Free-solution Electrophoresis Research Articles

Simultaneous detection of 19 K-ras mutations by free-solution conjugate electrophoresis of ligase detection reaction products on glass microchips.

We demonstrate here the power and flexibility of free-solution conjugate electrophoresis (FSCE) as a method of separating DNA fragments by electrophoresis with no sieving polymer network. Previous work introduced the coupling of FSCE with ligase detection reaction (LDR) to detect point mutations, even at low abundance compared to the wild-type DNA. Here, four large drag-tags are used to achieve free-solution electrophoretic separation of 19 LDR products ranging in size from 42 to 66 nt that correspond to mutations in the K-ras oncogene. LDR-FSCE enabled electrophoretic resolution of these 19 LDR-FSCE products by CE in 13.5 min (E = 310 V/cm) and by microchip electrophoresis in 140 s (E = 350 V/cm). The power of FSCE is demonstrated in the unique characteristic of free-solution separations where the separation resolution is constant no matter the electric field strength. By microchip electrophoresis, the electric field was increased to the maximum of the power supply (E = 700 V/cm), and the 19 LDR-FSCE products were separated in less than 70 s with almost identical resolution to the separation at E = 350 V/cm. These results will aid the goal of screening K-ras mutations on integrated "sample-in/answer-out" devices with amplification, LDR, and detection all on one platform.

Rapid separation of synthetic oligonucleotides on polymer modified capillary surfaces using short-end injection capillary electrophoresis in free solution

Here we use short-end electrokinetic injection capillary electrophoresis (CE) to investigate the free solution mobility of short strands of double-stranded oligonucleotides (dsODNs) on polymer modified capillaries. Single base pair (bp) resolution (Rs) of dsODNs ranging from 16-20 bp was achieved in free solution on an 8 cm capillary dynamically coated with poly(ethylpyrrolidine methacrylate-co-methyl methacrylate) (PEPyM-co-PMMA) random copolymer. Interestingly, separation of a dsODN mixture containing two 16 bp strands of different sequences resulted in partial resolution (0.52) implying that the free solution mobility of dsODNs was sequence dependent. The single bp resolution achieved for the complementary sequence strands (the sequence of all strands in the mixtures contained the same 16 bp sequence) was improved by up to 37% for separation of dsODNs containing non-complementary sequences. The 16 bp peak was not additive within each mixture, indicating the presence of ODN-ODN interactions. Investigation of these interactions (and ODN-buffer interactions) showed that they can be influenced by the ionic strength and conductivity of the background electrolyte (BGE). Increasing the ionic strength reduced the ODN-ODN interactions and improved the resolution, whereas, increasing the conductivity reduced ODN-buffer interactions, increasing the mobility, at the consequence of promoting ODN-ODN interactions, and hence decreasing the resolution.

Optimal Design of Microfluidic Devices for Rapid DNA Separations

DNA separation is required to be rapid to be a useful component in DNA analysis devices. Different microfluidic device structures can be exploited to separate DNA with high throughput. We presents a framework for determining the optimal microfluidic device structure for rapid DNA separation through solving a nonlinear programming problem. Optimally designed spiral and serpentine microfluidic device configurations are shown to give comparable results for separating up to 425 bases of DNA using the micelle end-labeled free solution electrophoresis technique. The minimum run time for the serpentine microfluidic device configuration separating up to 425 bases of DNA is 5.1 minutes.

Simulations of Free-Solution Electrophoresis of Polyelectrolytes with a Finite Debye Length Using the Debye-Hückel Approximation

We introduce a mesoscale simulation method based on multiparticle collision dynamics (MPCD) for the electrohydrodynamics of polyelectrolytes with finite Debye lengths. By applying the Debye-Hückel approximation to assign an effective charge to MPCD particles near charged monomers, our simulations are able to reproduce the rapid rise in the electrophoretic mobility with respect to the degree of polymerization for the shortest polymer lengths followed by a small decrease for longer polymers due to charge condensation. Moreover, these simulations demonstrate the importance of a finite Debye length in accurately determining the mobility of uniformly charged polyelectrolytes and net neutral polyampholytes.

