Polyelectrolyte effects in G-quadruplexes

Abstract

The role of counterion condensation as a dominant force governing the stability of DNA duplexes and triplexes is well established. In contrast, the effect of counterion condensation on the stability of G-quadrupex conformations is poorly understood. Unlike other ordered nucleic acid structures, G-quadruplexes exhibit a specific binding of counterions (typically, Na+ or K+) which are buried inside the central cavity and coordinated to the O6 carbonyls of the guanines forming the G-quartets. While it has been known that the G-quadruplex-to-coil transition temperature, TM, increases with an increase in the concentration of the stabilizing ion, the contributions of the specific (coordination in the central cavity) and nonspecific (condensation) ion binding have not been resolved. In this work, we separate the two contributions by studying the change in TM of preformed G-quadruplexes following the addition of nonstabilizing ions Li+, Cs+, and TMA+ (tetramethylammonium). In our studies, we used two G-quadruplexes formed by the human telomeric sequences which are distinct with respect to the folding topology and the identity and the number of sequestered stabilizing ions. Our data suggest that the predominant ionic contribution to G-quadruplex stability comes from the specifically bound Na+ or K+ ions and not from counterion condensation. We offer molecular rationalizations to the observed insensitivity of G-quadruplex stability to counterion condensation and emphasize the need to expand such studies to assess the generality of our findings.