High‐resolution quantification by charge‐dominant electrophoretic mobility shift of quantum dots

Conjugation of biomolecules to colloidal nanoparticles, such as quantum dots (QDs), often leads to change in mobility. We discover that linking DNA molecules to quantum dots alters their surface charge density without significantly increasing the hydrodynamic radius, causing a prominent shift in electrophoretic mobility. In this study, a high‐resolution molecular quantification method named quantification by QDs electrophoretic mobility shift (qQEMS) is developed based on the charge‐dominant transformation that closely associates DNA quantity to QDs electrophoretic mobility. The versatility of qQEMS is demonstrated by a number of quantification assays in which DNA molecules functioned as enzyme substrates, target‐specific probes, and competitive charge carriers. qQEMS shows a great potential as a generic and versatile quantification platform for a wide range of applications.     

Mobility of single DNA chain under electric field during its transient contact with solid surfaces

The motion of DNA chain under electric field when it is in transient contact with the solid surfaces in aqueous solution was studied by single molecule fluorescence microscopy at the total internal reflection geometry (TIRFM). In situ observation discovered that single λ-DNA chains driven by electric field made transient contact with the solid surface and made hitting–sliding–leaving-like motion along the surface. By varying the surface chemistry, from the negative-charged silanol group-rich surface to positive-charged amino group-rich surface, as well as hydrophobic surfaces, the dependence of DNA mobility on the surface–DNA interaction was studied. The results show that a dependence of the mobility of DNA on the surface polarity with respect to DNA itself. The study on different surfaces rich of silanol, amide, amino, and methyl groups show a sequence of DNA mobility of silanol > amide > amino. The mobility of DNA on methyl terminated surface was found to be similar to that on amino surface. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 2541–2546, 2009     

Conformation dependence of DNA electrophoretic mobility in a converging channel

The electrophoresis of λ‐DNA is observed in a microscale converging channel where the center‐of‐masses trajectories of DNA molecules are tracked to measure instantaneous electrophoretic (EP) mobilities of DNA molecules of various stretch lengths and conformations. Contrary to the usual assumption that DNA mobility is a constant, independent of field and DNA length in free solution, we find DNA EP mobility varies along the axis in the contracting geometry. We correlate this mobility variation with the local stretch and conformational changes of the DNA, which are induced by the electric field gradient produced by the contraction. A “shish‐kebab” model of a rigid polymer segment is developed, which consists of aligned spheres acting as charge and drag centers. The EP mobility of the shish‐kebab is obtained by determining the electrohydrodynamic interactions of aligned spheres driven by the electric field. Multiple shish‐kebabs are then connected end‐to‐end to form a freely jointed chain model for a flexible DNA chain. DNA EP mobility is finally obtained as an ensemble average over the shish‐kebab orientations that are biased to match the overall stretch of the DNA chain. Using physically reasonable parameters, the model agrees well with experimental results for the dependence of EP mobility on stretch and conformation. We find that the magnitude of the EP mobility increases with DNA stretch, and that this increase is more pronounced for folded conformations.     

Monitoring of single nicks in duplex DNA by gel electrophoretic mobility-shift assay

We demonstrate that the gel electrophoretic mobility-shift assay (EMSA) can be used for site-selective and quantitative monitoring of nicks in linear double-stranded DNA (dsDNA) thus allowing to expediently follow the nicking activity of enzymes or other agents targeted to a designated dsDNA site. At elevated temperature and/or in the presence of urea, DNA fragments carrying a single nick produced by the nicking enzyme N.BstNBI exhibit a well-detectable gel retardation effect. On the basis of permutation analysis, the decreased electrophoretic mobility of nicked dsDNA fragments is attributed to a bend (or hinge) in the DNA double helix sequence-specifically generated by a nick. Since nick-induced DNA bending depends on interaction between base pairs adjacent to a nick, the change in mobility is different for nicked DNA sites with different sequences. Therefore, EMSA monitoring of differential mobility change caused by nicks within various DNA sequences could be useful for studying the differential base stacking and nearest-neighbor energetics.     

Effect of topological asymmetry on the electrophoretic mobility of branched DNA structures with and without single-base mismatches

