Base-Stacking Disorder and Excited-State Dynamics in Single-Stranded Adenine Homo-oligonucleotides

Abstract

Single-stranded adenine homo-oligonucleotides were investigated in aqueous solution by femtosecond transient absorption spectroscopy in order to study the effect of strand length on the nature and dynamics of excited states formed by UV absorption. Global fitting analysis of bleach recovery signals recorded at a probe wavelength of 250 nm and pH 7 reveals that the same lifetimes of 2.72 and 183 ps reproduce the pronounced biexponential decays observed in all (dA)n oligomers, containing between 2 and 18 residues. Although the lifetimes are invariant, the amplitudes of the short- and long-lived components depend sensitively on the number of residues. For example, the 183 ps component increases with strand length and is greater for DNA vs RNA single strands with the same number of adenines. Inhomogeneous kinetics arising from two classes of adenine bases in each oligomer best explains the observations. A subset of adenine residues produce short-lived excited states upon excitation, while absorption by the remaining adenines yields long-lived excited states that are responsible for the long-lived signal. By assuming that each short-lived excited state in the oligomer makes the same contribution to the transient absorption signal as an excited state of the adenine mononucleotide, the fraction of each type of base in the oligomer can be estimated along with the quantum yield of long-lived excited states. The fraction of oligonucleotides that yield long-lived excited states increases with oligomer length in precisely the same manner as the fraction of bases that are found in base stacks. Corroborating evidence that base stacking leads to distinct decay channels comes from experiments conducted at low pH on (dA)2. Coulombic repulsion between the two protonated bases at pH 2 results in open, unstacked conformations causing the long-lived component seen in (dA)2 at neutral pH to vanish completely. The fast component seen in oligomers with two or more bases is assigned to vibrational cooling following ultrafast internal conversion to the electronic ground state. This monomer-like decay channel is operative for the subset of adenine residues that are either poorly or not at all stacked with neighboring bases. This study shows that static base stacking disorder fully accounts for the length-dependent transient absorption signals. Although absorption likely creates delocalized excitons of unknown spatial extent, the results from this study suggest that long-lived excitations in single-stranded A tracts are already fully localized on no more than two bases no later than 1 ps after UV excitation.