Novel hydroxyethylcellulose-graft-poly acrylamide copolymer for separation of double-stranded DNA fragments by CE

A novel separation medium, hydroxyethylcellulose-graft-polyacrylamide (HEC-g-PAM) synthesized by atom transfer radical polymerization (ATRP), used for dsDNA separation by CE is presented. The separation performance of HEC-g-PAM, which has the same graft density and different graft length, has been investigated in Tris-boric acid-EDTA (TBE) buffer solvent mixtures. The temperature-dependent rheological behavior of HEC-g-PAM was also studied by steady-shear rheometry. The results showed that dsDNA fragments between 72 and 1353 bp was achieved with a 30 cm effective capillary length at 150 V/cm using this type of graft copolymer as a separation medium in bare fused-silica capillaries, and separation improvement is obtained in HEC-g-PAM compared with HEC and poly(dimethylacrylamide (PDMA).     

Spatial open-network formed by mixed triblock copolymers as a new medium for double-stranded DNA separation by capillary electrophoresis

A mixture of two polyoxybutylene-polyoxyethylene-polyoxybutylene (BEB) triblock copolymers (B6E46B6 and B10E271B10, respectively) was used as a new separation medium for separating double-stranded DNA (dsDNA) fragments by capillary electrophoresis (CE). The two block copolymer mixtures were designed to form mixed flower-like micelles in dilute solution and a homogeneous gel-like open-network with hydrophobic clusters as cross-linking points at higher polymer concentrations. Being a polyoxyalkylene block copolymer gel, the separation medium has some special advantages, including the temperature-dependent sol-gel transition that makes sample injection easy, and the self-coating of the inner capillary wall that makes experimental procedures simple and reproducible. Furthermore, it can shorten the elution time and further improve the separation resolution, especially for small dsDNA fragments, when compared with EPE-type separation media, e.g., F127 (E99P69E99, with P being polyoxypropylene) block copolymer gels formed by the closed packing of spherical micelles. Single base pair resolution can be achieved by using the new separation medium for dsDNA fragments up to over 100 base pairs.     

Brush-like copolymer as a physically adsorbed coating for protein separation by capillary electrophoresis

A brush-like copolymer consisting of poly(ethylene glycol) methyl ether methacrylate and N,N-dimethylacrylamide (PEGMA-DMA) was synthesized and used as a novel static physically adsorbed coating for protein separation by capillary electrophoresis for the first time, in order to stabilize electroosmotic flow (EOF) and suppress adsorption of proteins onto the capillary wall. Very stable and low EOF was obtained in PEGMA-DMA-coated capillary at pH 2.2-7.8. The effects of molar ratio of PEGMA to DMA, copolymer molecular mass, and pH on the separation of basic proteins were discussed. A comparative study of bare capillary with PEGMA-DMA-coated capillary for protein separation was also performed. The basic proteins could be well separated in PEGMA-DMA-coated capillary over the investigated pH range of 2.8-6.8 with good repeatability and high separation efficiency because the copolymer coating combines good protein-resistant property of PEG side chains with excellent coating ability of PDMA-contained backbone. Finally, the coating was successfully applied to the fast separation of other protein samples, such as protein mixture and egg white, which reveals that it is a potential coating for further proteomics analysis.     

Synthesis of poly(N,N‐dimethylacrylamide)‐block‐poly(ethylene oxide)‐block‐poly(N,N‐dimethylacrylamide) and its application for separation of proteins by capillary zone electrophoresis