Quantitative experimental determination of primer–dimer formation risk by free‐solution conjugate electrophoresis

DNA barcodes are short, unique ssDNA primers that "mark" individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer-barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer-dimer cases comprised two 30-mer primers, one of which was covalently conjugated to a lab-made, chemically synthesized poly-N-methoxyethylglycine drag-tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer-dimers. The drag-tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer-dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free-solution conjugate CE at different temperatures, to assess effects on primer-dimer formation. When less than 30 out of 30 base-pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base-pairs formed, yet non-consecutive base-pairs did not create stable dimers even when 20 out of 30 possible base-pairs bonded. The use of free-solution electrophoresis in combination with a peptoid drag-tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer-dimer formation.

Monodisperse, “Highly” Positively Charged Protein Polymer Drag-Tags Generated in an Intein-Mediated Purification System Used in Free-Solution Electrophoretic Separations of DNA

Free-solution conjugate electrophoresis (FSCE) is a method of DNA sequencing that eliminates the need for viscous polymer solutions by tethering a carefully designed, mobility modifying "drag-tag" to each DNA molecule to achieve size-based separations of DNA. The most successful drag-tags to date are genetically engineered, highly repetitive polypeptides ("protein polymers") that are designed to be large, water-soluble, and completely monodisperse. Positively charged arginines were deliberately introduced at regular intervals into the amino acid sequence to increase the hydrodynamic drag without increasing drag-tag length. Additionally, a one-step purification method that combines affinity chromatography and on-column tag cleavage was devised to achieve the required drag-tag monodispersity. Sequencing with a read length of approximately 180 bases was successfully achieved with a known sequence in free-solution electrophoresis using one of these positively charged drag-tags. This preliminary result is expected to lead to further progress in FSCE sequencing with ~400 bases read length possible when more "highly" positively charged protein polymers of larger size are generated with the intein system.

Separation of Metallic and Semiconducting Single-Wall Carbon Nanotube Solution by Vertical Electric Field

A novel method to separate metallic and semiconducting single-wall carbon nanotubes (SWCNTs) by free solution electrophoresis was investigated. A vertical electrophoretic cell was used to separate SWCNT aqueous solution by the application of electric field along the vertical cell. In contrast with conventional electrophoresis, electric-field-induced layer formation was found in the cell with clear horizontal boundaries. Both the optical absorbance spectra and resonant Raman spectra of these layers revealed the enrichment of metallic and semiconducting SWCNTs with 95% semiconducting SWCNTs in a layer. This method was successfully applied for SWCNTs with diameters from 1.0 to 1.7 nm. Thin-film transistors fabricated by the direct deposition of the semiconductor-enriched nanotubes onto the substrate showed excellent transport properties with an on/off current ratio of 4.4 × 105 and a mobility of 6.8 cm2 V–1 s–1.

Completely monodisperse, highly repetitive proteins for bioconjugate capillary electrophoresis: development and characterization.

Protein-based polymers are increasingly being used in biomaterial applications because of their ease of customization and potential monodispersity. These advantages make protein polymers excellent candidates for bioanalytical applications. Here we describe improved methods for producing drag-tags for free-solution conjugate electrophoresis (FSCE). FSCE utilizes a pure, monodisperse recombinant protein, tethered end-on to a ssDNA molecule, to enable DNA size separation in aqueous buffer. FSCE also provides a highly sensitive method to evaluate the polydispersity of a protein drag-tag and thus its suitability for bioanalytical uses. This method is able to detect slight differences in drag-tag charge or mass. We have devised an improved cloning, expression, and purification strategy that enables us to generate, for the first time, a truly monodisperse 20 kDa protein polymer and a nearly monodisperse 38 kDa protein. These newly produced proteins can be used as drag-tags to enable longer read DNA sequencing by free-solution microchannel electrophoresis.

Purification and fractionation of single-walled carbon nanotubes

This study presents the approach to the purification and subsequent metallic/semiconductive (M/S) fractionation of single-walled carbon nanotubes (SWCNTs) with diameter from 1.04 to 1.60 nm produced via laser ablation. SWCNTs were purified through 3-fold refluxing processes in nitric acid followed by the multiple washings with sodium hydroxide and hydrochloric acid. The purified-annealed SWCNTs sample was divided into seven batches. One batch was dispersed in acetone as a reference sample. Each of the remaining batches were dispersed in one of the following surface agents: sodium dodecyl sulfate, sodium cholate acid (SCA), sodium deoxycholate, cetrimonium bromide, cetylpyridinium chloride, and benzalkonium chloride (BKC). SWCNT suspensions were fractionated via free solution electrophoresis technique. The recovered fractions from electrode and control areas were analyzed via optical absorption spectroscopy in UV–Vis–NIR range to evaluate the efficiency of the separation process. Raman spectroscopy was applied to analyze the purity of the samples. The catalyst content was estimated by atomic absorption spectroscopy. The morphology of the investigated samples was observed via high-resolution transmission electron microscopy. This contribution clearly shows that among the investigated surfactants there are two promising candidates (SCA and BKC) which can efficiently enrich the bulk sample in one electronic type of carbon nanotubes when FSE is applied.

