Kinetics and mechanism of G-quadruplex formation and conformational switch in a G-quadruplex of PS2.M induced by Pb2+

Abstract

DNA sequences with guanine repeats can form G-quartets that adopt G-quadruplex structures in the presence of specific metal ions. Using circular dichroism (CD) and ultraviolet-visible (UV-Vis) spectroscopy, we determined the spectral characteristics and the overall conformation of a G-quadruplex of PS2.M with an oligonucleotide sequence, d(GTG3TAG3CG3TTG2). UV-melting curves demonstrate that the Pb2+-induced G-quadruplex formed unimolecularly and the highest melting temperature (Tm) is 72°C. The analysis of the UV titration results reveals that the binding stoichiometry of Pb2+ ions to PS2.M is two, suggesting that the Pb2+ ions coordinate between adjacent G-quartets. Binding of ions to G-rich DNA is a complex multiple-pathway process, which is strongly affected by the type of the cations. Kinetic studies suggest that the Pb2+-induced folding of PS2.M to G-quadruplex probably proceeds through a three-step pathway involving two intermediates. Structural transition occurs after adding Pb(NO3)2 to the Na+-or K+-induced G-quadruplexes, which may be attributed to the replacement of Na+ or K+ by Pb2+ ions and the generation of a more compact Pb2+-PS2.M structure. Comparison of the relaxation times shows that the Na+→Pb2+ exchange is more facile than the K+→Pb2+ exchange process, and the mechanisms for these processes are proposed. © 2012 The Author(s).