Quadruplexes with a grain of salt: influence of cation type and concentration on DNA G4 stability

G-quadruplexes (G4) are stabilized by intra-quartet hydrogen bonds stacking between quartets, as well as specific and non-specific ionic interactions. Cation effects on G-quadruplexes differ significantly from those on duplexes, and specific cation coordination is indeed required to stabilize G4 structures. Most studies so far involve "standard" concentrations of potassium or sodium cations because of their prevalence in human cells, but several other monovalent and divalent cations may promote quadruplex formation. In addition, ionic strength may be different in other organisms such as Halophiles: the intracellular cation (potassium) concentration in salt-loving organisms such as Haloferax volcanii can be extremely high. In this study, we first performed a bioinformatics analysis of G4 propensity in halophiles and analyzed the impact of altering ionic strength or ionic balance on G4 or hairpin duplex stability. We then present a detailed and quantitative assessment of salt effect on a variety of duplex and quadruplex sequences. Over a dozen different quadruplex and duplex sequences were investigated by FRET melting and UV melting experiments. In addition, changes in sodium/potassium balance possibly occurring in human cells have a modest effect on G4-duplex competition. We also confirm that lithium is rather a "G4-indifferent" than a G4-destabilizing cation.