Free-solution electrophoretic separations of DNA-drag-tag conjugates on glass microchips with no polymer network and no loss of resolution at increased electric field strength.

Here, we demonstrate the potential for high-resolution electrophoretic separations of ssDNA-protein conjugates in borosilicate glass microfluidic chips, with no sieving media and excellent repeatability. Using polynucleotides of two different lengths conjugated to moderately cationic protein polymer drag-tags, we measured separation efficiency as a function of applied electric field. In excellent agreement with prior theoretical predictions of Slater et al., resolution is found to remain constant as applied field is increased up to 700 V/cm, the highest field we were able to apply. This remarkable result illustrates the fundamentally different physical limitations of free-solution conjugate electrophoresis (FSCE)-based DNA separations relative to matrix-based DNA electrophoresis. ssDNA separations in "gels" have always shown rapidly declining resolution as the field strength is increased; this is especially true for ssDNA > 400 bases in length. FSCE's ability to decouple DNA peak resolution from applied electric field suggests the future possibility of ultra-rapid FSCE sequencing on chips. We investigated sources of peak broadening for FSCE separations on borosilicate glass microchips, using six different protein polymer drag-tags. For drag-tags with four or more positive charges, electrostatic and adsorptive interactions with poly(N-hydroxyethylacrylamide)-coated microchannel walls led to appreciable band-broadening, while much sharper peaks were seen for bioconjugates with nearly charge-neutral protein drag-tags.

Separation of surfactant functionalized single-walled carbon nanotubes via free solution electrophoresis method

Abstract This work presents the application of the free solution electrophoresis method (FSE) in the metallic / semiconductive (M/S) separation process of the surfactant functionalized single-walled carbon nanotubes (SWCNTs). The SWCNTs synthesized via laser ablation were purified through high vacuum annealing and subsequent refluxing processes in aqua regia solution. The purified and annealed material was divided into six batches. First three batches were dispersed in anionic surfactants: sodium dodecyl sulfate (SDS), sodium cholate (SC) and sodium deoxycholate (DOC). The next three batches were dispersed in cationic surfactants: cetrimonium bromide (CTAB), benzalkonium chloride (BKC) and cetylpyridinium chloride (CPC). All the prepared SWCNTs samples were subjected to FSE separation process. The fractionated samples were recovered from control and electrode areas and annealed in order to remove the adsorbed surfactants on carbon nanotubes (CNTs) surface. The changes of the van Hove singularities (vHS) present in SWCNTs spectra were investigated via UV-Vis-NIR optical absorption spectroscopy (OAS).

Single-walled carbon nanotubes fractionation via electrophoresis

Single-walled carbon nanotubes fractionation via electrophoresis This work presents the influence of the sonication time on the efficiency of the metallic/semiconducting (M/S) fractionation of diazonium salt functionalized single-walled carbon nanotubes (SWCNTs) via free solution electrophoresis (FSE) method. The SWCNTs synthesized via laser ablation were purified from amorphous carbon and catalyst particles through high vacuum annealing and subsequent refluxing processes in aqua regia solutions, respectively. The purified material was divided into two batches. The SWCNTs samples were dispersed in 1% SDS solution in ultrasound bath for 2 and 12 hours. Both dispersed SWCNTs samples were functionalized with p-aminobenzoic acid diazonium salt and fractionated via free solution electrophoresis method. Afterwards, the fractionated samples were recovered, purified from surfactant/functionalities by annealing and investigated via UV-Vis-NIR optical absorption spectroscopy (OAS). The efficiency of the fractionation process was estimated through the comparison of the van Hove singularities (vHS) presented in the obtained fractions to the starting SWCNTs.

