Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides.

Area of Science:

• Genomic structural biology
• Medicinal chemistry
• Oligonucleotide therapeutics

Background:

• Guanine-rich genomic regions form G-quadruplex structures crucial for gene regulation.
• G-quadruplexes are therapeutic targets, with polyaromatic ligands showing promise for specific binding.
• Modulating G-quadruplex stability via base stacking offers a potential therapeutic approach.

Purpose of the Study:

• To investigate the impact of pyrene-modified uridine nucleotides on G-quadruplex stability and structure.
• To explore pyrene-guanine interactions within the thrombin binding aptamer (TBA) model system.
• To assess the therapeutic potential of pyrene-induced structural modifications.

Main Methods:

• Incorporation of pyrene-modified uridine nucleotides into the thrombin binding aptamer (TBA).
• Characterization using spectroscopic and biophysical techniques.
• Nuclear Magnetic Resonance (NMR) spectroscopy to elucidate structural changes.

Main Results:

• Pyrene incorporation induced significant alterations in the 3D structure of the TBA, including novel dimeric topologies.
• Spectroscopic and biophysical analyses revealed specific interaction modes between pyrene groups and the G-quadruplex core.
• Structural changes correlated with altered thrombin binding affinities and enhanced nuclease resistance.

Conclusions:

• Pyrene modification provides a method to predictably stabilize or destabilize specific G-quadruplex structures.
• The study demonstrates the potential of pyrene-modified oligonucleotides as therapeutic agents targeting G-quadruplexes.
• Site-specific structural modulation by pyrene stacking offers a tunable approach for aptamer-based therapies.