Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes

The central loop of G-quadruplex molecular beacons is a key element to sense target DNA or RNA sequences. In this study, circular dichroism spectroscopy (CD), thermal difference spectrum (TDS), non-denatured non-denaturing gel electrophoresis, and thermal stability analysis were used to investigate the effect of the central loop length on G-quadruplex features. Two series of G-quadruplexes, AG(3)TTAG(3)-(TTA)n-G(3)TTAG(3)T (n = 1–8) (named TTA series) and AG(3)TTTG(3)-(TTA)n-G(3)TTTG(3)T (n = 1–8) (named TTT series) were examined in K(+) and Na(+) solutions, respectively. CD and TDS spectral data indicated that TTA series adopted an antiparallel G-quadruplex structure in Na(+) solution and a hybrid G-quadruplex structure in K(+) solution respectively. TTT series exhibited a hybrid G-quadruplex structure in both Na(+) and K(+) solutions. UV melting curves indicated that the stability of G-quadruplex in both series was reduced by the elongation of central loop. Thermal stability analysis concluded that the G-quadruplex destabilization with long central loop is an entropy-driven process due to more flexible and longer central loops.