Base Stacking Configuration is a Major Determinant of Excited State Dynamics in A.T DNA and LNA

Abstract

Base stacking plays an important role in excited state dynamics in polynucleotides. However, it is poorly un- derstood how stacking geometries influence the formation of and relaxation from excites states. Natural poly(dA)·poly(dT) adopts a B-form structure with extensive geometrical overlap between adjacent stacked adenines while the synthetic, locked ribose analogue (LNA), adopts the A-form structure where such overlap between adjacent adenines is reduced. We have used pump-probe transient absorption measurements on DNA and LNA, with excitation at 260 nm and absorption monitored at 440 and 260 nm, to examine the differences in excited state dynamics in B- and A-form con- formations. We observed slow decay times, both early and late stage, from the excited states of B-form and fast decay times from the excited states of analogous homopolymeric A-form structures. Within similar conformations, relaxation times are dependent on the number of stacked adenines as determined by either chain length or sequence. An increase in excited state lifetimes with increase in the number of stacked adenines shows that these excited states can be delocalized over several bases. Thus excited state lifetimes are highly dependent on how the bases are stacked. We conclude from our results that, for identical sequences, conformations that exhibit a high degree of adenine base overlap favor initial coop- erative excitation as well as subsequent evolution to delocalized excited states, but hinder the formation of out-of-plane geometries required for fast relaxation to the electronic ground state thus prolonging excited state lifetimes.