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.

How to study G-quadruplex structures

“…CD spectroscopy can also provide information on conformational changes induced by altered solution conditions. Using this technique one is able to follow the kinetics of quadruplex formation (Liu et al, 2012). It is also possible to analyze the map of conformational changes because the same molecule can isomerize due to many factors.…”

Spinach RNA aptamer detects lead(ii) with high selectivity

“…Micromolar concentrations of Pb 2+ induce the formation of DNA G-quadruplexes even in the absence of K + or Na + , the two most common cations associated with G-quadruplexes. Pb 2+ -stabilized G-quadruplexes adopt a more compact structure than those stabilized by monovalent cations due to the smaller size and high charge density of Pb 2+ 6a,10,11,12a,b . We wondered whether these observations extend to the RNA G-quadruplex in Spinach.…”

Plasmonic Circular Dichroism Study of Gold Nanorod-Quadruplex Nanobioconjugates

“…PS2.M is 18 nucleotides guanine-rich sequence capable to form Anti-parallel and parallel Gquadruplex in the presence of various concentrations of metal ions (scheme.1) [10].…”