A series of well‐defined triblock copolymers, poly(N, N‐dimethylacrylamide)‐block‐poly(ethylene oxide)‐block‐poly(N, N‐dimethylacrylamide) (PDMA‐b‐PEO‐b‐PDMA) synthesized by atom transfer radical polymerization, were used as physical coatings for protein separation. A comparative study of EOF showed that the triblock copolymer presented good capillary coating ability and EOF efficient suppression. The effects of the M_r of PDMA block in PDMA‐b‐PEO‐b‐PDMA triblock copolymer and buffer pH on the separation of basic protein for CE were investigated. Moreover, the influence of the copolymer structure on separation of basic protein was studied by comparing the performance of PDMA‐b‐PEO‐b‐PDMA triblock copolymer with PEO‐b‐PDMA diblock copolymer. Furthermore, the triblock copolymer coating showed higher separation efficiency and better migration time repeatability than fused‐silica capillary when used in protein mixture separation and milk powder samples separation, respectively. The results demonstrated that the triblock copolymer coatings would have a wide application in the field of protein separation.     

Effect of quasi‐interpenetrating network of polyacrylamide and poly(N,N‐dimethylacrylamide) on separation of dsDNA fragments and basic protein using CE

Quasi‐interpenetrating network (quasi‐IPN) of linear polyacrylamide (LPA) with low molecular mass and poly(N,N‐dimethylacrylamide) (PDMA), which is shown to uniquely combine the superior sieving ability of LPA with the coating ability of PDMA, has been synthesized for application in dsDNA and basic protein separation by CE. The performance of quasi‐IPN on dsDNA separation was determined by polymer concentration, electric field strength, LPA molecular masses and different acrylamide (AM) to N,N‐dimethylacrylamide (DMA) ratio. The results showed that all fragments in Φ×174/HaeIII digest were achieved with a 30 cm effective capillary length at –6 kV at an appropriate polymer solution concentration in bare silica capillaries. Furthermore, EOF measurement results showed that quasi‐IPN exhibited good capillary coating ability, via adsorption from aqueous solution, efficiently suppressing EOF. The effect of the buffer pH values on the separation of basic proteins was investigated in detail. The separation efficiencies and analysis reproducibility demonstrated the good potentiality of quasi‐IPN matrix for suppressing the adsorption of basic proteins onto the silica capillary wall. In addition, when quasi‐IPN was used both as sieving matrix and dynamic coating in bare silica capillaries, higher peak separation efficiencies, and better migration time reproducibility were obtained.     

Poly(N,N-dimethylacrylamide)-grafted polyacrylamide: a self-coating copolymer for sieving separation of native proteins by CE

The potential of a series of newly synthesized poly(N,N-dimethylacrylamide) (PDMA) grafted polyacrylamide (PAM) copolymers (P(AM-PDMA)) as a replaceable separation medium for protein analysis was studied. A comparative study with and without copolymers was performed; the separation efficiency, analysis reproducibility and protein recovery proved that the P(AM-PDMA) copolymers were efficient in suppressing the adsorption of basic proteins onto the silica capillary wall. Furthermore, the size-dependent retardation of native proteins in a representative P(AM-PDMA) copolymer was demonstrated by Ferguson analysis. The results showed that the P(AM-PDMA) copolymers combine the good coating property of PDMA and the sieving property of PAM and could be applied as a sieving matrix for the analysis of native proteins.     

Thermoresponsive N,N-dialkylacrylamide copolymer blends as DNA sieving matrices with a thermally tunable mesh size

