Selectivity and affinity of DNA triplex forming oligonucleotides containing the nucleoside analogues 2′-O-methyl-5-(3-amino-1-propynyl)uridine and 2′-O-methyl-5-propynyluridine

Triplex forming oligonucleotides (TFOs) containing the nucleoside analogues 2′-O-methyl-5-propynyluridine (1) and 2′-O-methyl-5-(3-amino-1- propynyl)uridine (2) were synthesized. The affinity and selectivity of triplex formation by these TFOs were studied by gel shift analysis, T_m value measurement, and association rate assays. The results show that the introduction of 1 and 2 into TFOs can improve the stability of the triplexes under physiological conditions. Optimized distribution of 1 or 2 in the TFOs combined with a cluster of contiguous nucleosides with 2′-aminoethoxy sugars resulted in formation of triplexes with further enhanced stability and improved selectivity.