RNA and Triple Helices

Biological processes such as transcription and recombination may involve triple- stranded nucleic acid structures in vivo (1). Triple helices have also been used as biological tools like artificial nucleases or as highly sequence-specific repressors which modulate protein recognition of DNA (1). Polypurine and polypyrimidine sequences form either pyrimidine motif (Py*Pu·Py) or purine motif (Pu*Pu·Py) triplexes, where · and * indicate the Watson-Crick and Hoogsteen base pairing, respectively. In the pyrimidine motif, a pyrimidine oligonucleotide binds to the major groove of a double helix in a parallel orientation with respect to the purine strand, through formation of Hoogsteen hydrogen bonds between T*A·T and protonated C+*G·C. In the purine motif, oligonucleotides bind antiparallel to the purine strand of the duplex by reverse Hoogsteen hydrogen bonds, A*A·T and G*G·C. The Pu-motif is generally regarded as more applicable under physiological conditions since it does not involve protonation of cytidine.