Recognition of nucleic acid double helices by homopyrimidine 2′,5′-linked RNA

We have studied the effect of a 2′,5′-RNA third strand backbone on the stability of triple helices with a ‘pyrimidine motif ’ targeting the polypurine strand of duplex DNA, duplex RNA and DNA/RNA hybrids. Comparative experiments were run in parallel with DNA and the regioisomeric RNA as third strands adopting the experimental design of Roberts and Crothers. The results reveal that 2′,5′-RNA is indeed able to recognize double helical DNA (DD) and DNA (purine):RNA (pyrimidine) hybrids (DR). However, when the duplex purine strand is RNA and the duplex pyrimidine strand is DNA or RNA (i.e. RD or RR), triplex formation is not observed. These results exactly parallel what is observed for DNA third strands. Based on Tm data, the affinities of 2′,5′-RNA and DNA third strands towards DD and DR duplexes were similar. The RNA third strand formed triplexes with all four hairpins, as previously demonstrated. In analogy to the arabinose and 2′-deoxyribose third strands, the possible C2′-endo pucker of 2′,5′-linked riboses together with the lack of an α-2′-OH group are believed to be responsible for the selective binding of 2′,5′-RNA to DD and DR duplexes, over RR and RD duplexes. These studies indicate that the use of other oligonucleotide analogues will prove extremely useful in dissecting the contributions of backbone and/or sugar puckering to the recognition of nucleic acid duplexes