Unlocked nucleic acids: implications of increased conformational flexibility for RNA/DNA triplex formation

Unlocked nucleic acids (UNAs) have been introduced at specific positions in short model DNA hairpins and RNA/DNA triplexes for the first time. UNA residues destabilize the hairpins and decrease triplex thermodynamic stability or suppress triplex formation for most of the evaluated structures. Nevertheless, the incorporation of UNA residues at certain positions of dsDNA was found to be energetically favourable or at least did not affect triplex stability. Notably, the most thermodynamically stable UNA-modified triplexes exhibited improved stability at both acidic and physiological pH. The specificity of the interactions between the triplex-forming oligonucleotide and dsDNA was characterized using EMSA for the most thermodynamically stable structures, and triplex dissociation constants were determined. One of the modified triplexes exhibited an improved Kd in comparison with the unmodified triplex. CD and thermal difference spectra indicated that UNA residues do not alter the overall structure of the most thermodynamically stable triplexes. In addition, incubation of the modified oligonucleotides with human serum indicated that the UNAs demonstrate the potential to improve the biological stability of nucleic acids.