High physiological thermal triplex stability optimization of twisted intercalating nucleic acids (TINA)

The structure of the monomer (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl] glycerol (1) in twisted intercalating nucleic acids (TINA) was optimized for stabilizing interactions between the intercalator and surrounding nucleobases when used as a triplex forming oligonucleotide (TFO). Enhancement of π-π interactions with nucleobases of the TFO was achieved by increasing the aromatic surface using the (R)-1-O-[4-(1-pyrenylethynyl)naphthylmethyl]glycerol monomer (2). Bulge insertion of 2 in the middle of a Hoogsteen-type triplex increased the triplex thermal stability, ΔT_m = +2.0 °C compared with 1 at pH 7.2. Syntheses and thermal denaturation studies of triplexes and duplexes are described for three novel TINA monomers. The influence of π-π interactions, link length and the positioning of the ether in the linker in the TINA derivatives are described.