Tracing Effects of Fluorine Substitutions on G-Quadruplex Conformational Changes

Area of Science:

• Structural Biology
• Nucleic Acid Chemistry
• Biophysical Chemistry

Background:

• G-quadruplexes are nucleic acid structures with diverse biological roles.
• Hybrid G-quadruplexes exhibit unique folding patterns.
• The syn/anti glycosidic torsion angle and sugar pucker influence G-quadruplex stability and conformation.

Purpose of the Study:

• To investigate the effect of 2 -fluoro-2 -deoxyriboguanosine (^FG) incorporation on the polarity of G-tetrads in a human telomere hybrid G-quadruplex.
• To explore the conformational flexibility and structural rearrangements induced by ^FG substitution.
• To re-evaluate the role of sugar pucker in G-quadruplex tetrad flipping.

Main Methods:

• Synthesis of modified human telomere G-quadruplex sequences containing ^FG at specific positions.
• Circular dichroism (CD) spectroscopy to monitor structural changes.
• Nuclear Magnetic Resonance (NMR) spectroscopy for detailed structural analysis and determination of three-dimensional structures.

Main Results:

• ^FG incorporation induced a nearly quantitative switch in G-tetrad polarity, involving concerted syn↔anti transitions of all four guanine residues.
• Two of the three ^FG analogs exhibited an S-type sugar pucker, challenging the sole requirement of N-type sugars for anti glycosidic torsion angles.
• NMR structures revealed conserved overall folds but significant rearrangements in overhang and loop regions capping the flipped tetrad.

Conclusions:

• Hybrid G-quadruplexes demonstrate a propensity for tetrad polarity reversal upon ^FG substitution, suggesting a general mechanism.
• The observed sugar pucker preferences of ^FG analogs can be rationalized by fluorine atom orientation and steric/electrostatic interactions within the quadruplex.
• These findings provide new insights into the structural plasticity of G-quadruplexes and the factors governing their conformational dynamics.