In an earlier study we showed that a blend of thermoresponsive and nonthermoresponsive hydroxyalkylcelluloses could be used to create a thermally tunable polymer network for double-stranded (ds) DNA separation. Here, we show the generality of this approach using a family of polymers suited to a wider range of DNA separations: a blended mixture of N,N-dialkylacrylamide copolymers with different thermoresponsive behaviors. A mixture of 47% w/w N,N-diethylacrylamide (DEA)/53% w/w N,N-dimethylacrylamide (DMA) (DEA47; thermoresponsive, transition temperature = 55 degrees C in water) and 30% w/w DEA/70% w/w DMA (DEA30; nonthermoresponsive, transition temperature > 85 degrees C in water) copolymers in the ratio of 1:5 w/w DEA47:DEA30 was used to separate a dsDNA restriction digest (PhiX174-HaeIII). We investigated the effects of changing mesh size on dsDNA separation, as controlled by temperature. We observed good DNA separation performance with the copolymer blend at temperatures ranging from 25 degrees C to 48 degrees C. The separation selectivity was evaluated quantitatively for certain DNA fragment pairs as a function of temperature. The results were compared with those obtained with a control matrix consisting only of the nonthermoresponsive DEA30. Different DNA fragment pairs of various sizes show distinct temperature-dependent selectivities. Over the same temperature range, no significant temperature dependence of selectivity is observed for these DNA fragment pairs in the nonthermoresponsive control matrix. Overall, the results show similar trends in the temperature dependency of separation selectivity to what was previously observed in hydroxyalkylcellulose blends, for the same DNA fragment pairs. Finally, we showed that a ramped temperature scheme enables improved separation in the blended copolymer matrix for both small and large DNA fragments, simultaneously in a single capillary electrophoresis (CE) run.     

Graft copolymer composed of cationic backbone and bottle brush-like side chains as a physically adsorbed coating for protein separation by capillary electrophoresis

To stabilize electroosmotic flow (EOF) and suppress protein adsorption onto the silica capillary inner wall, a cationic hydroxyethylcellulose-graft-poly (poly(ethylene glycol) methyl ether methacrylate) (cat-HEC-g-PPEGMA) graft copolymer composed of cationic backbone and bottle brush-like side chains was synthesized for the first time and used as a novel physically adsorbed coating for protein separation by capillary electrophoresis. Reversed (anodal) and very stable EOF was obtained in cat-HEC-g-PPEGMA-coated capillary at pH 2.2-7.8. The effects of degree of cationization, PEGMA grafting ratio, PEGMA molecular mass, and buffer pH on the separation of basic proteins were investigated. A systematic comparative study of protein separation in bare and HEC-coated capillaries and in cat-HEC-g-PPEGMA-coated capillary was also performed. The basic proteins can be well separated in cat-HEC-g-PPEGMA-coated capillary over the pH range of 2.8-6.8 with good repeatability and high separation efficiency, because the coating combines good protein-resistant property of bottle brush-like PPEGMA side chains with excellent coating ability of cat-HEC backbone. Besides its success in separation of basic proteins, the cat-HEC-g-PPEGMA coating was also superior in the fast separation of other protein samples, such as protein mixture, egg white, and saliva, which indicates that it is a promising coating for further proteomics analysis.     

Ultrafast, efficient separations of large-sized dsDNA in a blended polymer matrix by microfluidic chip electrophoresis: a design of experiments approach

Double-stranded (ds) DNA fragments over a wide size range were successfully separated in blended polymer matrices by microfluidic chip electrophoresis. Novel blended polymer matrices composed of two types of polymers with three different molar masses were developed to provide improved separations of large dsDNA without negatively impacting the separation of small dsDNA. Hydroxyethyl celluloses with average molar masses of ～27 kDa and ～1 MDa were blended with a second class of polymer, high-molar mass (～7 MDa) linear polyacrylamide. Fast and highly efficient separations of commercially available DNA ladders were achieved on a borosilicate glass microchip. A distinct separation of a 1-kb DNA extension ladder (200-40,000 bp) was completed in 2 min. An orthogonal design of experiments was used to optimize experimental parameters for DNA separations over a wide size range. We find that the two dominant factors are the applied electric field strength and the inclusion of a high concentration of low-molar mass polymer in the matrix solution. These two factors exerted different effects on the separations of small dsDNA fragments below 1 kbp, medium dsDNA fragments between 1 and 10 kbp, and large dsDNA fragments above 10 kbp.     

Separation of double-stranded DNA fragments in plastic capillary electrophoresis chips by using E99P69E99 as separation medium.

