Thermodynamic Stability of DNA Duplexes Comprising the Simplest T → du Substitutions

Carolyn E. Carr, Irine Khutsishvili, Barry Gold, Luis A Marky

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)5666-5671
Number of pages6
JournalBiochemistry
Volume57
Issue number39
DOIs
StatePublished - Oct 2 2018

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Uracil
Thermodynamics
Thermodynamic stability
Substitution reactions
Uracil-DNA Glycosidase
Base Pairing
DNA
Deoxyribose
Thymine
Enzymes
Catalysis
Immobilization
Conformations
Hot Temperature
Binding Sites
Water
Population

ASJC Scopus subject areas

  • Biochemistry

Cite this

Thermodynamic Stability of DNA Duplexes Comprising the Simplest T → du Substitutions. / Carr, Carolyn E.; Khutsishvili, Irine; Gold, Barry; Marky, Luis A.

In: Biochemistry, Vol. 57, No. 39, 02.10.2018, p. 5666-5671.

Research output: Contribution to journalArticle

Carr, Carolyn E. ; Khutsishvili, Irine ; Gold, Barry ; Marky, Luis A. / Thermodynamic Stability of DNA Duplexes Comprising the Simplest T → du Substitutions. In: Biochemistry. 2018 ; Vol. 57, No. 39. pp. 5666-5671.
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