Electronic Excitations and Spectra in Single-Stranded DNA

Abstract

Using density functional theory and molecular dynamics simulations, we show that delocalized states extending over three bases can be directly excited in single-stranded poly(A) DNA. The results are in semiquantitative agreement with recent experimental results for the delocalization length of these states in single- and double-stranded DNA. The structures used in these molecular dynamics calculations are validated by comparing calculated circular dichroic spectra for d(A)2 and d(A)4 with experiment. These spectra, which arise from highly stacked structures, are in good agreement with experiment, suggesting that the short delocalization in ssDNA arises in spite of strong stacking.

Absorption Spectrum of A–T DNA Unraveled by Quantum Mechanical Calculations in Solution on the (dA)2⋅(dT)2 Tetramer

“…Nonetheless, the good agreement between our predictions and the experimental absorption spectrum indicates that our model captures the essential physics of the absorption process within A-T DNA. Confirming the results obtained on A multimers, [15,16] although the presence of multiple stacking interactions can modulate the excited-state behavior of DNA, [7,10] a stacked dimer is the key unit for understanding the most significant processes triggered in DNA by UV absorption, in agreement with the indication of a very recent experimental study. [37] Finally, from the methodological point of view, we confirm [16] that an accurate treatment of solvent effects on the electronic transitions (including those with CT character) and the use of a suitable density functional is necessary to correctly describe the excited states of single and double DNA strands.…”

“…[4] Interestingly, our current results give evidence that the bright excited states of poly(dT) and poly(dA) single and double strands are not localized on a single base, thus confirming the results we obtained on longer 9Me-A oligomers, [15,16] in agreement with very recent experimental indications. [7,10] Both for adenine and thymine strands, part of the oscillator strength of the T-S B and A-S B bright states is predicted to be loss upon stacking. As shown in Figure 2, where the intensities of the computational absorption bands are normalized with respect to the number of chromophores, our calculations correctly predict that the formation of the double strand leads to a strong decrease of the total absorption intensity.…”

Progress and Challenges in the Calculation of Electronic Excited States

“…Therefore, a large part of the initially absorbed energy will decay in sub-ps time by the same channels as those found in the monomers. Intrastrand stacked excimers/exciplexes, which are the origin of the red-shifted fluorescence observed in several oligonucleotides, as has been seen experimentally [285,293] and theoretically confirmed [294] and which are known to be formed mainly by stacks of two nucleobases, will be formed as well as neutral and charge-transfer dimers, which will all finally evolve to the same monomer decay channel after surmounting an energy barrier. [288] These potential barriers are the explanation for the deactivation mechanisms that lead to the slowest transients (> 4 ps) detected experimentally.…”

Exciton delocalization, charge transfer, and electronic coupling for singlet excitation energy transfer between stacked nucleobases in DNA: An MS-CASPT2 study

“…Excitonic and charge transfer states have been made responsible for this difference, and the role of these states has been discussed extensively on the basis of experimental 2,3,[15][16][17][19][20][21][22][23][24][25] and theoretical 14,24,[26][27][28] work. Most theoretical ab initio approaches on the excited states of DNA have considered small polymers, for which the excited states are calculated using time-dependent density functional theory 24,[26][27][28] (TD-DFT) or wave function based methods. 14 The excited state studies are often preceded by molecular dynamics calculations to account for the structural fluctuations of the polymer.…”