Effects of an abasic site on triple helix formation characterized by affinity cleaving

The stability of triple helical complexes of pyrimidine oligodeoxyribonucleotides containing one abasic 1,2-dideoxy-D-ribose (phi) residue was examined by affinity cleaving. Within a pyrimidine third strand, the triplets phi.AT, phi.GC, phi.TA and phi.CG are significantly less stable than the triplets, T.AT, C+GC and G.TA. The decrease in binding produced by an abasic residue is similar to that observed with imperfectly matched natural base triplets, with phi.AT and phi.GC being less stable than phi.TA and phi.CG triplets for the sequences studied.