title: Effect of base stacking on the acid-base properties of the adenine cation radical [A*+] in solution: ESR and DFT studies.
abstract: In this study, the acid-base properties of the adenine cation radical are investigated by means of experiment and theory. Adenine cation radical (A*(+)) is produced by one-electron oxidation of dAdo and of the stacked DNA-oligomer (dA)6 by Cl2*(-) in aqueous glass (7.5 M LiCl in H2O and in D2O) and investigated by ESR spectroscopy. Theoretical calculations and deuterium substitution at C8-H and N6-H in dAdo aid in our assignments of structure. We find the pKa value of A*(+) in this system to be ca. 8 at 150 K in seeming contradiction to the accepted value of < or = 1 at ambient temperature. However, upon thermal annealing to > or = 160 K, complete deprotonation of A*(+) occurs in dAdo in these glassy systems even at pH ca. 3. A*(+) found in (dA)6 at 150 K also deprotonates on thermal annealing. The stability of A*(+) at 150 K in these systems is attributed to charge delocalization between stacked bases. Theoretical calculations at various levels (DFT B3LYP/6-31G*, MPWB95, and HF-MP2) predict binding energies for the adenine stacked dimer cation radical of 12 to 16 kcal/mol. Further DFT B3LYP/6-31G* calculations predict that, in aqueous solution, monomeric A*(+) should deprotonate spontaneously (a predicted pKa of ca. -0.3 for A*(+)). However, the charge resonance stabilized dimer AA*(+) is predicted to result in a significant barrier to deprotonation and a calculated pKa of ca. 7 for the AA*(+) dimer which is 7 pH units higher than the monomer. These theoretical and experimental results suggest that A*(+) isolated in solution and A*(+) in adenine stacks have highly differing acid-base properties resulting from the stabilization induced by hole delocalization within adenine stacks.
authors.affiliation: Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA.
authors.forename: Amitava
authors.initials: A
authors.lastname: Adhikary
authors.forename: Anil
authors.initials: A
authors.lastname: Kumar
authors.forename: Deepti
authors.initials: D
authors.lastname: Khanduri
authors.forename: Michael D
authors.initials: MD
authors.lastname: Sevilla
mesh_terms: D000225:Adenine / Q000737:chemistry*; D002412:Cations; D004578:Electron Spin Resonance Spectroscopy; D005609:Free Radicals / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D012996:Solutions
chemical_list: D002412:Cations; D005609:Free Radicals; D009838:Oligodeoxyribonucleotides; D012996:Solutions; C030570:oligodeoxyadenylic acid; D000225:Adenine