COMPARATIVE STABILITY OF 8 DIFFERENT TRIPLE HELICES FORMED BY DIFFERENTLY MODIFIED DNA OR RNA PYRIMIDINE STRANDS AND A DNA HAIRPIN

The comparative stability of eight different triplexes constituted wit h 16-mer pyrimidine-modified oligodeoxynucleotides (wild-type ODN, PS- ODN, alpha-ODN, or alpha-PS-ODN) or oligoribonucleotides (wild-type OR N, alpha-ORN, 4'-thio-ORN, or 2'-O-MeORN) and a DNA hairpin, termed H3 6, 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 concen tration (100 mM and 1 M Na+), and in the presence or absence of divale nt cation (0 or 3 mM Mg2+) or, Spermine (0 or 1 mM), At pH 5.5, the ei ght triplexes are formed with T-m values ranging from 24.7 degrees C t o 50.9 degrees C (Delta G(298K) between -8.1 and -16.8 kcal/mol). At p H 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 tripler for mation, An increase of salt concentration or the presence of spermine stabilizes the triplexes, whereas Mg2+ has a destabilizing effect (exc epted for alpha-ORN), In general ORN:H36 and 2'-O-MeORN:H36 triplexes were the most stable, Finally, introduction of alpha-anomeric nucleosi des led to an alpha-ORN analog that showed low binding with H36 and to alpha-ODN and alpha-PS-ODN analogs, Triplexes formed with alpha-ODN w ere slightly less stable than those formed with unmodified ODN, Surpri singly, introduction of phosphorothioate in an alpha analog led only t o a low destabilization.