Diverse polymorphism of G-quadruplexes as a kinetic phenomenon

Knowledge of forces that drive conformational transitions of G-quadruplexes is crucial for understanding the molecular basis of several key cellular processes. It can only be acquired by combining structural, thermodynamic and kinetic information. Existing biophysical and structural evidences on polymorphism of intermolecular G-quadruplexes have shown that the formation of a number of these structures is a kinetically controlled process. Reported kinetic models that have been used to describe the association of single strands into quadruplex structures seem to be inappropriate since the corresponding model-predicted activation energies turn out to be negative. By contrast, we propose here a novel kinetic model that successfully describes experimentally monitored folding/unfolding transitions of G-quadruplexes and gives positive activation energies for all elementary steps, including those describing association of two single strands into bimolecular quadruplex structures. It is based on a combined thermodynamic and kinetic investigation of polymorphic behavior of bimolecular G-quadruplexes formed from d(G4T4G4) and d(G4T4G3) strands in the presence of Na(+) ions, monitored by spectroscopic (UV, CD) and calorimetric (DSC) techniques. According to our experiment and model analysis the topology of the measured G-quadruplexes is clearly flexible with the conformational forms that respond to the rate of temperature change at which global unfolding/folding transitions occur.