Star-shaped polymers for DNA sequencing by capillary electrophoresis

The separation and sequencing of DNA are the main objectives of the Human Genome Project, and this project has also been very useful for gene analysis and disease diagnosis. Capillary electrophoresis (CE) is one of the most common techniques for the separation and analysis of DNA. DNA separations are usually achieved using capillary gel electrophoresis (CGE) mode, in which polymer gel is packed into the capillary. Compared with a traditional CGE matrix, a hydrophilic polymer matrix, which can be adsorb by the capillary wall has numerous advantages, including stability, reproducibility and ease of automation. Various water-soluble additives, such as linear poly(acrylamide) (PAA) and poly(N,N-dimethylacrylamide) (PDMA), have been employed as media. In this study, different star-shaped PDMA polymers were designed and synthesized to achieve lower polymer solution viscosity. DNA separations with these polymers avoid the disadvantages of high viscosity and long separation time while maintaining high resolution (10 bp between 271 bp and 281 bp). The influences of the polymer concentration and structure on DNA separation were also determined in this study; higher polymer concentration yielded better separation performance, and star-like polymers were superior to linear polymers. This work indicates that modification of the polymer structure is a potential strategy for optimizing DNA separation.     

A DNA sieving matrix with thermally tunable mesh size

We present a "proof-of-concept" study showing that a blend of thermo-responsive and nonthermo-responsive polymers can be used to create a DNA sieving matrix with a thermally tunable mesh size, or "dynamic porosity". Various blends of two well-studied sieving polymers for CE, including hydroxypropylcellulose (HPC), a thermo-responsive polymer, and hydroxyethylcellulose (HEC), a nonthermo-responsive polymer, were used to separate a double-stranded DNA restriction digest (Phi X174-HaeIII). HPC exhibits a volume-phase transition in aqueous solution which results in a collapse in polymer coil volume at approximately 39 degrees C. Utilizing a blend of HPC and HEC in a ratio of 1:5 by weight, we investigated the effects of changing mesh size on DNA separation, as controlled by temperature. High-resolution DNA separations were obtained with the blended matrix at temperatures ranging from 25 degrees C to 38 degrees C. We evaluated changes in the selectivity of DNA separation with increasing temperature for certain pairs of small and large fragments. A pure HEC (nonthermo-responsive) matrix was used over the same temperature range as a negative control. In the blended matrix, we observe a maximum in selectivity at approximately 31 degrees C for small DNA, while a significant increase in the selectivity of large-DNA separation occurs at approximately 36 degrees C as the polymer mesh "opens". We also demonstrate, through a temperature ramping experiment, that this matrix can be utilized to obtain high-resolution separation of both small and large DNA fragments simultaneously in a single CE run. Blended polymer matrices with "dynamic porosity" have the potential to provide enhanced genomic analysis by capillary array or microchip electrophoresis in microfluidic devices with advanced temperature control.     

Application of water-soluble polymers as modifiers in electrophoretic analysis of phenols

A review of application of water-soluble cationic, anionic and nonionic polymers as pseudostationary phases in capillary electrophoresis (CE) and micellar electrokinetic capillary chromatography (MEKC) is presented. The effect of the structure of the polymers on the selectivity and efficiency of separation is discussed. A novel specially designed cationic polymer, 2,10-ionene, has been used for the separation of phenols. The polymer has hydrophilic and hydrophobic parts in its backbone. The polymer shows the best selectivity as a modifier in capillary zone electrophoresis (CZE)-mode, which allows the selective determination of both hydrophilic and hydrophobic phenols.     

The use of light scattering for precise characterization of polymers for DNA sequencing by capillary electrophoresis

The ability of a polymer matrix to separate DNA by capillary electrophoresis (CE) is strongly dependent upon polymer physical properties. In particular, recent results have shown that DNA sequencing performance is very sensitive to both the average molar mass and the average coil radius of the separation matrix polymers, which are affected by both polymer structure and polymer-solvent affinity. Large polymers with high average molar mass provide the best DNA sequencing separations for CE, but are also the most challenging to characterize with accuracy. The methods most commonly used for the characterization of water-soluble polymers with application in microchannel electrophoresis have been gel permeation chromatography (GPC) and intrinsic viscosity measurements, but the limitations and potential inaccuracies of these approaches, particularly for large or novel polymers and copolymers, press the need for a more universally accurate method of polymer molar mass profiling for advanced DNA separation matrices. Here, we show that multi-angle laser light scattering (MALLS) measurements, carried out either alone or in tandem with prior on-line sample fractionation by GPC, can provide accurate molar mass and coil radius information for polymer samples that are useful for DNA sequencing by CE. Wider employment of MALLS for characterization of novel polymers designed as DNA separation matrices for microchannel electrophoresis should enable more rapid optimization of matrix properties and formulation, and assist in the development of novel classes of polymer matrices.     

