pKa values of guanine in water: Density functional theory calculations combined with Poisson-Boltzmann continuum-solvation model

Yun Hee Jang, William A. Goddard, Katherine T. Noyes, Lawrence C. Sowers, Sungu Hwang, Doo Soo Chung

Research output: Contribution to journalArticle

175 Scopus citations

Abstract

It has long been postulated that rare tautomeric or ionized forms of DNA bases may play a role in mispair formation. To investigate the role this phenomenon plays in the mispairing of guanine and to develop a calculation methodology that can be extended to mutagenic DNA damage products, we used first principles quantum mechanics (density functional theory (B3LYP) with the Poisson-Boltzmann continuum-solvation model) to calculate the relative stabilities of tautomers of guanine in various environments and their pKa values in aqueous solution. This method allows us to calculate site specific pKa values - information that is experimentally inaccessible - as well as overall pKa values for each stage, wherein our numbers are in agreement with experimental values. We find that neutral guanine exists in aqueous phase as a mixture of two major keto tautomers, the N9H form (1) and a N7H form (3). These keto forms are also major species present in the gas phase, as well as the O6H enol tautomer (7a). These results show that tautomeric configurations can be drastically different depending on the environment. Here, we discuss the reasons for this environmental variability and suggest some possible implications. Finally, we estimate that the relative population of deprotonated guanine is 0.2-2% in the range of pH 7-8, a significant enough population to potentially play a role in mispair formation.

Original languageEnglish (US)
Pages (from-to)344-357
Number of pages14
JournalJournal of Physical Chemistry B
Volume107
Issue number1
DOIs
StatePublished - Jan 9 2003
Externally publishedYes

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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