Conformational and Thermodynamic Properties of Parallel Intramolecular Triple Helices Containing a DNA, RNA, or 2‘-OMeDNA Third Strand

Abstract

The thermodynamic stability and solution conformational properties of three intramolecular triple helices based on the sequence AGAAGA-x-TCTTCT-x-TCTTCT (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 contains the 2‘-OMe third strand, followed by the triplex containing RNA in the third strand. Comparison of the NMR spectroscopic data for the RNA hybrid triplex with those of the all-DNA triplex 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 triplex γ has a substantial fraction of the trans rotamer for both of the internal adenine residues (A3 and A4), whereas in the free duplex γ is g+ for these residues. In the RNA-containing triplex, only A3 shows the presence of γ(t), and in the 2‘-OMe state, both A3 and A4 are γ(g+). In addition, the 2‘-OMe triplex shows conforma...