The Alkali Ion-DNA Interaction as Reflected in the Nuclear Relaxation Rates of ²³ Na and ⁸⁷ Rb

Abstract

Longitudinal relaxation rates of "Na and '7Rb in aqueous solutions of DNA were measured and interpreted in terms of contributions of "bound" and free species. The frequency dependence of the 2'Na relaxation rate sets an upper limit of 5.5 nsec for the correlation time characteristic of the alkali ion-DNA interaction. The plausible description of the alkali ion-DNA interaction emerging from the results is one in which the "bound" ions comprise a highly mobile ionic cloud around the lattice of phosphate groups with a population characterized by an apparent dissociation constant of 10.9 mM. Any specific binding to phosphate groups involving severe restrictions of motional freedom must be much (at least two orders of magnitude) weaker and of a very short duration (<5.5 nsec).The interaction of metal ions with DNA plays a key role both in maintaining the conformation of the macromolecule and in governing its biological activity. Of particular interest seems to be the interaction with alkali-metal ions, in view of their relatively high abundance in biological fluids. The alkali ion-DNA interaction has been studied by a variety of physical methods (the subject has been extensively reviewed; cf., e.g., refs. 1-4). It appears, however, that different experimental approaches result in different qualitative pictures of the mode of this interaction. The two presently held views describe the alkali ion-DNA interaction either as a specific binding to phosphate groups or as an ionic cloud, forming a positively charged atmosphere around the lattice of negatively charged phosphate groups (1-4). In their report of a sodium-23 nuclear magnetic resonance (NMR) study of the sodium ion-RNA interaction, James and Noggle have discussed the shortcomings of some of the techniques employed in studying cation-macromolecule interactions and suggested that the NMR relaxation method is advantageous and should provide information regarding the electronic environment and the motional freedom of the bound metal ion (5).Presented in this communication are the results of a 2"Na NMR relaxation study of the alkali ion-DNA interaction. In addition to the usual titrations, measurements of 21Na relaxation rates were also done at several resonance frequencies. In this way details of the relaxation mechanism were elucidated and the mode of the cation-DNA interaction was delineated. Further support of our interpretation was obtained from measurements of 87Rb relaxation rates.

Distribution of ions around DNA, probed by energy transfer.

“…On the other hand, experimental techniques for studying these properties usually have been limited to observing either the effect of DNA on bulk thermodynamic properties of the solution (6,(15)(16)(17) or the dependence of ligand binding on electrolyte concentration (18,19). NMR spectroscopy of 23Na+ can report directly on ions near DNA, but interpretation is complicated because of the mechanisms of nuclear relaxation involved (20)(21)(22)(23)(24).In principle, the effect of a polyelectrolyte on ion-ion collision frequencies can be used to test theoretical descriptions of the distribution of ions around the polyion (25). However, despite numerous reports concerning the effects of polyelectrolytes on bimolecular chemical reaction rates (refs.…”

Excited-State Properties of Thymidine and Their Relevance to Its Heterogeneous Emission in Double-Stranded DNA

“…The results of the present study, taken together, imply that as a result of the motions of the T bases in DNA and the concomitant changes in the (1) rigidity of the stacked geometries, ( 2 ) strength of the dispersion forces and ( 3 ) extent of interaction with polar groups, the emission will be heterogeneous. An additional source of heterogeneity stems from the loose association of Na-with the phosphate groups (36). The ensuing Na' mobility, which takes place on the picosecond-nanosecond time scales (36), would result in a distribution of phosphate-ion interactions that could give rise to a population of emitting species, perhaps through effects on T mediated by the backbone.…”

Biological Magnetic Resonance

“…The precise basis for the small frequency dependence noted by Reuben et al (1975) is unclear. One possibility is that a fraction of the condensed Na + was immobilized and in rapid exchange with the remaining condensed Na +.…”

“…The slightly greater enhancement for 39K is likely to arise from the greater number of electrons and therefore greater value of its Sternheimer antishielding factor (Deverell, 1969). Such a mechanism also appears responsible for the greater enhancements of the relaxation rates of 87Rb over those of 23N a by aqueous solutions of DNA (Reuben et at., 1975); 87Rb is characterized by a larger antishielding factor than either 23Na or 39K (Deverell, 1969). The larger the alkali cation, the more effectively will its electronic cloud be polarized by a given electrostatic field, resulting in a larger electric field gradient.…”