Are Adenine Strands Helical H-Aggregates?

Abstract

On the basis of our quantum mechanical calculation, we propose that homogeneous single-stranded adenine bases (Ade-DNA) form helical H aggregates, and the photoexcited states can be described as Frenkel excitons. The calculated excitonic coupling between adjacent transition dipoles is in good agreement with the measured absorption spectrum of 20-base homogeneous adenine stacks that exhibits a blue shift of 2.6 nm relative to that of the monomeric species.

Monomeric adenine decay dynamics influenced by the DNA environment

“…Despite this inherent limitation of our presently adopted model, the QM/MM results for a single QM adenine compare reasonably well with experiment, as the absorption maxima of oligonucleotides are observed at 4.82 eV [(dA) 20 ] for single strands [12] and at 4.78 eV…”

“…give reasonable results for the excitation energies of homogeneous adenine single strands [12] and delocalized excitonic states. [24] Voityuk [25] showed the merits of the semiempirical INDO/S method in dealing with bulky systems as large as double-stranded DNA polymers.…”

“…There is a small red shift (0.06 eV) when going from the gas phase to aqueous solution, and a small blue shift (0.09-0.17 eV) when going from the latter to the DNA strands. Various experimental spectra show similar red shifts [1,52] (0.14-0.31 eV) and blue shifts [12,53,54] (0.01-0.07 eV). These shifts are induced by the complex electrostatic and steric environment in the condensed phase.…”

“…The simplest models, stacked base dimers (as well as trimers) and base pairs, have been studied most. Density functional theory (DFT), complete-active-space self-consistent-field (CASSCF) methodology, and configuration interaction approaches have been applied to model virtually every aspect of DNA photochemistry, including energetics, [12,13] p-stacking and/or base pairing, [14,15] electrostatic interactions, [16] damage and repair reactions, [17] excited-state delocalization (charge transfer, excimer/exciplex, exciton), [18] and decay dynamics. [19] Spectroscopic measurements of DNA strands are usually done in solution, and hence, solvent effects may play a crucial role.…”

Superradiance at the localization-delocalization crossover in tubular chlorosomes

“…There is, then, a competition between localization and collectiveness (or state coherence) and the more optical active region where superradiance occurs coincides with the crossover region between localization and delocalization. The results found in this work should be applicable to other different supramolecu-lar aggregates [52,53]. These states where the absorption is largest are also the ones expected to dominate the energy transfer.…”