structural water for all substituted duplexes regardless of the neighbor identity or number of substitutions.
AB - Members of the uracil-DNA glycosylase (UDG) enzyme family recognize and bind uracil, sequestering it within the binding site pocket and catalyzing the cleavage of the base from the deoxyribose, leaving an abasic site. The recognition and binding are passive and rely on innate dynamic motions of DNA wherein base pairs undergo thermally induced breakage and conformational fluctuations. Once the uracil breaks from its base pair, it can be recognized and bound by the enzyme, which then alters its conformation for sequestration and catalysis. Our results suggest that the thymine to uracil substitution, which differs only by a single methyl group, causes a destabilization of the duplex thermodynamics, which would lead to an increase in the population of the extrahelical state and increase the probability of uracil being recognized and excised from DNA by UDG. This destabilization is dependent on the identity of the nearest-neighbor base-pair stacks; a G·C nearest neighbor leads to thermal and enthalpic destabilization that is weaker that that seen with two A·T neighbors. In addition, uracil substitution yields a nearest-neighbor increase in the counterion uptake of the duplexes but decreases the level of immobilization of structural water for all substituted duplexes regardless of the neighbor identity or number of substitutions.
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U2 - 10.1021/acs.biochem.8b00676
DO - 10.1021/acs.biochem.8b00676
M3 - Article
C2 - 30185020
AN - SCOPUS:85053703719
SN - 0006-2960
VL - 57
SP - 5666
EP - 5671
JO - Biochemistry
JF - Biochemistry
IS - 39
ER -