Ultrafast Excited-State Dynamics in Hexaethyleneglycol-Linked DNA Homoduplexes Made of A·T Base Pairs

Abstract

Double-stranded DNA conjugates with the sequence (dA)₁₀·(dT)₁₀ and hexaethylene glycol linkers at one end (hairpin) or both ends (dumbbell) were studied in buffer solution by deep UV femtosecond transient absorption spectroscopy. These covalently constrained duplexes have greatly enhanced thermal stability compared to A·T duplex oligonucleotides that lack linkers. The conjugates eliminate the slipped-strand and end-frayed structures that form readily in unlinked (dA)_<i>n</i>·(dT)_<i>n</i> sequences, allowing the excited-state dynamics of stacked A·T base pairs to be observed without interference from structures with stacking or pairing defects. Transient absorption signals show that subpicosecond internal conversion to the electronic ground state takes place in addition to the formation of long-lived excited states having lifetimes of approximately 70 ps. Watson–Crick base-pairing slows the rate of vibrational cooling compared to monomeric bases or single-stranded DNA, possibly by reducing the total number of solute–solvent hydrogen bonds. Long-lived excited states in intact A·T base pairs decay several times more quickly than long-lived excited states observed in single-stranded (dA)_<i>n</i> sequences. These results show that base-pairing can measurably affect nonradiative decay pathways in A·T duplexes