Hole delocalization over adenine tracts in single stranded DNA oligonucleotides

Abstract

Adiabatic ionization energies of single stranded DNA oligonucleotides containing adenine tracts of different sizes have been computed at the DFT level and compared with the oxidation potentials determined by differential pulse voltammetry. Geometry optimizations have been performed at the full quantum mechanical level, including the sugar phosphate backbone and solvent effects. The observed progressive lowering of the ionization energy upon increasing the number of consecutive adenines is well predicted, the computed ionization potential shifts being in very good agreement with the experimental outcomes, both by using pure and hybrid functionals. The spin density of the oligonucleotide radical cations is distributed almost over the whole adenine tract, forming delocalized polaron

Length-independent transport rates in biomolecules by quantum mechanical unfurling

“…A remarkable characteristic of these hole orbitals is that (regardless of N ) each one can be related specifically to the donor ([G] + ), to the poly-A bridge ([(T) N ] + ), or to the acceptor ([GGG] + ). Similarly to the results of other experimental observations and model computations 48 – 50 for poly-A DNA in various conformations, orbitals that are related to the bridge are not restricted to specific nucleobases. Moreover, our model for rigid [5′-G(T) N GGG-3′] + shows that most of the bridge orbitals are delocalized over the entire poly-A sequence.…”

DFT predictions of the oxidation potential of organic dyes for opto-electronic devices

“…Several reports show that the widely used B3LYP functional is capable of predicting reliable ionization energies, for aromatic systems, even for difficult cases such as the oxidation of DNA nucleobases, nucleosides and oligonucleotides in solution [11][12][13][14][15][16][17][18]. However B3LYP was found to underestimate oxidation free energies of triphenylamine-based dipolar chromophores for dye-sensitized solar cells, while meta functionals furnished more accurate results [19].…”

Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies

“…[59][60][61][62] On the other hand, guanine rich oligonucleotides are known to exhibit opposite behavior. [59][60][61][62] On the other hand, guanine rich oligonucleotides are known to exhibit opposite behavior.…”