DFT studies on the pairing abilities of the one-electron reduced or oxidized adenine-thymine base pair

Using density functional theory (DFT), the hydrogen bonds making up the adenine-thymine (A-T) base pair are found to increase in total energy upon one-electron oxidation or reduction by 10.9 and 13.3 kcal mol(-1), respectively. Due to unsymmetric changes in the H-bond lengths, this strengthening affects an expansion of the base pair length (N1'-N9) by similar to0.27 Angstrom. In the oxidized pair, A(.+)-T, deprotonation from N-6, and with the reduced pair, A(.-)-T, protonation on N3 or N7 lead to base pairs which have similar base pairing energies as their parent A-T, i.e., the stabilization by the change in oxidation state is annihilated by (de)protonation. The calculated proton affinities of A(.-)-T are large enough to explain its protonation by H2O, which involves heterolytic bond cleavage of a water molecule. The N1 protonated electron adduct of A is a powerful H-bond donor; it is able to mismatch with cytosine (-28.9 kcal mol(-1)). In DNA this could compete with the legitimate guanine-cytosine pairing. The pairing abilities of 2-aminopurine, an unnatural isomer of A, used as a fluorescent probe in DNA assemblies, are calculated to resemble those of A closely.