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

Abstract

The structure of the monomer (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol () 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 pi-pi interactions with nucleobases of the TFO was achieved by increasing the aromatic surface using the (R)-1-O-[4-(1-pyrenylethynyl)naphthylmethyl]glycerol monomer (). Bulge insertion of in the middle of a Hoogsteen-type triplex increased the triplex thermal stability, DeltaT(m) = +2.0 degrees C compared with at pH 7.2. Syntheses and thermal denaturation studies of triplexes and duplexes are described for three novel TINA monomers. The influence of pi-pi interactions, link length and the positioning of the ether in the linker in the TINA derivatives are described.

Unexpected Hydration of a Triple Bond During DNA Synthesis: Conjugating 3‐(Pyren‐1‐ylethynyl)indole to DNA for Triplex Studies

“…Molecular modeling studies were performed on truncated triplexes with four base triplets on both sides of the intercalator, which was incorporated in the center of the sequence (i.e., ON2 and ON4 ) and the complementary duplex D1 . The starting structure was taken from a previous calculation on the same sequence with an inserted intercalator, which was replaced with Z and X . Representative low‐energy structures were generated with the AMBER* force field in MacroModel 9.2 from Schrödinger (Figure ).…”

“…This approach has been developed further to include twisted intercalating nucleic acid (TINA), which has a monomer inserted into the backbone in which two aromatic ring systems are connected together through an acetylenic bond. The triple bond allows propeller twisting between the two aromatic ring systems that results in better stacking to the surrounding nucleobases in the triplex, as observed for ( R )‐1‐ O ‐[4‐(1‐pyrenylethynyl)phenylmethyl]glycerol ( W ; Figure ) and similar examples . The TINA monomer not only stabilizes parallel CT‐based triplexes, but also GA/GT‐based antiparallel triplexes, even in the presence of RNA .…”

Next-generation bis-locked nucleic acids with stacking linker and 2′-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes

“…Among other modifications available, twisted intercalating nucleic acid (TINA) is a flexible intercalator inserted as a bulge to considerably stabilize the triple helix ( 26 ). Modified linkers with aromatic moieties confer the ability of stacking to adjacent nucleobases to form highly stable and sequence-specific triplexes ( 27 , 28 ).…”

Optimizing anti-gene oligonucleotide ‘Zorro-LNA’ for improved strand invasion into duplex DNA

“…However, TFOs are only able to target stretches of polypurines/polypyrimidines (14–16). Moreover, the Hoogsteen mechanism of binding, through which TFOs are working, is considered weak and can be interrupted by the nucleotide excision repair machinery in the cell (17,18). Therefore, agents that bind via Watson–Crick hybridization mechanisms constitute appealing alternatives.…”