Femtosecond time-resolved guanine oxidation in acridine modified alanyl peptide nucleic acids

Alanyl peptide nucleic acids have been designed to generate linear and rigid pairing complexes. Femtosecond time resolved electron transfer dynamics studies of alanyl-PNA double strands where both strands contain an intercalated 9-amino-6-chloro-2-methoxy-acridine in its protonated state reveal a strong similarity to nearest neighbor interstrand/intrastrand guanine oxidation in the corresponding B-DNA fragment. This observation implies that the combined influence of electronic couplings and energetic parameters, driving force and reorganization energy, on electron transfer dynamics is similar in both structures. With respect to the alanyl-PNA structure, this result is consistent with the notion of stacking distances in the nucleobase staple similar to the one in B-DNA and thus provides additional structural evidence for nucleobase stacking in alanyl-PNA double strands.