Comparative Stability of Eight Different Triple Helices Formed by Differently Modified DNA or RNA Pyrimidine Strands and a DNA Hairpin

Abstract

The comparative stability of eight different triplexes constituted with 16-mer pyrimidine-modified oligodeoxynucleotides (wild-type ODN, PS-ODN, α-ODN, or α-PS-ODN) or oligoribonucleotides (wild-type ORN, α-ORN, 4‵-thio-ORN, or 2‵-O-MeORN) and a DNA hairpin, termed H36, was studied in five different buffers by UV melting curve analysis. The composition of buffers varied in pH (5.5 and 6.5), in salt concentration (100 mM and 1 M Na⁺), and in the presence or absence of divalent cation (0 or 3 mM Mg²⁺) or spermine (0 or 1 mM). At pH 5.5, the eight triplexes are formed with T_m values ranging from 24.7°C to 50.9°C (△G_298K between —8.1 and —16.8 kcal/mol). At pH 6.5, the triplexes are less stable, and thus 4‵-thio-ORN and PS-ODN showed broad transitions that did not allow us to conclude triplex formation. An increase of salt concentration or the presence of spermine stabilizes the triplexes, whereas Mg²⁺ has a destabilizing effect (excepted for α-ORN). In general ORN:H36 and 2‵-0-MeORN:H36 triplexes were the most stable. Finally, introduction of α-anomeric nucleosides led to an α-ORN analog that showed low binding with H36 and to α-ODN and α-PS-ODN analogs. Triplexes formed with α-ODN were slightly less stable than those formed with unmodified ODN. Surprisingly, introduction of phosphorothioate in an α analog led only to a low destabilization.