Conformational and thermodynamic properties of parallel intramolecular triple helices containing a DNA, RNA, or 2 '-OMeDNA third strand

The thermodynamic stability and solution conformational properties of three intramolecular triple helices based on the sequence AGAAGA-x-TCTTCT-x-TCTT CT (x is a non-nucleotide linker) comprising a DNA duplex and DNA, RNA, or 2'-OMeDNA third strands have been compared. The most stable triple helix co ntains the 2'-OMe third strand, followed by the tripler containing RNA in t he third strand. Comparison of the NMR spectroscopic data for the RNA hybri d tripler with those of the all-DNA tripler shows that the duplex parts of the structure are very similar; the major difference is that the RNA strand is characterized by C3'-endo sugars (except the two terminal residues). In the all-DNA tripler gamma has a substantial fraction of the trans rotamer for both of the internal adenine residues (A3 and A4), whereas in the free duplex gamma is g(+) for these residues. In the RNA-containing tripler, onl y A3 shows the presence of gamma(t), and in the 2'-OMe state, both A3 and A 4 are gamma(g(+)). In addition, the 2'-OMe tripler shows conformational het erogeneity. Thus, there are sugar-dependent differences in the degree of di stortion in the purine strand imposed by the third strand binding. The heli cal parameters for the underlying duplexes are very similar in all three tr iplexes. However, the helical parameters for the third strands are differen t for the DNA versus the RNA and 2'-OMe strands, reflecting their different sugar conformations. The lower degree of distortion of the underlying dupl ex in the presence of the 2'-OMe third strand is consistent with higher the rmodynamic stability of this tripler compared with the greater distortion o f the duplex induced by both DNA and RNA third strands.