A chemically synthesized peptoid‐based drag‐tag enhances free‐solution DNA sequencing by capillary electrophoresis

We report a capillary-based DNA sequencing read length of 100 bases in 16 min using end-labeled free-solution conjugate electrophoresis (FSCE) with a monodisperse poly-N-substituted glycine (polypeptoid) as a synthetic drag-tag. FSCE enabled rapid separation of single-stranded (ss) DNA sequencing fragments with single-base resolution without the need for a viscous DNA separation matrix. Protein-based drag-tags previously used for FSCE sequencing, for example, streptavidin, are heterogeneous in molar mass (polydisperse); the resultant band-broadening can make it difficult to obtain the single-base resolution necessary for DNA sequencing. In this study, we synthesized and HPLC-purified a 70mer poly-N-(methoxyethyl)glycine (NMEG) drag-tag with a molar mass of - 11 kDa. The NMEG monomers that comprise this peptoid drag-tag are interesting for bioanalytical applications, because the methoxyethyl side chain's chemical structure is reminiscent of the basic monomer unit of polyethylene glycol, a highly biocompatible commercially available polymer, which, however, is not available in monodisperse preparation at an - 11 kDa molar mass. This is the first report of ssDNA separation and of four-color, base-by-base DNA sequencing by FSCE through the use of a chemically synthesized drag-tag. These results show that high-molar mass, chemically synthesized drag-tags based on the polyNMEG structure, if obtained in monodisperse preparation, would serve as ideal drag-tags and could help FSCE reach the commercially relevant read lengths of 100 bases or more.

NMEGylation: A novel modification to enhance the bioavailability of therapeutic peptides

We have evaluated "NMEGylation"--the covalent attachment of an oligo-N-methoxyethylglycine (NMEG) chain--as a new form of peptide/protein modification to enhance the bioavailability of short peptides. OligoNMEGs are hydrophilic polyethylene glycol-like molecules made by solid-phase synthesis, typically up to 40 monomers in length. They have been studied as nonfouling surface coatings and as monodisperse mobility modifiers for free-solution conjugate capillary electrophoresis. However, polyNMEGs have not been demonstrated before this work as modifiers of therapeutic proteins. In prior published work, we identified a short peptide, "C20," as a potential extracellular inhibitor of the fusion of human respiratory syncytial virus with mammalian cells. The present study was aimed at improving the C20 peptide's stability and solubility. To this end, we synthesized and studied a series of NMEGylated C20 peptide-peptoid bioconjugates comprising different numbers of NMEGs at either the N- or C-terminus of C20. NMEGylation was found to greatly improve this peptide's solubility and serum stability; however, longer polyNMEGs (n > 3) deleteriously affected peptide binding to the target protein. By incorporating just one NMEG monomer, along with a glycine monomer as a flexible spacer, at C20's N-terminus (NMEG-Gly-C20), we increased both solubility and serum stability greatly, while recovering a binding affinity comparable to that of unmodified C20 peptide. Our results suggest that NMEGylation with an optimized number of NMEG monomers and a proper linker could be useful, more broadly, as a novel modification to enhance bioavailability and efficacy of therapeutic peptides.

A 265-base DNA sequencing read by capillary electrophoresis with no separation matrix.

Electrophoretic DNA sequencing without a polymer matrix is currently possible only with the use of some kind of "drag-tag" as a mobility modifier. In free-solution conjugate electrophoresis (FSCE), a drag-tag attached to each DNA fragment breaks linear charge-to-friction scaling, enabling size-based separation in aqueous buffer alone. Here we report a 265-base read for free-solution DNA sequencing by capillary electrophoresis using a random-coil protein drag-tag of unprecedented length and purity. We identified certain methods of protein expression and purification that allow the production of highly monodisperse drag-tags as long as 516 amino acids, which are almost charge neutral (+1 to +6) and yet highly water-soluble. Using a four-color LIF detector, 265 bases could be read in 30 min with a 267-amino acid drag-tag, on par with the average read of current next-gen sequencing systems. New types of multichannel systems that allow much higher throughput electrophoretic sequencing should be much more accessible in the absence of a requirement for viscous separation matrix.

