Electrophoresis of DNA. II. Specific interactions of univalent and divalent cations with DNA

Ross, Philip D.; Scruggs, Robert L.

doi:10.1002/bip.1964.360020111

Cited by 91 publications

(45 citation statements)

References 24 publications

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“…2 For example, MnCl 2 is more effective in bending DNA than MgCl 2 . This is consistent with electrophoretic data by Ross and Scruggs,29 which show that Mn 2ϩ ions adsorb more strongly than Mg 2ϩ ions to DNA. Depending on the adsorption of the multivalent ions to DNA one expects multiple bends that change the statistics of DNA.…”

Section: Discussionsupporting

confidence: 92%

An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA

Stigter

1998

Biopolymers

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We have studied electrostatic properties of DNA with a discrete charge model consisting of a cylindrical dielectric core with a radius of 8 Å and a dielectric constant Di = 4, surrounded by two helical strings of phosphate point charges at 10 Å from the axis, immersed in an aqueous medium with dielectric constant Dw = 78.54. Eliminating the dielectric core makes potentials in the phosphate surface less negative by about 0.5 kT/e. Salt effects are evaluated for the model without a dielectric core, using the shielded Coulomb potential. Smearing the phosphate charges increases their potential by about 2.5 kT/e, due mostly to the self‐potential of the smeared charge. Potentials in the center of the minor and major grooves vary less than 0.02 kT/e along their helical path. The potential in the center of the minor groove is from 1.0 to 1.7 kT/e, more negative than in the center of the major groove, depending on dielectric core and salt concentration. So multivalent cations and also larger cationic ligands, such as some antibiotics, are likely to adsorb in the minor groove, in agreement with earlier computations by A. and B. Pullman. Dielectric effects on the surface potential and the local potential variations are found to be relatively small. Bending of DNA is studied by placing a multivalent cation, MZ+, in the center of the minor or major groove, curving DNA around it for a certain length, and calculating the free energy difference between the bent and the straight configuration. Boltzmann averaged bending angles, 〈β〉, are found to be maximal in 0.03M monovalent salt, for a length of about 50 or 25 Å of curved DNA when an MZ+ ion is adsorbed in the minor or the major groove, respectively. When the dielectric constant of water is used throughout the calculation, we find maximal bends of 〈β〉 = 11° for M2+ and 〈β〉 = 16° for M3+ in the minor groove, 〈β〉 = 13° for M3+ in the major groove. The absence of bends in DNA adsorbed to mica in the presence of Mg salts supports the role of Mg2+ in “ion bridging” between DNA and mica. The treatment of the effective dielectric constant between two points outside a dielectric cylinder in water is appended. © 1998 John Wiley & Sons, Inc. Biopoly 46: 503–516, 1998

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Section: Discussionsupporting

confidence: 92%

An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA

Stigter

1998

Biopolymers

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“…These results, together with other studies in the literature (1)(2)(3)(4)(5)(6)(7)(8)(9), suggest that all, or nearly all, monovalent cations bind to randomsequence dsDNA in aqueous solutions. The apparent K D observed for the binding of Tris + to ds26 is somewhat smaller than observed for the binding of other cations, suggesting that Tris-DNA complexes are stabilized by the formation of hydrogen bonds with the DNA bases (45), as well as by electrostatic interactions with the phosphate residues.…”

Section: Discussionsupporting

confidence: 81%

“…If the residual EOF mobility is negligible in comparison with the mobilities of the analytes, as in the present case, the apparent mobilities can be calculated from the migration times, using Eq. (1): (1) where μ is the observed mobility, L d is the distance to the detector (in cm), E is the electric field strength (in V/cm), and t is the time required for the sample to migrate to the detector (in seconds). The migration times were very reproducible: the average standard deviation of the mobility measured for a given sample on a given day was ±0.2%.…”

Section: Capillary Electrophoresismentioning

confidence: 99%

Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

2007

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A variation of affinity capillary electrophoresis, called the Replacement Ion (RI) method, has been developed to measure the binding of monovalent cations to random sequence, double-stranded (ds) DNA. In this method, the ionic strength is kept constant by gradually replacing a non-binding ion in the solution with a binding ion, and measuring the mobility of binding and non-binding analytes as a function of binding ion concentration. The binding of monovalent cations to DNA and other polynucleotides has been studied for many years. Early free boundary electrophoresis and conductivity studies (1-3) showed that the affinity of cations for calf thymus DNA decreases in the order Li + > Na + > K + ≫ tetramethylammonium (TMA + ). Competitive dialysis measurements (4) showed that Li + , Na + , K + , Cs + and tetrabutylammonium (TBA + ) ions bind to double-stranded (ds) DNA in a sequence-independent manner, while TMA + and tetraethylammonium (TEA + ) ions are

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“…The value of KD for the rubidium ion-DNA interaction is consistent with the findings that the strength of the alkali ion-DNA interaction decreases along the alkali series (11). The similarity in the order of magnitude of KD for Na+ and Rb+ suggests, in view of the marked differences in the hydration state of these ions (12), that the alkali ion-DNA interaction is of an electrostatic nature.…”

Section: Discussionsupporting

confidence: 85%

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

Reuben

Shporer²,

Gabbay³

1975

Proc. Natl. Acad. Sci. U.S.A.

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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.

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Electrophoresis of DNA. II. Specific interactions of univalent and divalent cations with DNA

Cited by 91 publications

References 24 publications

An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA

An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA

Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

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

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Electrophoresis of DNA. II. Specific interactions of univalent and divalent cations with DNA

Cited by 91 publications

References 24 publications

An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA

An electrostatic model for the dielectric effects, the adsorption of multivalent ions, and the bending of B-DNA

Quantitative Analysis of Monovalent Counterion Binding to Random-Sequence, Double-Stranded DNA Using the Replacement Ion Method

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

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