The separation of double-stranded DNA (dsDNA) fragments in polymethylmethacrylate (PMMA) capillary electrophoresis (CE) chips by using E99P69E99 as a separation medium has been demonstrated. The PMMA CE chips were simply manufactured by micromachining and adhesive tape sealing. To make the separation channel compatible with the separation medium, a dynamic nonionic surfactant coating procedure was developed, which made the plastic separation channel sufficiently hydrophilic to allow the separation medium to fill the channel by capillary action. Subsequent separation of DNA fragments was successful with a separation efficiency of the order of 10(4) theoretical plates over an effective separation distance of 1.5 cm. By using an applied electric field strength of 200 V/cm, the separation of low DNA mass ladder was completed within 5 min. The simple coating procedure, together with the self-assembled viscosity-adjustable separation medium, should be useful to meet some of the essential requirements for developing single-use disposable CE chips. Coating the channels with polymer blends of PMMA and the separation medium also showed promise.     

Polymer mixtures with enhanced compatibility and extremely low viscosity used as DNA separation media

Poor compatibility was the major drawback of polymer mixtures when used as DNA separation media. Using poly(ethylene oxide)‐b‐poly(N, N‐dimethylacrylamide) (PEO₄₄‐b‐PDMA₈₈) and PEO (M_w: 1.3 MDa) as an example, we demonstrated the concept that the compatibility was significantly improved when mixing a homopolymer with its copolymer. Laser light scattering indicated that the major interaction between PEO and PEO‐b‐PDMA in dilute solution was the weak hydrodynamic interaction, which showed almost no effect on the viscosity and the static scattering pattern. In semidilute or concentrated solution, viscosity measurement also suggested good compatibility between the two components. When tested as DNA separation medium by CE, the viscosity of the mixture was extremely low, only 5 cP for 5.0 m/v% PEO‐b‐PDMA+0.1 m/v% PEO at 25°C. The performance on DNA separation could be tuned by varying the concentration of each component as well as the component ratio. Good separation on both dsDNA and ssDNA was achieved.     

A Novel Sieving Medium for Separation of DNA Fragments- Poly(acrylamide-dimethylacrylamide)

IntroductionCapillary electrophoresis (CE) in polymer solution has become an attractive alternative to slab gel electrophoresis for DNA analysis1, 2. This technique has been successfully applied for mutation detection, genotyping, DNA sequencing and gene expression3-7. In order to perform DNA analysis, the inner surface of the capillary must be modified, usually by covalent bonding of hydrophilic polymers. However, the covalent coating will increase the cost and often causes problems rela…     

Hydroxyethylcellulose-graft-poly(2-(dimethylamino)ethyl methacrylate) as physically adsorbed coating for protein separation by CE

In this work, a novel graft copolymer, hydroxyethylcellulose-graft-poly(2-(dimethylamino)ethyl methacrylate) (HEC-g-PDMAEMA), used as physical coatings of the bare fused-silica capillaries, was synthesized by using ceric ammonium nitrate initiator in aqueous nitric acid solution. EOF measurement results showed that the synthesized HEC-g-PDMAEMA graft copolymer-coated capillary in this paper could suppress EOF effectively compared to the bare fused-silica capillary, and efficient separations of basic proteins were also achieved. The electrical charge of the coated capillary wall could be modulated by varying not only the pH of the running buffer, but also the grafting ratio of poly(2-(dimethylamino)ethyl methacrylate) grafts, which makes possible the analysis of basic and acidic proteins in the same capillary. The effects of poly(2-(dimethylamino)ethyl methacrylate) grafting ratio in HEC-g-PDMAEMA and buffer pH on the separation of basic proteins for capillary electrophoresis were investigated in detail. Furthermore, egg white proteins and milk powder samples were separated by the HEC-g-PDMAEMA-coated capillary. The results demonstrated that the HEC-g-PDMAEMA copolymer coatings have great potential in the field of diagnosis and proteomics.     

