NMR study of the exchange rate between two stacked conformers of a model Holliday junction

Our investigations into the folding behavior of a series of small model Holliday junctions in the presence of magnesium ions revealed a sequence (junction J9a) displaying a 71/29 population ratio between the two differently folded stacked X-conformers in slow exchange on the NMR chemical shift time scale. For the first time we report the rates of interconversion between two stacked X-conformers and their lifetimes as measured by chemical exchange (EXSY) NMR spectroscopy: k1 5.6 (+/-0.5) s-1, k-1 2.3 (+/-0.2) s-1. The corresponding lifetimes (tau=1/k) are: tau1 430 ms, tau2 180 ms and the conformational transition barrier amounts to DeltaGdouble dagger294 68 kJ/mol (16.2 kcal/mol). It is argued that this free-energy barrier reflects the maximum barrier that separates stacked X-conformers in junction 9a from the unfolded structure.