Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations

doi:10.1073/pnas.0703298104

Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations

^†Istituto per i Processi Chimico–Fisici, Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca del CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy;
^‡Dipartimento di Chimica and Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali, Università Federico II, Complesso Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy; and
^§Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy

Communicated by George C. Schatz, Northwestern University, Evanston, IL, April 11, 2007 (received for review January 16, 2007)

Abstract

A thorough study of the excited-state properties of the stacked dimers and trimers of 9-methyladenine in B-DNA conformation has been performed in aqueous solution by using time-dependent density functional calculations and the solvent polarizable continuum model, and results were compared with experimental results on polyadenine oligomers. The effect of base stacking on the absorption and emission spectra is fully reproduced by our calculations. Although light absorption leads to a state (S_B) delocalized over several nucleobases, excited-state geometry optimization indicates that S_B subsequently evolves into a state in which the excitation is localized on a single base. Analysis of the excited-state potential energy surfaces shows that S_B can easily decay into the lowest energy excited state, S_CT, which is a dark excimer produced by intermonomer charge transfer between two stacked bases. The subpicosecond features of the time-resolved experiments are interpreted in terms of ultrafast decay from S_B. After localization, two easy, radiationless decay channels are indeed open for S_B: (i) ground-state recovery, according to the same mechanisms proposed for isolated adenine and/or (ii) decay to S_CT. Our calculations suggest that the slowest part of the excited-state dynamics detected experimentally involves the S_CT state.

Footnotes

^¶To whom correspondence should be addressed. E-mail: robimp{at}unina.it
Author contributions: F.S., V.B., and R.I. designed research; F.S. and R.I. performed research; and F.S., V.B., and R.I. wrote the paper.
The authors declare no conflict of interest.
This article contains supporting information online at www.pnas.org/cgi/content/full/0703298104/DC1.
Abbreviations:

9-MA,

9-methyladenine;

CT,

charge transfer;

FC,

Franck–Condon (region);

TD-DFT,

time-dependent density functional theory;

PCM,

polarizable continuum model;

PES,

potential energy surface(s);

VEE,

vertical excitation energy.