Electrophoresis of DNA. III. The effect of several univalent electrolytes on the mobility of DNA

Ross, Philip D.; Scruggs, Robert L.

doi:10.1002/bip.1964.360020304

Cited by 93 publications

(45 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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%

“…Since the EOF mobility and the analyte mobility are additive (52,54), the mobilities observed in the second and subsequent capillaries were corrected to the mobility that would have been observed in the original capillary, using Eq. (2): (2) where μ ss26,new cap is the observed mobility of ss26 (for example) in the new capillary, μ ss26,orig cap is the observed mobility of ss26 in the original capillary and Δμ is the difference between the mobilities observed in the two capillaries. The correction was typically less than 2%, but ranged up to 20% for one of the capillaries.…”

Section: Capillary Electrophoresismentioning

confidence: 99%

See 1 more Smart Citation

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

2007

View full text Add to dashboard Cite

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

show abstract

Section: Discussionsupporting

confidence: 81%

Section: Capillary Electrophoresismentioning

confidence: 99%

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

2007

View full text Add to dashboard Cite

show abstract

“…Actually, the dielectric constant at the surface of DNA is a rather elusive quantity that has not been measured directly. Electrophoresis 25 and binding experiments 26 support the adsorption of cationic charges at the DNA surface. 27,28 This suggests that there is no important change in the Born energy of such adsorbed ions and, hence, that water at or very near the DNA surface behaves as bulk water.…”

Section: Discussionmentioning

confidence: 90%

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

Stigter

1998

Biopolymers

View full text Add to dashboard Cite

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

show abstract

“…The electrophoresed DNA (A and C) was transferred to nitrocellulose filter paper and hybridized sequentially with probes YRp7 and Mp8HIS3 (B and D), which detect the electrophoretic bands corresponding to chromosomes IV and XV, respectively. The autoradiograms were exposed for 24 (32). The number of pores housing a molecule-i.e., the number of segments corresponding to a given fragment size (in kbp)-was evaluated using the procedure suggested in ref.…”

mentioning

confidence: 99%

Pulsed-field electrophoresis: application of a computer model to the separation of large DNA molecules.

Lalande

Noolandi

Turmel

et al. 1987

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

View full text Add to dashboard Cite

The biased reptation theory has been applied to the pulsed-field electrophoresis of DNA in agarose gels. A computer simulation of the theoretical model that calculates the mobility of large DNA molecules as a function of agarose pore size, DNA chain properties, and electric field conditions has been used to generate mobility curves for DNA molecules in the size range of the larger yeast chromosomes. Pulsed-field electrophoresis experiments resulting in the establishment ofan electrophoretic karyotype for yeast, where the mobility of the DNA fragments is a monotonic function of molecular size for the entire size range that is resolved (200-2200 kilobase pairs), has been compared to the theoretical mobility curves generated by the computer model. The various physical mechanisms and experimental conditions responsible for band inversion and improved electrophoretic separation are identified and discussed in the framework of the model.The ability to resolve large [>100 kilobase pairs (kbp)] fragments of DNA using pulsed-field electrophoresis represents a major advance in molecular genetics. Schwartz and Cantor (1) demonstrated that yeast chromosomes could be separated in agarose gels by the application of alternately pulsed perpendicularly oriented electric fields. This apparatus as well as modifications of orthogonal field alternating gel electrophoresis systems (2-4) have been used to obtain electrophoretic karyotypes of several microorganisms (5)(6)(7)(8)(9)(10) and to perform long-range restriction mapping of DNA fragments (11)(12)(13)(14)(15)(16). Other electrophoretic configurations that have been developed to resolve large DNA molecules include the periodic inversion of a single electric field (17), the use of transverse fields in a vertical electrophoresis apparatus (18), the application of contour-clamped homogeneous electric fields (19), and the use of a rotating gel system (20). In all the pulsed-field electrophoretic systems used thus far, the pulse times have been determined empirically. In the present report, preliminary data are presented describing the separation of large DNA fragments based on a quantitative model of pulsed-field electrophoresis. Slater and Noolandi (21,22) derived a theoretical model describing the dynamics of DNA molecules electrophoresed in agarose gels. Briefly, the theory considers that the DNA molecule undergoes one-dimensional worm-like motion, termed reptation (23), in a "tube" formed by the consecutive pores housing the molecule in the three-dimensional mesh of the gel. Under the influence of the electric field and the thermal agitation (Brownian motion), the DNA chain drifts through the tube and new tube sections are continuously formed by the end segment leaving the original tube. Lateral movements of DNA in the gel matrix are not considered, as they cannot lead to net center-of-mass displacement. The equations describing the dynamics of the chain in its tube have been given in previous articles (21,22,24,25). The motion of the chain is further reduced to discrete...

show abstract

Electrophoresis of DNA. III. The effect of several univalent electrolytes on the mobility of DNA

Cited by 93 publications

References 9 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

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

Pulsed-field electrophoresis: application of a computer model to the separation of large DNA molecules.

Contact Info

Product

Resources

About