Parallel stranded duplex DNA.

Three linear 21-nt oligonucleotides (C2, C3, C7) have been synthesized with different sequences of A and T residues. One pairwise combination, (C3, C7), hybridizes to form a conventional antiparallel duplex (aps-C3.C7), whereas the pair C2, C3 forms a duplex (ps-C2.C3) in which the two strands are in a parallel orientation and the A.T base-pairs in a reverse Watson-Crick configuration. The existence of the novel ps helical structure was established from the following criteria: (i) The electrophoretic mobilities of the ps and aps duplexes in native and denaturing polyacrylamide gels are similar. (ii) The ps duplex is not a substrate for T4 DNA ligase. (iii) Salt-dependent thermal transitions are observed for the two duplexes, but the melting temperatures of the ps molecules are 15 degrees C lower. (iv) The ultraviolet absorption and circular dichroism spectra of the ps duplex are indicative of a base-paired structure, but differ systematically from that of the aps helix. (v) Based on fluorescent measurements, the bis-benzimidazole drug BBI-258 shows a lower affinity for the ps compared to the aps duplex, whereas the opposite preference holds for the intercalator ethidium bromide. We conclude from the present study that parallel stranded DNA is a stable conformation which can arise by interaction between two conventional strands with appropriate sequence homology.