Electrophoretic Mobilities of the Charge Variants of DNA and Other Polyelectrolytes: Similarities, Differences, and Comparison with Theory

Stellwagen, Nancy C.

doi:10.1021/acs.jpcb.6b10599

Cited by 6 publications

(12 citation statements)

References 43 publications

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“…(1). To compare the mobilities of ss-and dsDNAs with different charge densities, measured on different days in different BGEs, mobility ratios were calculated for each data set by dividing the mobility of each charge variant by the mobility of its fully charged, unmodified parent DNA, measured under the same experimental conditions [83,124]. The mobility ratios were then plotted as a function of the fractional charge of the charge variant.…”

Section: Dependence Of Dna Mobility On Charge Densitymentioning

confidence: 99%

“…The mobility ratios of the charge variants of the nucleic acids are compared in Fig. 14 with the mobility ratios calculated for the charge variants of other polyions, using data taken from the literature [124]. The mobility ratios calculated for carboxylate derivatives of benzene [47], sulfate derivatives of naphthalene [125], phosphate derivatives of adenosine [126], peptides containing different numbers of positively charged lysine residues [127], and bovine carbonic anhydrase II (BCA) derivatives containing different numbers of positive lysine residues [128], also increased linearly with the logarithm of the fractional charge, as shown in Fig.…”

Section: Dependence Of Dna Mobility On Charge Densitymentioning

confidence: 99%

“…Surprisingly, the mobility ratios of the charge variants of these very different polyions exhibited the same dependence on the logarithm of the fractional charge. By contrast, the mobility ratios calculated [124] for synthetic polyions containing different proportions of charged and uncharged monomers [47,[129][130][131] exhibited a different linear dependence on the logarithm of the fractional charge (Fig. 14).…”

Section: Dependence Of Dna Mobility On Charge Densitymentioning

confidence: 99%

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Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

Stellwagen

2021

Electrophoresis

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Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cationsThis review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss-and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss-and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.

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Section: Dependence Of Dna Mobility On Charge Densitymentioning

confidence: 99%

Section: Dependence Of Dna Mobility On Charge Densitymentioning

confidence: 99%

Section: Dependence Of Dna Mobility On Charge Densitymentioning

confidence: 99%

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Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

Stellwagen

2021

Electrophoresis

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“…The electrophoretic effect is caused by the migration of the solvated counterions and the polyion in opposite directions, increasing the viscous drag on the polyion. As a result, the observed mobility of a given polyion is a complicated function of the number of charged residues, the size of the polyion, counterion condensation, and the composition of the surrounding ionic medium (32,34).…”

Section: Electrophoretic Mobilitymentioning

confidence: 99%

“…We have been using free-solution capillary electrophoresis (CE) to evaluate the properties of small ssDNA and dsDNA in solutions containing various monovalent cations. Our previous studies have addressed the dependence of the electrophoretic mobility of DNA on molecular weight (22)(23)(24), ionic strength (25,26), curvature (27)(28)(29)(30), charge density (23,(30)(31)(32), and solution viscosity (33). Here, we have used CE to determine the dependence of the electrophoretic mobility of ssDNA and dsDNA on ionic strength in solutions containing high concentrations of Na þ ions.…”

Section: Introductionmentioning

confidence: 99%

Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

Stellwagen

2020

Biophysical Journal

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The free-solution mobilities of small single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) have been measured by capillary electrophoresis in solutions containing 0.01-1.0 M sodium acetate. The mobility of dsDNA is greater than that of ssDNA at all ionic strengths because of the greater charge density of dsDNA. The mobilities of both ssDNA and dsDNA decrease with increasing ionic strength until approaching plateau values at ionic strengths greater than $0.6 M. Hence, ssDNA and dsDNA appear to interact in a similar manner with the ions in the background electrolyte. For dsDNA, the mobilities predicted by the Manning electrophoresis equation are reasonably close to the observed mobilities, using no adjustable parameters, if the average distance between phosphate residues (the b parameter) is taken to be 1.7 Å . For ssDNA, the predicted mobilities are close to the observed mobilities at ionic strengths %0.01 M if the b-value is taken to be 4.1 Å . The predicted and observed mobilities diverge strongly at higher ionic strengths unless the b-value is reduced significantly. The results suggest that ssDNA strands exist as an ensemble of relatively compact conformations at high ionic strengths, with b-values corresponding to the relatively short phosphate-phosphate distances through space.

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In situ Surface Charge Density Visualization of Self‐assembled DNA Nanostructures after Ion Exchange

et al. 2020

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The charge density of DNA is a key parameter in strand hybridization and for the interactions occurring between DNA and molecules in biological systems. Due to the intricate structure of DNA, visualization of the surface charge density of DNA nanostructures under physiological conditions was not previously possible. Here, we perform a simultaneous analysis of the topography and surface charge density of DNA nanostructures using atomic force microscopy and scanning ion conductance microscopy. The effect of in situ ion exchange using various alkali metal ions is tested with respect to the adsorption of DNA origami onto mica, and a quantitative study of surface charge density reveals ion exchange phenomena in mica as a key parameter in DNA adsorption. This is important for structure‐function studies of DNA nanostructures. The research provides an efficient approach to study surface charge density of DNA origami nanostructures and other biological molecules at a single molecule level.

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Electrophoretic Mobilities of the Charge Variants of DNA and Other Polyelectrolytes: Similarities, Differences, and Comparison with Theory

Cited by 6 publications

References 43 publications

Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations

Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

In situ Surface Charge Density Visualization of Self‐assembled DNA Nanostructures after Ion Exchange

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