The electrophoretic mobility of three-arm star DNA structures with varying degrees of branch length asymmetry has been investigated in polyacrylamide (PAA) hydrogels. We report the effect of single-base mismatches, adjacent to the branch point, on the mobility of branched DNA with three different arm lengths. Branched DNA structures were formed using wild-type and mutated fragments of the p53 tumor suppressor gene, which is believed to play an important role in cancer development. Branching was directed at the site of several previously characterized mutations in exon 7 of p53. At a given gel concentration, the mobility of branched DNA with fully complementary base pairing is found to increase as the degree of branch length asymmetry is increased. Ferguson analysis of the gel electrophoresis data leads to a retardation coefficient that is strongly dependent on topology. This finding can be explained in terms of a minimum molecular cross-section for each molecule. Specifically, we show that structures with the smallest molecular cross-section can access more pores in the gel, which leads to higher mobility. Our results can also be understood by considering the rotational diffusivity of branched DNA. Asymmetric DNA stars with higher calculated rotational diffusivities also have higher mobilities. When a mutated base is present in junctions with low degrees of branch length asymmetry, adjacent to the branch point, the mobility increases in comparison to the fully complementary molecules. The reason for this increased mobility is unclear, here, we propose that the mismatched base introduces additional flexibility to the arm containing the mutation leading to higher conformational freedom and enhanced mobility in gels. When a mismatched base is present in junctions with high degrees of branch length asymmetry, the opposite result is obtained. Here, the mutated species has a lower mobility. This result is argued to arise from incomplete hybridization and/or frayed ends. Finally, we have shown that by using two of the branch point oligonucleotides as probe molecules, mutations known to occur at specific sites can be detected through the mobility shift. If the sequences of the probe chains are changed in a controlled manner, the location and base of the mutant can also be determined.     

Influence of electric field intensity, ionic strength, and migration distance on the mobility and diffusion in DNA surface electrophoresis

In order to increase the separation rate of surface electrophoresis while preserving the resolution for large DNA chains, e.g., genomic DNA, the mobility and diffusion of Lambda DNA chains adsorbed on flat silicon substrate under an applied electric field, as a function of migration distance, ionic strength, and field intensity, were studied using laser fluorescence microscope. The mobility was found to follow a power law with the field intensity beyond a certain threshold. The detected DNA peak width was shown to be constant with migration distance, slightly smaller with stronger field intensity, but significantly decreased with higher ionic strength. The molecular dynamics simulation demonstrated that the peak width was strongly related with the conformation of DNA chains adsorbed onto surface. The results also implied that there was no diffusion of DNA during migration on surface. Therefore, the Nernst-Einstein relation is not valid in the surface electrophoresis and the separation rate could be improved without losing resolution by decreasing separation distance, increasing buffer concentration, and field intensity. The results indicate the fast separation of genomic DNA chains by surface electrophoresis is possible.     

Electrophoresis of a toroid along the axis of a cylindrical pore

The electrophoresis of a toroid (doughnut-shaped entity) along the axis of a long cylindrical pore is analyzed under the conditions of low surface potential and weak applied electric field. The system under consideration is capable of modeling the electrophoretic behavior of various types of biocolloid such as bacterial DNA, plasmid DNA, and anabaenopsis, in a confined space. The influences of the key parameters of the problem, including the sizes of a toroid, the radius of a pore, and the thickness of the double layer, on the electrophoretic mobility of a toroid are discussed. We show that the electrophoretic behavior of a toroid under typical conditions can be different from that of an integrated entity. For instance, although the presence of the pore wall has the effect of retarding the movement of a particle, it becomes advantageous if a toroid is sufficiently close to the boundary. Several interesting behaviors are also observed, for example, the mobility of a toroid when the boundary effect is significant can be larger than that when it is insignificant.     

DNA separation at a liquid-solid interface

We demonstrate that it is possible to separate a broad band of DNA on a solid substrate without topological obstacles. The mobility was found to scale with molecular size (N) as N(-0.25), while the resolution scaled as N(0.75) indicating that diffusivity on this substrate was minimal. By varying the buffer concentration we were able to show that the mobility for a given chain length scaled with the persistent length (p) as p(1/2). This could be shown to be related to the Gaussian conformation of the chains adsorbed on the surface. A two-dimensional corrugated surface of nonporous silica beads was produced using a self-assembling process at the air/water interface. Even though the surface corrugations were comparable to persistence length we show that they do not affect the mobility, indicating that surface friction rather than topological constraints are the predominant mechanism of separation on a surface.     

Modeling the stability and the motion of DNA nucleobases on the gold surface

We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol(-1), and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considered.     

Effect of cosurfactant on the free-drainage regime of aqueous foams

We report results of drainage in aqueous foams of small bubble size D (D=180 microm) prepared with SDS-dodecanol solutions. We have performed free-drainage experiments in which local drainage rates are measured by electrical conductivity and by light scattering techniques. We have investigated the role of the surfactant-cosurfactant mass ratio on the drainage regime. The results confirm that a drainage regime corresponding to a high surface mobility can indeed be found for such small bubbles, and show that an increase in the cosurfactant content can induce a transition to a low surface mobility drainage regime. We show that the transition is not linked to variations of the bulk properties, but rather to variations of the interfacial properties. However, the results show that the added amount of dodecanol to trigger the transition is quite high, evidencing that the relevant control parameter for drainage regimes includes both bubble size and interfacial contributions.     

