Near threshold photo-oxidation of dinucleotides containing purines upon 266 nm nanosecond laser excitation.: The role of base stacking, conformation, and sequence

The 266 nm nanosecond laser photoionization (PI) of a wide range of dinucleotides containing purines, and related nucleosides and nucleotides, occurs through a combination of one- and two-photon pathways that can be considered as a near threshold PI process. The net PI yields of these DNA and RNA model compounds are of the order of 10(-2), whereas the monophotonic component is of the order of 10(-3). These yields increase with an increase in the initial ground-state concentration, which is interpreted in terms of a stabilization of their ionization potentials (lPs) due to an increase in the electronic coupling between the bases as the base stacking of the dinucleotides increases on going from 1 to 100 muM concentrations. Photodestruction yields for dinucleotides in the range 10(-3) to 10(-2) were determined using low-intensity 254 nm irradiation; these increased in the following order: GpC approximate to TpdG > CpG > ApG. Competition experiments using electron scavengers showed that the participation of the oxidized base in the photodestruction mechanism is 85% for GpC, 64% for TpdG, 59% for ApG, and 18% for CpG. The photoionization yields, estimated from the effect of electron scavengers on the photodestruction yield at low-intensity 254 nm irradiation, correlated well with the monophotonic PI yields of the dinucleotides examined. Differences in base stacking, conformation, and structural fluctuations of the various dinucleotides isomers are proposed to explain the sequence effect observed in the PI yields and photoreactivity at 254 nm. A linear correlation between the net PI yield of various dinucleotides and the calculated IPs reported by Saito and Rosch groups was obtained [Saito, I.; Nakamura, T.; Nakatani, K.; Yoshioka, Y.; Yamaguchi, K.; Sugiyama, H. J. Am. Chem. Soc. 1998,120,12686-12687; Voityuk, A. A.; Jortner, J.; Bixon, M.; Rosch, N. Chem. Phys. Lett. 2000, 324, 430-434]. Altogether, the results strongly suggest the use of near threshold PI yields of small oligonucleotides to estimate the effect of such properties as base stacking, sequence and conformation, base pairing, structural fluctuation, and solvation on the efficiency of hole-trapping and charge transport in DNA.