Sequence and solvent effects on telomeric DNA bimolecular G-quadruplex folding kinetics

Area of Science:

• Biochemistry
• Structural Biology
• Chemical Biology

Background:

• Telomeric DNA sequences form G-quadruplex structures sensitive to sequence and chemical environment.
• Solvation effects on G-quadruplex folding and unfolding kinetics are not well understood.

Purpose of the Study:

• To investigate how organic cosolvents influence the folding and unfolding rates of bimolecular telomeric G-quadruplexes.
• To elucidate the role of solvation in G-quadruplex formation kinetics and structure.

Main Methods:

• Utilized electrospray mass spectrometry to monitor bimolecular G-quadruplex formation from 12-mer telomeric strands.
• Analyzed ammonium ion distribution to differentiate parallel and antiparallel G-quadruplex structures and determine individual reaction rates.
• Quantified reaction rate dependence on varying percentages of organic cosolvents (methanol, ethanol, isopropanol, acetonitrile).

Main Results:

• Antiparallel G-quadruplex structures form faster than parallel ones.
• A dimeric reaction intermediate was identified in rapid equilibrium with single strands.
• Organic cosolvents significantly increase G-quadruplex stability by accelerating folding rates, with up to a 200-fold acceleration observed.
• Cosolvent molecules are involved in G-quadruplex formation, indicating direct interactions with DNA.
• Unfolding rates are largely insensitive to solvation but depend on sequence and structure (e.g., thymine at 5'-end affects parallel dimer dissociation).

Conclusions:

• Solvation plays a crucial role in modulating telomeric G-quadruplex folding pathways, primarily by influencing folding rates.
• The nature of the cosolvent (e.g., methanol favoring antiparallel structures) and reaction time scale dictate G-quadruplex structure in crowded environments.
• G-quadruplex unfolding is primarily determined by sequence and final structure, with minimal solvation influence.