Preparation of monodispersed vinylpyridine–divinylbenzene porous copolymer resins and their application to high-performance liquid chromatographic separation of aromatic amines

For the separation of aromatic amines, two types of monodispersed porous polymer resins were prepared by the copolymerization of 2-vinylpyridine and 4-vinylpyridine with divinylbenzene in the presence of template silica gel particles (particle size 5 μm), followed by dissolution of the template silica gel in an alkaline solution. The transmission electron micrographs and the scanning electron micrograph revealed that these templated polymer resins have a spherical morphology with a good monodispersity and porous structure. Using these monodispersed polymer resins, the high-performance liquid chromatographic separation of aromatic amines in the mobile phases of pHs 2.0, 2.9, 4.1, 7.2 and 11.7 were carried out. The 2-vinylpyridine–divinylbenzene copolymer resins showed slightly stronger retentions for aromatic amines than the 4-vinylpyridine–divinylbenzene copolymer resins. Under acidic conditions (around pH 2.0), aniline and the toluidines showed no retention on these copolymer resins due to the repulsion between the cationic forms of these amines and pyridinium cations in the stationary phase, whereas less basic aromatic amines or non-basic acetanilide showed slight retentions. Above pH 4.1, the separation of aromatic amines with these polymer resins showed a typical reversed-phase mode separation. Therefore, the separation patterns of aromatic amines are effectively tunable by changing the pH value of the mobile phases. A good separation of eight aromatic amines was achieved at pH 2.9 using the 2-vinylpyridine–divinylbenzene copolymer resins.     

Separation of basic proteins by capillary zone electrophoresis with coatings of a copolymer of vinylpyrrolidone and vinylimidazole

Capillary zone electrophoretic (CZE) separation of basic proteins has been achieved with capillary columns modified with copolymers of vinylpyrrolidone (VP) and vinylimidazole (VI). The copolymerization reaction is performed inside the capillary column and involves chemical bonding of the polymer to silica. The electroosmotic flow (EOF) is greatly decreased by this surface modification. The presence of positive charges on the coating surface, due to the cationic property of vinylimidazole at pH below 7, reduces the adsorption of basic proteins onto the silanol groups of the capillary surface. Acidic proteins are irreversibly adsorbed, but rapid separation and good performance reproducibility are obtained with basic proteins. In the case of capillaries modified with VP, the acidic and basic proteins are eluted within 10 min. In this work, we studied the effects of pH and buffer concentration on the magnitude of the EOF, as well as the effect of copolymer composition on the separation efficiency.     

DNA gel particles: particle preparation and release characteristics

Aqueous mixtures of oppositely charged polyelectrolytes undergo associative phase separation, resulting in coacervation, gelation, or precipitation. This phenomenon has been exploited here to form DNA gel particles by interfacial diffusion. We report the formation of DNA gel particles by mixing solutions of DNA (either single-stranded (ssDNA) or double-stranded (dsDNA)) with solutions of cationic surfactant CTAB and solutions of the protein lysozyme. Swelling, surface morphology, and DNA release determinations indicate different interaction of ssDNA and dsDNA with both the surfactant and the protein. By using CTAB and lysozyme as the base material, the formation of a DNA reservoir hydrogel, without adding any kind of cross-linker or organic solvent, was demostrated.     

Novel Porous Monolithic Column Using Poly(high internal phase emulsion) Methacrylate as Materials for Immunoglobulin Separation Performance on HPLC

A novel porous polymeric monolithic column based on poly(high internal phase emulsion) methacrylate monolith was prepared and applied to fast separation of proteins. The block copolymer chemistry of high internal phase emulsions was used in the experiment. These unique properties, together with high porosity, good mechanical property, chemical modification of the surface make themselves superior in monolithic medium applications. Morphology of the monolithic material was studied by scanning electron microscopy. The stability of the emulsion and the load of hydroxyl groups–the active group of the monolithic column were investigated. Additionally, the capabilities of separation of this column in conjunction with high performance liquid chromatography (HPLC) were investigated. Immunoglobulin was separated from human plasma and chicken egg yolk with high resolution on the hydrophobic interaction chromatographic column in a short time. The effects of pH and concentration of mobile phase (buffer) on the elution of immunoglobulin were investigated. Moreover, fast separation of a two mode protein mixture (α‐amylase and lysozyme) on the monolith was achieved within 1.5 min at a velocity of 1445 cm·h^?1. As a result, good separation was achieved, and stable low back pressure drop was ensured at high throughput elution with an even longer column.     

