First Principles Calculations of the pKa Values and Tautomers of Isoguanine and Xanthine

Katherine Noyes Rogstad, Yun Hee Jang, Lawrence Sowers, William A. Goddard

Research output: Contribution to journalArticle

61 Citations (Scopus)

Abstract

The accurate replication of DNA requires the formation of complementary hydrogen bonds between a template base and the base moiety of an incoming deoxynucleotide-5′-triphosphate. Recent structural studies suggest that some DNA polymerases contribute additional constraints by interrogating the minor groove face of the incoming and template bases. Therefore, the hydrogen bond-donating or -accepting properties of the base pairing as well as minor groove faces of the bases could be important determinants of correct base selection. In this paper, we investigate two purines that could arise by endogenous damage of the normal DNA bases: isoguanine (which can be generated by the oxidation of adenine) and xanthine (which can be generated by the deamination of guanine). In both cases, the potential exists for the placement of a proton in the N3 position, converting the N3 position from a hydrogen bond acceptor to a donor. In this paper, we use first principles quantum mechanical methods (density functional theory using the B3LYP functional and the 6-31G++G**basis set) to predict the ionization and tautomeric equilibria of both isoguanine and xanthine in the gas phase and aqueous solution. For isoguanine, we find that the N1H and N3H neutral tautomeric forms are about equally populated in aqueous solution, while the enol tauotomers are predominant in the gas phase. In contrast, we find that xanthine displays essentially no tautomeric shifts in aqueous solution but is nearly equally populated by both an anionic and a neutral form at physiological pH. To obtain these results, we carried out an extensive examination of the tautomeric and ionic configurations for both xanthine and isoguanine in solution and in the gas phase. The potential hydrogen-bonding characteristics of these damaged purines may be used to test predictions of the important components of base selection by different DNA polymerases during DNA replication.

Original languageEnglish (US)
Pages (from-to)1455-1462
Number of pages8
JournalChemical Research in Toxicology
Volume16
Issue number11
DOIs
StatePublished - Nov 2003
Externally publishedYes

Fingerprint

Xanthine
Hydrogen bonds
Hydrogen
Purines
Gases
DNA-Directed DNA Polymerase
DNA Replication
DNA
Deamination
Guanine
Adenine
Hydrogen Bonding
Base Pairing
DNA Damage
Ionization
Density functional theory
Protons
Oxidation
isoguanine

ASJC Scopus subject areas

  • Drug Discovery
  • Organic Chemistry
  • Chemistry(all)
  • Toxicology
  • Health, Toxicology and Mutagenesis

Cite this

First Principles Calculations of the pKa Values and Tautomers of Isoguanine and Xanthine. / Rogstad, Katherine Noyes; Jang, Yun Hee; Sowers, Lawrence; Goddard, William A.

In: Chemical Research in Toxicology, Vol. 16, No. 11, 11.2003, p. 1455-1462.

Research output: Contribution to journalArticle

Rogstad, Katherine Noyes ; Jang, Yun Hee ; Sowers, Lawrence ; Goddard, William A. / First Principles Calculations of the pKa Values and Tautomers of Isoguanine and Xanthine. In: Chemical Research in Toxicology. 2003 ; Vol. 16, No. 11. pp. 1455-1462.
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