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Multinuclear NMR study of cation binding to duplex and unusual DNA structures
Abstract
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 $\sp{25}$Mg lineshape analysis in polymeric DNA solution. A dynamic frequency shift was observed in the multiple-quantum filtered $\sp{25}$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 $\sp{59}$Co NMR in calf thymus DNA solution. $\sp{23}$Na intensity measurements demonstrate that Na$\sp+$ binds to the polymeric duplex DNA loosely, without loss of waters of hydration. Mg$\sp{2+}$ binds to a 16mer junction slightly tighter than to its complementary junction. The equilibrium between junction and duplex was regulated by Mg$\sp{2+}.$ Titrating the oligonucleotide d($\rm G\sb4C\sb4)$ with K+ shifted the equilibrium from the duplex toward the quadruplex form. Multiple-quantum $\sp{23}$Na NMR techniques were applied to characterize the biexponential relaxation for Na$\sp+$ bound to the tetrameric parallel-stranded quadruplex structure $\rm d(T\sb2G\sb4T).$ In contrast to the rapid exchange from $\rm d(T\sb2G\sb4T),\ Na\sp+$ bound to dimeric quadruplex structure $\rm d(G\sb4T\sb4G\sb4)$ exchanges slowly. Thymine bases of $\rm d(T\sb2G\sb4T)$ form three T-quartets in the presence of $\rm\sp{15}NH\sbsp{4}{+}$ at low pH. $\rm\sp{15}NH\sbsp{4}{+}$ 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$\sp{2+}$ bound to $\rm d(T\sb2G\sb4T)$ is in slow exchange, even in the presence of K$\sp+.$
Subject Area
Chemistry|Biochemistry|Biophysics
Recommended Citation
Deng, Hong, "Multinuclear NMR study of cation binding to duplex and unusual DNA structures" (1995). ETD collection for University of Nebraska-Lincoln. AAI9609430.
https://digitalcommons.unl.edu/dissertations/AAI9609430