Characteristics of migration patterns of DNA oligomers in gels and the relationship to the question of intrinsic DNA bending

We have developed a methodology that is capable of quantitatively describing the electrophoretic mobility patterns of oligomeric B-DNA through polyacrylamide gels (PAG) in the presence of varying concentration of the organic solvent 2-methyl-2,4-pentanediol (MPD), used routinely to induce DNA crystallization. The model includes the ion atmosphere and its polarization, electrostatic excluded volume, hydrodynamic interactions, and fluctuation effects that characterize the overall size of the migrating polyion. Using this model, and by critically examining the mobility patterns of linear random-sequence B-DNA molecules in PAG as a function of MPD, we address the question of the discrepancy between current models used to explain the molecular origins of A-tract-induced DNA bending. Direct analysis of the mobility of B-DNA oligomers on PAG, and comparison to the mobility of A-tract-containing oligomers, shows a significant apparent effect of MPD on the mobility of generic B-DNA sequences, which is larger than the effect on A-tract-containing oligomers. The effect is chain-length dependent, especially at lower MPD concentration. Thus, the apparent reduction in gel mobility, as a function of MPD, is not unique to A-tract regions or A-tract-containing molecules. However, our analysis suggests that MPD molecules are probably excluded from the surface of both B-DNA and A-tract molecules. This is supported by circular dichroism studies on A-tract and B-DNA molecules in solutions containing various MPD concentrations.     

Electrophoresis of a charge-regulated toroid normal to a large disk

The electrophoresis of a charge-regulated toroid (doughnut-shaped entity) normal to a large disk is investigated under the conditions of low surface potential and weak applied electric field. The system considered is capable of modeling the electrophoretic behavior of various types of biocolloids such as bacterial DNA, plasmid DNA, and anabaenopsis near a perfectly conducting planar wall. The influences of the size of the toroid, the separation distance between the toroid and the disk, the charged conditions on the surfaces of the toroid and the disk, and the thickness of electric double layer on the electrophoretic mobility of the toroid are discussed. The results of numerical simulation reveal that under typical conditions the electrophoretic behavior of the toroid can be different from that of an integrated entity. For instance, if the surface of the toroid carries both acidic and basic functional groups, its mobility may have a local maximum as the thickness of double layer varies. We show that the electrophoretic behavior of the toroid is different, both qualitatively and quantitatively, from that of the corresponding integrated particle (particle without hole).     

Free mobility determination by electrophoresis in polyacrylamide containing agarose at a nonrestrictive concentration

In the determination of the free mobility, related to the surface net charge, by quantitative gel electrophoresis, the previous arbitrary extrapolation of Ferguson plots from the lowest gel concentrations that give a mechanically stable gel to 0% T has recently been replaced by measurement of mobilities across that concentration range, using the addition of 0.5% agarose to polyacrylamide at the various low concentrations in application to a DNA fragment 155 bp in size (Orbán, L. et al., in preparation). The present study applies that approach to several proteins and DNA fragments smaller than 1300 bp, using 0.4% agarose in polyacrylamide gels of varying concentration. The intercepts of the plots with the mobility axis provide experimental data by which the free mobility in polyacrylamide gel electrophoresis can be estimated for molecules not significantly retarded in their migration at the agarose concentration admixed to polyacrylamide. Across the gel concentration range below 3% T, in the presence of agarose, the Ferguson plots of proteins and DNA fragments are convex. It was shown by mass spectrometry that this convex curvature of the plots in the mixed polymer is not significantly due to low polymerization efficiency in the concentration range of liquid polyacrylamide (below 3%T).     

Confinement effects on electromigration of long DNA molecules in an ordered cavity array

Confinement effects on the electromigration of long dsDNA molecules in an array of well-ordered, molecular sized cavities interconnected by nanopores are described. The array was prepared by replicating the structure of a colloidal crystal of microspheres in a polymer matrix. Both conformation and mobility studies show that the electrophoretic behavior of large DNA molecules is distinct from that in gels and other microfabricated sieves, showing a peak in mobility versus electric field, and an inversion in the separation order with field strength. A simple model was proposed to interpret this unexpected observation qualitatively. We conclude that the molecular behavior of DNA can be modified by the combination of entropic effect and electric trapping as a consequence of both unique geometry and conductivity of this cavity array material. This approach provides insights for design and optimization of on-chip molecular sieving structures for rapid separation of long DNA molecules. It may lead to a promising material for manipulation and size fractionation of other biological macromolecules.     

The electrophoretic mobility of DNA three-way junctions is affected by the sequence of overhanging single-stranded ends

The folding of three- and four-way DNA junctions is often assessed by comparing the electrophoretic mobility of restriction enzyme fragments, using the long-short arm assay. We have compared the mobility of synthetic three-way junctions that contain identical branch point sequences, but different restriction sites in the arms. We show that the mobility of fragments is affected by the sequence of the overhanging ends. In general, GC-rich overhangs produce fragments with anomalous mobilities. These anomalies can be prevented by treating the cleaved junctions with mung bean endonuclease, elevating the electrophoresis temperature or using blunt cleaving restriction endonucleases.     

