| Two series of DNA oligomers with anthraquinone (AQ) covalently linked to the 5'-terminus were designed to investigate the interaction of the electronically excited quinone with DNA duplexes that contain doublet- or triplet-guanine (G) sequence steps. Excitation of the quinone with light forms an excited state chromophore that injects a radical cation into the helix, and initiates its propagation through the duplex. When the irradiated DNA is treated with hot piperidine, strand scission is observed primarily at GG-steps that are close to and farther from the quinone.;In the first series, duplexes containing a single base bulge or a tandem base mis-pair were investigated. Previous studies have shown that these non-Watson-Crick base pairs are susceptible to radiation damage [1, 2]. However, our investigations reveal that there are minimal differences in the relative photocleavage efficiencies for the charge migrating through either the perturbed or fully complementary sequences.;The second series of oligonucleotides contain tandem G·A mis-pairs with either anti-anti ('head to head') or sheared, 'side to side', conformations. The sequence effects are traced to the effect of A-T base pairs flips (A/T → T/A) on charge migration.;The results for the irradiation experiments indicate that there is a significant reaction difference between anti-anti and sheared conformations. However, the control sequences show that this is not due to the conformation of the G·A tandem mis-pairs.;Based on the migration pattern that emerges from our results, charge migration by a "purine:purine staggered walk" is suggested. This may predict the efficiency and reactivity of electron transfer through select B-DNA duplexes.;A comparison of our findings with a theory [3] that incorporates superexchange through A/T base pairs does not fit our experimental data. |
