Recognition of a Guanine-Cytosine Base Pair by 8-Oxoadenine

Two oligodeoxyribonucleotides, d-CTTCTTTTTTATTTT, I(A), and d-ATTATTTTTTATTTT, 11(A), where C is 5-methylcytosine and A is 8-oxoadenine, were prepared and their interactions with the duplex d-GA5GAAAAAAYAAAA/d-TTTTZTTTTTTCTTC, III∙IV(Y∙Z), were studied. Oligomers I(A) and II(A) each form triplexes with III∙IV(G∙C) at temperatures below 20 °C as shown by continuous variation experiments, melting experiments, and circular dichroism (CD) spectroscopy. The CD spectra of these triplexes are almost identical to those formed by I(C) and II(C), oligomers which contain cytosine in place of 8-oxoadenine. This suggests that the 8-oxoadenine-containing triplexes have conformations which are very similar to those of the cytosine-containing triplexes. The melting temperature (T_m) for dissociation of the third strand of triplex II∙III∙IV(A∙G∙C) is 22 °C at pH 7.0 and 8.0, whereas the T_m of the corresponding transition in triplex II∙III∙IV(C∙G∙C) decreases from 28 °C at pH 7.0 to 17 °C at pH 8.0. The pH dependence of the T_m in the latter triplex reflects the necessity of protonating the N-3 of cytosine in order for it to form two hydrogen bonds with G of the G-C base pair. It appears that the keto form of 8-oxoadenine can potentially form two hydrogen bonds with the N-7 and 0-6 atoms of G of the G-C base pair, when the 8-oxoadenine is in the syn conformation and in contrast to cytosine does not require protonation of the base. Oligomer I(A) does not form triplexes with II∙III∙IV(Y∙Z) when Y∙Z is A∙T or T∙A. Triplex formation is observed when Y∙Z is C∙G or U∙A with the third strands melting at approximately 9 and 13 °C, respectively. The latter A∙U∙A triplex may be stabilized by formation of a single hydrogen bond between the N-6 exocyclic amino group of 8-oxoadenine and the O-4 or uracil of the U∙A base pair. The ability of 8-oxoadenine to form A∙G∙C triads suggests that this modified base may be a useful alternative to cytosine or 5-methylcytosineTor use in triplex formation at physiological pH.