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

Effect of Internal and Bulge Loops on the Thermal Stability of Small DNA Duplexes

The thermal stabilities of DNA duplexes analogous to the let-7 microRNA:lin-41 mRNA complex from Caenorhabditis elegans have been measured by free solution capillary electrophoresis. DNA duplexes with the same stems but different types of internal or bulge loops and a control with no loop have also been studied. The melting temperatures of the DNA derivatives increased linearly with the logarithm of the Na+ or K+ ion concentration in the solution. Peaks in the electropherograms corresponding to duplexes with internal or bulge loops exhibited extensive tailing at high temperatures, suggesting that denaturation occurred by slow exchange between the duplexes and their component single strands. The single strands did not separate completely from the duplexes in aqueous solutions; instead, they appeared as small subpeaks on the tails of the duplex peaks. However, complete separation of the duplexes from their component single strands was observed at 20 °C in solutions containing 300 mM tetrapropylammonium ions. In addition, counterion condensation appears to be significantly reduced in DNA duplexes containing internal or bulge loops.

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

This 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.

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

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.

Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

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.