Sodium-23 NMR studies of cation-DNA interactions

Anderson, Charles; Record, M. Thomas; Hart, Phillip A.

doi:10.1016/0301-4622(78)85007-8

Cited by 157 publications

(110 citation statements)

References 34 publications

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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%

“…However, with TBA + as the non-binding ion, the difference mobility profile exhibits a sigmoidal dependence on [Li + ]. Therefore, this difference mobility profile was analyzed using a four parameter Hill equation (64): (5) where n is the cooperativity parameter and the other terms have been defined above. The apparent K D values and the cooperativity parameters, n, obtained for Li + binding to ds26, using the four quaternary ammonium ions as the non-binding ions, are given in the top section of Table 2.…”

Section: Quantitative Analysis Of Monovalent Counterion Binding By Dsdnamentioning

confidence: 99%

“…23 Na NMR measurements (5) showed that Na + , TEA + and TBA + bind to DNA with relative affinities of 20:5:1, respectively. Tris (hydroxymethyl)aminomethane (Tris + ) ions also bind to DNA, with an affinity similar to that observed for Na + (5).…”

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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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Section: Discussionsupporting

confidence: 81%

Section: Quantitative Analysis Of Monovalent Counterion Binding By Dsdnamentioning

confidence: 99%

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

2007

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“…In fact, no significant effect on the magnitude of the k d is observed as a consequence of the substitution of Na ϩ with K ϩ . Since the affinities of Na ϩ and K ϩ for DNA are quite similar (41), this result suggests that cations are simply displaced from the nucleic acid and do not interact with Ku upon complex formation. Hence, the value of 10.2 should not need to be adjusted by the cation uptake component.…”

Section: Discussionmentioning

confidence: 91%

Fluorescence Anisotropy Studies on the Ku-DNA Interaction

Arosio

Costantini

Kong

et al. 2004

Journal of Biological Chemistry

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DNA non-homologous end joining starts with the binding of Ku heterodimers to double strand breaks. In this work, we characterized the thermodynamics of the Ku-DNA interaction by fluorescence anisotropy of the probe-labeled DNA. We determined that the microscopic dissociation constant (k d ) for the binding of Ku to a DNA binding site of the proper length (>20 bp) ranges from 22 to 29 nM at 300 mM NaCl. The binding isotherms for DNA duplexes with two or three heterodimers were analyzed with two independent models considering the presence and absence of overlapping binding sites. This analysis demonstrated that there is no or very weak nearestneighbor cooperativity among the Ku molecules. These models can most likely be applied to study the interaction of Ku with duplexes of any length. Furthermore, our salt dependence studies indicated that electrostatic interactions play a major role in the binding of Ku to DNA and that the k d decreases ϳ60-fold as the salt concentration is lowered from 300 to 200 mM. The slope (⌫ salt ) of the plot of log k d versus log[NaCl] is 12.4 ؎ 0.1. This value is among the highest reported in the literature for a protein-DNA interaction and suggests that ϳ12 ions are released upon formation of the Ku-DNA complex. In addition, comparison of the slope values measured upon varying the type of cation and anion indicated that approximately nine cations and three anions are released from DNA and Ku, respectively, when the complex is formed.

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“…It is known that when spin-spin relaxation is extremely efficient, e.g., for quadrupolar nuclei such as 23 Na, a good estimate of T2 (spin-spin relaxation time) can be obtained simply by measuring the peak width. It has been shown that T2-1 value is roughly related to the peak width at half height, W1/2, in the following way [6], Since the relaxation of 23 Na nucleus is mainly due to interactions between its quadrupole nucleus, an increase in the relaxation rate is expected if "ion-condensation" occurs [7]. Thus the peak width reflects the fractions of condensed Na+ ion to total Na+ ions present in the sample solution.…”

Section: Experimental Chemicalsmentioning

confidence: 99%

Counterion Binding to Inorganic Polyphosphate Anions (I)

Miyajima

Kakehashi

1993

Phosphorus Research Bulletin

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The change in the Na+ ion binding properties of a series of the anions of inorganic phosphates (phosphinate, cyclic polyphosphate, and linear polyphosphate) has been studied in order to see the transition from simple electrolyte to polyelectrolyte. Na+ ion activity measurement together with 23 Na NMR peak width measurement gave a consistent conclusion that about 100 of the chain-length is needed to show the binding properties independent of the chain-length in salt-free system.

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Sodium-23 NMR studies of cation-DNA interactions

Cited by 157 publications

References 34 publications

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

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

Fluorescence Anisotropy Studies on the Ku-DNA Interaction

Counterion Binding to Inorganic Polyphosphate Anions (I)

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