The thrombin aptamer (5'-d-GGTTGGTGTGGTTGG) can fold itself into a chair-type G-quadruplex in a suitable solution. The formation and the structural stability of G-quadruplex was studied by UV-VIS melting experiments and circular dichroism spectra to conduct quantative and qualitaive analyses.
According to the experimental result, the structural stability of chair-type G-quadruplex of thrombin aptamer was closely related to the nature and concentration of anions. The electrostatic repulsion between the divalent anion SO42－and phosphate backbone would destabilize the structure of the G-quadruplex. This phenomenon also reflected on the UV absorption. The hypochromic effect (ΔAbs:0.063→0.037) at 295 nm of G-quadruplex was decreasing as the concentration of SO42－was elevated. On the other hand, the electrostatic replusion between Na+ (a monovalent anion) and phosphate backbone was smaller than that between SO42－ and phosphate backbone. The hypochromic values did not change a lot when the concentrations of chloride were elevated from 0.1 mM to 145 mM.
Cations (such as K+, Na+, etc.) stabilize chair-type G-quadruplex. When 140 mM potassium chloride was added into sample solution, the melting temperature of chair-type G-quadruplex with K+ was about 51 ℃. In the case of sodium chloride, the melting temperature of chair-type G-quadruplex with Na+ was at most 21 ℃ as the concentration of Na+ above 1.2 mM. This result indicates that K+ enhance chair-type G-quadruplex formation better than Na+ does.
