Kinetics of double-chain reversals bridgingcontiguous quartets in tetramolecular quadruplexes

Repetitive 50GGXGG DNA segments abound in, ornear, regulatory regions of the genome and mayform unusual structures called G-quadruplexes.Using NMR spectroscopy, we demonstrate that afamily of 50GCGGXGGY sequences adopts a foldingtopology containing double-chain reversals. Thetopology is composed of two bistranded quadruplexmonomeric units linked by formation of G:C:G:Ctetrads. We provide a complete thermodynamic andkinetic analysis of 13 different sequences usingabsorbance spectroscopy and DSC, and comparetheir kinetics with a canonical tetrameric parallelstrandedquadruplex formed by TG4T. We demonstratelarge differences (up to 105-fold) in the associationconstants of these quadruplexes depending onprimary sequence; the fastest samples exhibitingassociation rate equal or higher than the canonicalTG4T quadruplex. In contrast, all sequences studiedhere unfold at a lower temperature than this quadruplex.Some sequences have thermodynamic stabilitycomparable to the canonical TG4T tetramolecularquadruplex, but with faster association and dissociation.Sequence effects on the dissociation processesare discussed in light of structural data.