Chapter 90 - Ultrasfast excited-state dynamics in DNA and RNA polymers

Abstract

Recent progress in understanding the photophysics of single nucleobases has now focused attention on the challenging problem of excited-state dynamics in DNA and RNA polymers. It is often stated that ultrafast non-radiative decay by the monomeric nucleobases greatly reduces the likelihood of their photochemical damage. This is a tempting explanation for why the present-day bases may have been favored over alternative compounds as the carriers of genomic information in all living organisms. However, it is yet to be shown that the DNA and RNA polymers enjoy the same degree of photostability as the monomeric nucleobases. In fact, evidence is now accumulating that considerably longer-lived excitations are formed in natural and synthetic nucleic acid polymers. This chapter discusses how the noncovalent interactions responsible for nucleic acid secondary structure (that is, base stacking and base pairing) affect the photophysics of these multi-chromophoric systems. It describes initial experimental results that demonstrate dramatic differences in excited-state dynamics of nucleic acid polymers compared to their constituent monomers. Although ultrafast internal conversion is the dominant relaxation pathway for single bases, electronic energy relaxation in single-stranded polynucleotides occurs over a wide range of time scales extending from femtoseconds to nanoseconds. Since base stacking increases the electronic coupling between adjacent nucleobases, polymer conformation significantly affects the electronic structure of these important macromolecules. The experiments in the chapter demonstrate that the intrinsic UV chromophores of nucleic acids, the DNA and RNA bases, are useful ultrafast optical probes of secondary polymer structure.