Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions

Suresh Gorle, Siladitya Padhi, Indrajit Patil, U. Deva Priyakumar

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Urea lesions are formed in DNA because of free radical damage of the thymine base, and their occurrence in DNA blocks DNA polymerases, which has deleterious consequences. Recently, it has been shown that urea is capable of forming hydrogen bonding and stacking interactions with nucleobases, which are responsible for the unfolding of RNA in aqueous urea. Base pairing and stacking are inherent properties of nucleobases; because urea is able to form both, this study attempts to investigate if urea can mimic nucleobases in the context of nucleic acid structures by examining the effect of introducing urea lesions complementary to the four different nucleobases on the overall helical integrity of B-DNA duplexes and their thermodynamic stabilities using molecular dynamics (MD) simulations. The MD simulations resulted in stable duplexes without significant changes in the global B-DNA conformation. The urea lesions occupy intrahelical positions by forming hydrogen bonds with nitrogenous nucleobases, in agreement with experimental results. Furthermore, these urea lesions form hydrogen bonding and stacking interactions with other nucleobases of the same and partner strands, analogous to nucleobases in typical B-DNA duplexes. Direct hydrogen bond interactions are observed for the urea-purine pairs within DNA duplexes, whereas two different modes of pairing, namely, direct hydrogen bonds and water-mediated hydrogen bonds, are observed for the urea-pyrimidine pairs. The latter explains the complexities involved in interpreting the experimental nuclear magnetic resonance data reported previously. Binding free energy calculations were further performed to confirm the thermodynamic stability of the urea-incorporated DNA duplexes with respect to pure duplexes. This study suggests that urea mimics nucleobases by pairing opposite all four nucleobases and maintains the overall structure of the B-DNA duplexes.

Original languageEnglish (US)
Pages (from-to)5653-5664
Number of pages12
JournalBiochemistry
Volume55
Issue number40
DOIs
StatePublished - Oct 11 2016
Externally publishedYes

Fingerprint

B-Form DNA
Hydrogen Bonding
Urea
Hydrogen bonds
Hydrogen
DNA
Molecular Dynamics Simulation
Thermodynamics
Molecular dynamics
Thermodynamic stability
RNA Folding
Thymine
Computer simulation
DNA-Directed DNA Polymerase
Base Pairing
Nucleic Acids
Free energy
Free Radicals
Conformations

ASJC Scopus subject areas

  • Biochemistry

Cite this

Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions. / Gorle, Suresh; Padhi, Siladitya; Patil, Indrajit; Priyakumar, U. Deva.

In: Biochemistry, Vol. 55, No. 40, 11.10.2016, p. 5653-5664.

Research output: Contribution to journalArticle

Gorle, Suresh ; Padhi, Siladitya ; Patil, Indrajit ; Priyakumar, U. Deva. / Urea Mimics Nucleobases by Preserving the Helical Integrity of B-DNA Duplexes via Hydrogen Bonding and Stacking Interactions. In: Biochemistry. 2016 ; Vol. 55, No. 40. pp. 5653-5664.
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