Electrophoresis of end-labeled DNA: Theory and experiment

The dynamic behavior of end-labeled DNA during free-solution electrophoresis is investigated using a simple dumbbell model for the labeled DNA. We study the effect of the applied field, label size, and chain stiffness on DNA conformation and electrophoretic mobility. High applied fields are predicted to magnify the size-dependence of mobility and to yield a nonmonotonic dependence of electrophoretic mobility on applied field. The effectiveness of leveraging label size and DNA chain stiffness for improving resolution is also discussed in the context of DNA deformation. To evaluate the most salient model predictions, we use capillary electrophoresis experiments to characterize the size- and field-dependent mobility of dsDNA fragments (300 bp-2 kbp) end-functionalized with streptavidin. Our experimental results are found to be in generally good accord with expectations based on the dumb-bell model. We discuss implications of these findings for fast, size-based separation of DNA in free solution.

Integrated microfluidic device for automated single cell analysis using electrophoretic separation and electrospray ionization mass spectrometry.

A microfabricated fluidic device was developed for the automated real-time analysis of individual cells using capillary electrophoresis (CE) and electrospray ionization-mass spectrometry (ESI-MS). The microfluidic structure incorporates a means for rapid lysis of single cells within a free solution electrophoresis channel, where cellular constituents were separated, and an integrated electrospray emitter for ionization of separated components. The eluent was characterized using mass spectrometry. Human erythrocytes were used as a model system for this study. In this monolithically integrated device, cell lysis occurs at a channel intersection using a combination of rapid buffer exchange and an increase in electric field strength. An electroosmotic pump is incorporated at the end of the electrophoretic separation channel to direct eluent to the integrated electrospray emitter. The dissociated heme group and the alpha and beta subunits of hemoglobin from individual erythrocytes were detected as cells continuously flowed through the device. The average analysis throughput was approximately 12 cells per minute, demonstrating the potential of this method for high-throughput single cell analysis.

Mesoscale modelling of polyelectrolyteelectrophoresis

The electrophoretic behaviour of flexible polyelectrolyte chains ranging from single monomers up to long fragments of hundred repeat units is studied by a mesoscopic simulation approach. Abstracting from the atomistic details of the polyelectrolyte and the fluid, a coarse-grained molecular dynamics model connected to a mesoscopic fluid described by the Lattice Boltzmann approach is used to investigate free-solution electrophoresis. Our study demonstrates the importance of hydrodynamic interactions for the electrophoretic motion of polyelectrolytes and quantifies the influence of surrounding ions. The length-dependence of the electrophoretic mobility can be understood by evaluating the scaling behavior of the effective charge and the effective friction. The perfect agreement of our results with experimental measurements shows that all chemical details and fluid structure can be safely neglected, and a suitable coarse-grained approach can yield an accurate description of the physics of the problem, provided that electrostatic and hydrodynamic interactions between all entities in the system, i.e., the polyelectrolyte, dissociated counterions, additional salt and the solvent, are properly accounted for. Our model is able to bridge the single molecule regime of a few nm up to macromolecules with contour lengths of more than 100 nm, a length scale that is currently not accessible to atomistic simulations.

Optimizing End-Labeled Free-Solution Electrophoresis by Increasing the Hydrodynamic Friction of the Drag Tag

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.

Unfolding polyelectrolytes in trivalent salt solutions using dc electric fields: A study by Langevin dynamics simulations

We study the behavior of single linear polyelectrolytes condensed by trivalent salt under the action of electric fields through computer simulations. The chain is unfolded when the strength of the electric field is stronger than a critical value. This critical electric field follows a scaling law against chain length, and the exponent of the scaling law is -0.77(1), smaller than the theoretical prediction, -3nu2 [R. R. Netz, Phys. Rev. Lett. 90, 128104 (2003)], and the one obtained by simulations in tetravalent salt solutions, -0.453(3) [P.-Y. Hsiao and K.-M. Wu, J. Phys. Chem. B 112, 13177 (2008)]. It demonstrates that the scaling exponent depends sensitively on the salt valence. Hence, it is easier to unfold chains condensed by multivalent salt of a smaller valence. Moreover, the absolute value of chain electrophoretic mobility increases drastically when the chain is unfolded in an electric field. The fact that the mobility depends on electric field and on chain length provides a plausible way to impart chain-length dependence in free-solution electrophoresis via chain unfolding transition induced by electric fields. Finally, we show that, in addition to an elongated structure, a condensed chain can be unfolded into a U-shaped structure. The formation of this structure in our study is purely a result of the electric polarization, not of the elastohydrodynamics dominated in sedimentation of polymers.