Multinuclear NMR study of cation binding to duplex and unusual DNA structures

Cation binding environments on duplex, four-way junction and G-quadruplex DNA structures were investigated by multinuclear NMR. The fraction of strong binding sites on oligomeric DNAs correlates with the percentages of GC base pairs and GG dinucleotides. A higher order relaxation contribution, which has the same origin as the second-order frequency shift, must be included in {dollar}sp{lcub}25{rcub}{dollar}Mg lineshape analysis in polymeric DNA solution. A dynamic frequency shift was observed in the multiple-quantum filtered {dollar}sp{lcub}25{rcub}{dollar}Mg spectrum. Multiple-quantum NMR techniques for spin-7/2 nuclei were analyzed by the irreducible spherical tensor operator formalism. These techniques were applied to {dollar}sp{lcub}59{rcub}{dollar}Co NMR in calf thymus DNA solution. {dollar}sp{lcub}23{rcub}{dollar}Na intensity measurements demonstrate that Na{dollar}sp+{dollar} binds to the polymeric duplex DNA loosely, without loss of waters of hydration. Mg{dollar}sp{lcub}2+{rcub}{dollar} binds to a 16mer junction slightly tighter than to its complementary junction. The equilibrium between junction and duplex was regulated by Mg{dollar}sp{lcub}2+{rcub}.{dollar}; Titrating the oligonucleotide d({dollar}rm Gsb4Csb4){dollar} with K+ shifted the equilibrium from the duplex toward the quadruplex form. Multiple-quantum {dollar}sp{lcub}23{rcub}{dollar}Na NMR techniques were applied to characterize the biexponential relaxation for Na{dollar}sp+{dollar} bound to the tetrameric parallel-stranded quadruplex structure {dollar}rm d(Tsb2Gsb4T).{dollar} In contrast to the rapid exchange from {dollar}rm d(Tsb2Gsb4T), Nasp+{dollar} bound to dimeric quadruplex structure {dollar}rm d(Gsb4Tsb4Gsb4){dollar} exchanges slowly. Thymine bases of {dollar}rm d(Tsb2Gsb4T){dollar} form three T-quartets in the presence of {dollar}rmsp{lcub}15{rcub}NHsbsp{lcub}4{rcub}{lcub}+{rcub}{dollar} at low pH. {dollar}rmsp{lcub}15{rcub}NHsbsp{lcub}4{rcub}{lcub}+{rcub}{dollar} specifically binds to these T-quartets rather than to G-quartets, which suggests that the T-quartet could be a preferential binding site for cations. Consistent with this model, Mg{dollar}sp{lcub}2+{rcub}{dollar} bound to {dollar}rm d(Tsb2Gsb4T){dollar} is in slow exchange, even in the presence of K{dollar}sp+.{dollar}...