Electrophoretic Mobility of DNA in Solutions of High Ionic Strength

Abstract

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.

Out-of-plane faradaic ion concentration polarization: stable focusing of charged analytes at a three-dimensional porous electrode

“…cm 2 /V•s) 39 that is similar to that of nucleic acids (2 − 3 × 10 !" cm 2 /V•s, depending on ionic strength), 40 and therefore, the degree to which it is enriched and the location at which it focuses approximate the performance of our device for nucleic acid preconcentration and separation from other sample components (e.g., albumin) such as has been reported previously. 41 We next investigated CVC characteristics obtained at a planar Au electrode as a function of the concentration of Tris buffer.…”

Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution

“…We show in this study that the fluorescence amplitude of the probe at each position within a ssDNA lattice otherwise consisting solely of dT residues (and also within lattices of mixed base composition in earlier studies ( 12 )) is essentially the same, indicating that by this criterion the unperturbed ssDNA lattice has, on average, a fairly uniform conformation. Under our experimental conditions, the ssDNA bases likely fluctuate non-cooperatively around a largely stacked Watson-Crick B-form conformation with an average right-handed helical pitch of ∼3.4 Å per nucleotide residue ( 32 , also E. Beyerle et al, unpublished results).…”

Out-of-plane faradaic ion concentration polarization: stable focusing of charged analytes at a three-dimensional porous electrode

“…We next evaluated the distribution of two anionic fluorescent tracers (BODIPY 2and dyelinked albumin (Texas Red BSA)) in these solutions under conditions appropriate for electrokinetic enrichment. First, the channel was filled with the BGE, and then a constant flow rate of 100 nL min key point is that BODIPY 2has an electrophoretic mobility ( cm 2 /V s) 39 that is 2.11 × 10 -4 • similar to that of nucleic acids ( cm 2 /V s, depending on ionic strength), 40 and 2 -3 × 10 -4 • therefore, the degree to which it is enriched and the location at which it focuses approximate the performance of our device for nucleic acid preconcentration and separation from other sample components (e.g., albumin). Such a separation has been reported previously by Ouyang et al 41 who utilized pressure modulation at the device inlet to push dye-linked albumin past the locally enhanced electric field.…”

“…Focusing of these species by fICP was not observed in KNO 3 or phosphate buffer solutions. A key point is that BODIPY 2− has an electrophoretic mobility (2.11 × 10 −4 cm 2 V −1 s −1 ) 39 that is similar to that of nucleic acids (2 -3 × 10 −4 cm 2 V −1 s −1 , depending on ionic strength), 40 and therefore, the degree to which it is enriched and the location at which it focuses approximate the performance of our device for nucleic acid preconcentration and separation from other sample components (e.g., albumin). Such a separation has been reported previously by Ouyang et al 41 who utilized pressure modulation at the device inlet to push dye-linked albumin past the locally enhanced electric field.…”