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

Area of Science:

• Chemical Biology
• Oligonucleotide Chemistry
• Biophysical Chemistry

Background:

• Twisted intercalating nucleic acids (TINA) are designed for specific DNA/RNA binding.
• Optimizing intercalator-nucleobase interactions is key to enhancing TINA stability and function.
• Pyrene-based monomers offer extended aromatic systems for improved pi-pi stacking.

Purpose of the Study:

• To synthesize and characterize novel TINA monomers with enhanced aromaticity.
• To investigate the impact of these monomers on triplex-forming oligonucleotide (TFO) stability.
• To elucidate the role of pi-pi interactions, linker length, and ether positioning in TINA derivatives.

Main Methods:

• Chemical synthesis of three novel TINA monomers.
• Thermal denaturation studies (UV-Vis spectroscopy) of TFO duplexes and triplexes.
• Analysis of structural modifications on triplex thermal stability (ΔTm).

Main Results:

• Incorporation of (R)-1-O-[4-(1-pyrenylethynyl)naphthylmethyl]glycerol monomer into TFOs increased thermal stability by +2.0 °C at pH 7.2.
• Enhanced pi-pi interactions were observed due to increased aromatic surface area of the modified monomers.
• Systematic evaluation of linker modifications demonstrated their influence on TINA stability.

Conclusions:

• Novel pyrene-containing TINA monomers significantly enhance pi-pi interactions with nucleobases.
• Bulge insertion of these monomers into Hoogsteen-type triplexes improves thermal stability.
• These findings provide a basis for designing more stable and effective TINA-based nucleic acid structures.