Influence of branch length asymmetry on the electrophoretic mobility of rigid rod-like DNA

The electrophoretic mobility of three-arm asymmetric star DNA molecules, produced by incorporating a short DNA branch at the midpoint of rigid-rod linear DNA fragments, is investigated in polyacrylamide gels. We determine how long the added branch must be to separate asymmetric star DNA from linear DNA with the same total molecular weight. This work focuses on two different geometric progressions of small DNA molecules. First, branches of increasing length were introduced at the center of a linear DNA fragment of constant length. At a given gel concentration, we find that relatively small branch lengths are enough to cause a detectable reduction in electrophoretic mobility. The second geometric progression starts with a small branch on a linear DNA fragment. As the length of this branch is increased, the DNA backbone length is decreased such that the total molar mass of the molecule remains constant. The branch length was then increased until the asymmetric branched molecule becomes a symmetric three-arm star polymer, allowing the effect of molecular topology on mobility to be studied independent of size effects. DNA molecules with very short branches have a mobility smaller than linear DNA of identical molar mass. The reason for this change in mobility when branching is introduced is not known, however, we explore two possible explanations in this article. (i) The branched DNA could have a greater interaction with the gel than linear DNA, causing it to move slower; (ii) the linear DNA could have modes of motion or access to pores that are unavailable to the branched DNA.     

DNA mediated assembly of single walled carbon nanotubes: role of DNA linkers and annealing

With the high demand for nanoelectronic devices, extensive research has focused on the use of single walled carbon nanotubes (CNTs) due to their high electron carrier mobility, large tensile strength, and single nanometer dimensions. Despite their promise, however, their applicability has been greatly hindered by the inherent difficulties of both separating nanotubes of different chiralities and diameters and positioning them from metallic tubes and positioning them in a precise location on a surface. In recent years, single stranded DNA (ssDNA) has been identified as a potential solution for both of these problems since DNA can be used to both separate the different types of CNTs as well as direct their organization. We demonstrate here the first principles on how to guide CNT assembly directly on surfaces from solution by specific DNA hybridization. It was found that the specific DNA sequence used to disperse the carbon nanotubes greatly influences the adsorption and specificity of nanotube binding to the surface. Furthermore, we demonstrate here that thermal annealing can correct misaligned tubes or incorrect binding. These studies provide an excellent foundation for employing two-dimensional DNA templates for CNT organization for nanoelectronic logic and memory based applications. Furthermore, using a single biomaterial to both sort and place CNTs in minimal steps would greatly help the throughput, manufacturability, and cost of such devices.     

Polypeptide friction and adhesion on hydrophobic and hydrophilic surfaces: a molecular dynamics case study

Using all-atomistic MD simulations including explicit water, the mobility and adhesion of a mildly hydrophobic single polypeptide chain adsorbed on hydrophobic and hydrophilic diamond surfaces is investigated by application of lateral and vertical pulling forces. Forced motion on the hydrophilic surface exhibits stick-slip due to breaking and reformation of hydrogen bonds; in contrast, on the hydrophobic surface, the motion is smooth. By carefully tuning the driving force magnitude, the linear-response regime is reached on a hydrophobic surface and equilibrium values for mobility and adhesive strength are obtained. On the hydrophilic surface, on the other hand, slow hydrogen-bond kinetics prevents equilibration and only upper bounds for adhesion force and mobility can be estimated. Whereas the desorption force is rather comparable on the two surfaces and differs at most by a factor of 2, the mobility on the hydrophilic surface is at least 30-fold reduced compared to the hydrophobic one. A simple model based on a single particle diffusing in a corrugated potential landscape suggests that cooperativity is rather limited and that the small mobility on a hydrophilic surface can be rationalized in terms of incoherently moving monomers. The experimentally well-known peptide mobility in bulk water is quantitatively reproduced in our simulations, which serves as a sensitive test on our methodology employed.     

Tension and mobility of a DNA fragment in the lakes-straits model

We consider numerically, in the framework of the lakes-straits model, the mobility of a DNA chain under field-inversion gel-electrophoresis (FIGE). Here we investigate the role of the gel's structure on the mobility. We consider two situations: (i) a DNA chain fragment is bounded by two straits (narrow gateways) at a fixed distance, but is otherwise free, and (ii) the fragment is, in addition, confined with in a closed volume (pore). We calculate the tension on the DNA fragment in the two cases. For Gaussian chains we evaluate the corresponding statistical weights exactly, using a cellular automation algorithm. We find that the resulting tension differs drastically in the two models considered. Nonetheless this difference influences only weakly the overall FIGE mobility.