Pyrimidine motif triplexes containing polypurine RNA or DNA with oligo 2'-O-methyl or DNA triplex forming oligonucleotides.

Triplex forming oligonucleotides (TFOs) are potentially useful in targeting RNA for antisense therapeutic applications. To determine the feasibility of targeting polypurine RNA with nuclease-resistant oligonucleotides, TFOs containing 2'-deoxy or 2'-O-methyl (2'-OMe) backbones, designed to form pyrimidine motif triplexes with RNA, were synthesized. TFOs were made which can form trimolecular triplexes, or bimolecular, 'clamp' triplexes with polypurine RNA and DNA. It was found that the relative stabilities of the triplexes formed followed the order: M.DM(clamp)>>>D.DD approximately M.DD>M. RM>D.DM>M.RD approximately M.DM, where M is a 2'-OMe, D is a DNA and R is an RNA backbone. The third strand is listed first, separated by a dot from the purine strand of the Watson-Crick duplex, followed by the pyrimidine strand of the duplex. The results described here provide insight into the feasibility of using TFOs containing a 2'-OMe backbone as antisense agents.