Probing the mechanical stability of DNA in the presence of monovalent cations

We examine the interaction between monovalent cations and DNA using several different assays that measure the stability of double-stranded DNA (dsDNA). The thermal melting of dsDNA and the mechanical separation of dsDNA into two single strands both depend on the stability of dsDNA with respect to ssDNA and are sensitive to the interstrand phosphate repulsion. We find that the experimentally measured melting temperatures and unzipping forces are approximately the same for all of the ions considered in this study. Likewise, the force required to transform B-DNA into the overstretched form is also similar for all of the ions. In contrast, for a given ion concentration, the force at which the overstretched state fully relaxes back to the canonical B-DNA form depends on the cation; however, for all cations, the overstretching force decreases with decreasing ion concentration, suggesting that this force is sensitive to screening. We observe a general trend for smaller ions to produce more efficient relaxation. Finally, for a given cation, the relaxation can also depend on the anion.     

Composition analysis of poly(ethylene glycol)-poly(L-lactide) diblock copolymer studied by two-dimensional column chromatography

We used two-dimensional column chromatography to analyze the composition of a sample of presumably a diblock copolymer of poly(ethylene glycol) (PEG) and poly(L-lactide) synthesized from monomethoxy-terminated PEG. The first dimension of the separation is phase fluctuation chromatography to prepare fractions that contain various components of the copolymer in different ratios. The second dimension is size-exclusion chromatography, NMR, and HPLC at the critical condition of PEG. The PEG initiator has small amounts of diol-terminated dimeric components. We found that the copolymer sample contains a triblock copolymer and low-molecular-mass components in addition to the main part of the diblock copolymer. The SEC chromatograms show that the main part consists of two components with distinct peak lengths for the PLLA block. The low-molecular-mass components have a broad distribution in chemical composition. Phase fluctuation chromatography enriched the triblock copolymer and the diblock copolymer with the longer PLLA block in early fractions when the column was packed with carboxymethyl-modified porous silica. When the porous medium was PLLA-grafted silica, size exclusion dominated, but the low-molecular-mass components were separated according to their chemical composition.     

A new quasi-interpenetrating network formed by poly(N-acryloyl-tris-(hydroxymethyl)aminomethane and polyvinylpyrrolidone: separation matrix for double-stranded DNA and single-stranded DNA fragments by capillary electrophoresis with UV detection

The preparation of a new separation matrix, quasi-interpenetrating networks (quasi-IPNs) formed by poly(N-acryloyl-Tris) (poly(tris-A)) and PVP, and its application for dsDNA and ssDNA fragments separation by CE with UV detection, are presented. This new quasi-IPN exhibited high sieving performance, good dynamic coating ability, and low viscosity. Single-base resolutions of dsDNA fragments (Rs = 0.92 for 123/124 bp) and ssDNA fragments (Rs = 0.65 for 123/124 base, Rs = 0.48 for 309/310 base) were achieved by using the quasi-IPN of poly(tris-A)/PVP (2% + 2%) solution in a 31 cm effective length linear polyacrylamide (LPA)-coated column. Single-base separation of dsDNA fragments (Rs = 0.92 for 123/124 bp) was also obtained within 28 min in a 46.7 cm effective length bare column at higher 160 V/cm electric field strength by using the same quasi-IPN solution. The RSD of the migration time measured for each DNA fragments was less than 1.5% in the bare column for nine continuous runs. The effects of temperature and electric field strength on the DNA separation were also investigated.