Volumetric contributions of loop regions of G-quadruplex DNA to the formation of the tertiary structure.

DNA guanine-quadruplexes (G-quadruplexes) are unique DNA structures formed by guanine-rich sequences. The loop regions of G-quadruplexes play key roles in stability and topology of G-quadruplexes. Here, we investigated volumetric changes induced by pressure in the folding of the G-quadruplex formed by the thrombin binding aptamer (TBA) with mutations within the loop regions. The change of partial molar volume in the transition from coil to G-quadruplex, ∆Vtr , of TBA with a mutation from T to A in the 5' most loop (TBA T3A) was 75.5cm3 mol-1 , which was larger than that of TBA (54.6cm3 mol-1 ). TBA with a G to T mutation in the central loop (TBA G8T) had thermal stability similar to TBA T3A but a smaller ∆Vtr of 41.1cm3 mol-1 . In the presence of poly(ethylene)glycol 200 (PEG200), ∆Vtr values were 14.7cm3 mol-1 for TBA T3A and 13.2cm3 mol-1 for TBA G8T. These results suggest that the two mutations destabilize the G-quadruplex structure differently. Thus, volumetric data obtained using pressure-based thermodynamic analyses provides information about the dynamics of the loop regions and the roles of loops in the stabilities and folding of G-quadruplex structures.