Nonconventional synthesis and characterization of ultrahigh-molar-mass polyacrylamides

In spite of the significant progresses in the field of replaceable sieving matrices for separating DNA in capillary electrophoresis (CE), an intense research activity is still going on to improve the separation of large size DNA sequencing fragments. There are evidences, both from experimental and theoretical sides that the resolution of these fragments, at the single base, requires the use of sieving matrices comprised of long chain linear polymers. In the separation of DNA fragments by CE are of upmost importance: (i) the complete solubility of the polymer, (ii) the linearity of the chain, (iii) the achievement of ultrahigh viscosity in dilute solutions. The aim of this work is the synthesis of ultrahigh-molecular-weight polymers which possess the three requirements mentioned above by employing a nonconventional method. We demonstrate that the sieving performance of polyacrylamide is directly correlated to its intrinsic viscosity.     

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.     

Low viscosity DNA sieving matrices for capillary electrophoresis

The rapid development of DNA capillary electrophoresis (CE) technology has increased the demand of new low viscosity sieving matrices with high separation capacity. The high throughput, resolution and automatic operation of CE systems have stimulated the application of the technique to different kinds of DNA analysis, including DNA sequencing, separation of restriction fragments, PCR products and synthetic oligonucleotides. In addition specific methods for PCR-based mutation assays for the study of known and unknown point mutations have been developed for use in CE. The key component for a large scale application of CE to DNA analysis is the availability of appropriate sieving matrices. This article gives an overview of the linear polymers used as DNA separation matrices with particular emphasis on the polymers that combine high sieving capacity, low viscosity and chemical resistance.     

Thermally Rearranged Polymer Membranes Containing Tröger's Base Units Have Exceptional Performance for Air Separations

The influence of segmental chain motion on the gas separation performance of thermally rearranged (TR) polymer membranes is established for TR polybenzoxazoles featuring Tröger's base (TB) monomer subunits as exceptionally rigid sites of contortion along the polymer backbone. These polymers are accessed from solution‐processable ortho‐acetate functionalized polyimides, which are readily synthesized as high‐molecular‐weight polymers for membrane casting. We find that thermal rearrangement leads to a small increase in d‐spacing between polymer chains and a dramatic pore‐network reconfiguration that increases both membrane permeability and O₂/N₂ selectivity, putting its performance above the 2015 upper bound.     

Sieving polymer synthesis by reversible addition fragmentation chain transfer polymerization

Replaceable sieving polymers are the fundamental component for high‐resolution nucleic acids separation in CE. The choice of polymer and its physical properties play significant roles in influencing separation performance. Recently, reversible addition fragmentation chain transfer (RAFT) polymerization has been shown to be a versatile polymerization technique capable of yielding well‐defined polymers previously unattainable by conventional free‐radical polymerization. In this study, a high molecular weight poly‐(N,N‐dimethylacrylamide) (PDMA) at 765 000 gmol^?1 with a polydispersity index of 1.55 was successfully synthesized with the use of chain transfer agent—2‐propionic acidyl butyl trithiocarbonate in a multistep sequential RAFT polymerization approach. This study represents the first demonstration of RAFT polymerization for synthesizing polymers with the molecular weight range suitable for high‐resolution DNA separation in sieving electrophoresis. Adjustment of pH in the reaction was found to be crucial for the successful RAFT polymerization of high molecular weight polymer as the buffered condition minimizes the effect of hydrolysis and aminolysis commonly associated with trithiocarbonate chain transfer agents. The separation efficiency of 2‐propionic acidyl butyl trithiocarbonate PDMA was found to have marginally superior separation performance compared to a commercial PDMA formulation, POP?‐CAP, of similar molecular weight range.     

Influence of side chains assembly on the structure and transport properties of comb-like polysiloxanes in hydrocarbon separation

We have synthesized a number of comb-like polysiloxanes with linear, branched, cyclic and silicon-containing substituents; most of them are new and previously not studied polymers. The physicochemical properties of comb-like polysiloxanes have been systematically investigated. Differential-scanning calorimetry and wide-angle X-ray scattering data revealed the side-chain microphase assembly for polymers with linear aliphatic substituents, while the polymers with bulky substituents did not form a microphase. It is shown that the ratio of microphase in the polymer is greater, the closer the values of the thickness of the microphase layer and the length of the cross-link. The effect of the side-chain substituent on the hydrocarbon transport properties of comb-like polysiloxanes was studied. All synthesized polymers are promising as membrane materials for a vital process of hydrocarbon separation. This is associated with an increase in the solubility selectivity of n-butane/methane because the solubility coefficient of methane sharply decreases when long side chains are introduced into the polysiloxane. It was shown for the first time that microphase forming polymers have a significantly higher butane/methane selectivity (23.2–27.5) than polysiloxanes not forming a microphase (selectivity 12.3–20.0). The effect is demonstrated on polysiloxanes with various types of side substituents. It was revealed that for the comb-like polysiloxanes, the diffusivity selectivity and permselectivity are proportional to the fraction of the side-chain microphase in the polymer. With the increase in the hydrocarbon microphase share, the diffusion coefficient of the permanent gas methane is decreasing more rapidly than n-butane, which dissolves well in hydrocarbons and plasticizes polymer. Consequently, the polymers forming the microphase have a higher selectivity C₃₊/CH₄ in the separation of a multicomponent hydrocarbons mixture.     

Potential of prodendronic polyamines with modulated segmental charge density as novel coating for fast and efficient analysis of peptides and basic proteins by CE and CE‐MS

In this work, the suitability of a new polymer family has been investigated as capillary coatings for the analysis of peptides and basic proteins by CE. This polymer family has been designed to minimize or completely prevent protein–capillary wall interactions and to modify the EOF. These coating materials are linear polymeric chains bearing as side cationizable moiety a dentronic triamine derived from N,N,N’,N’‐tetraethyldiethylenetriamine (TEDETA), which is linked to the backbone through a spacer (unit labeled as TEDETAMA). Four different polymers have been prepared and evaluated: a homopolymer which comprised only of those cationizable repetitive units of TEDETAMA, and three copolymers that randomly incorporate TEDETAMA together with neutral hydrosoluble units of N‐(2‐hydroxypropyl) methacrylamide (HPMA) at different molar percentages (25:75, 50:50 and 75:25). It has been demonstrated that the composition of the copolymers influences the EOF and therefore the separation of the investigated biopolymers. Among the novel polymers studied, poly‐(TEDETAMA‐co‐HPMA) 50:50 copolymer was successfully applied as coating material of the inner capillary surface in CE‐UV and CE‐MS, providing EOF reversing together with fast and efficient baseline separation of peptides and basic proteins. Finally, the feasibility of the polymer‐coated capillary was shown through the analysis of lysozyme in a cheese sample.     

Silicon surface modification with trialkoxysilyl‐functionalized star‐shaped polymers

The synthesis of trimethoxysilane end‐capped linear polystyrene (PS) and star‐branched PS and subsequent silicon (Si) surface modification with linear and star polymers are described. Trimethoxysilane terminated PS was synthesized using sec‐butyl lithium initiated anionic polymerization of styrene and subsequent end‐capping of the living anions with p‐chloromethylphenyl trimethoxysilane (CMPTMS). ¹H and ²⁹Si NMR spectroscopy confirmed the successful end‐capping of polystyryllithium with the trimethoxysilane functional group. The effect of a molar excess of end‐capper on the efficiency of functionalization was also investigated, and the required excess increased for higher molar mass oligomers. Acid catalyzed hydrolysis and condensation of the trimethoxysilane end‐groups resulted in star‐branched PS, and NMR spectroscopy and SEC analysis were used to characterize the star polymers. This is the first report of core‐functionalized star‐shaped polymers as surface modifiers and the first comparative study showing differences in surface topography between star and linear polymer modified surfaces. Surface‐sensitive techniques such as ellipsometry, contact angle goniometry, and AFM were used to confirm the attachment of star PS, as well as to compare the characteristics of the star and linear PS modified Si surfaces. The polymer film properties were referenced to polymer dimensions in dilute solution, which revealed that linear PS chains were in the intermediate brush regime and the star‐branched PS produced a surface with covalently attached chains in the mushroom regime. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 3655–3666, 2005     

Anomalous reinforcing effects in cellulose gel-based polymeric nanocomposites

Cellulose-synthetic polymer nanocomposite films were prepared by immersion of cellulose gel in polymer solutions followed by dry casting. The cellulose hydrogel was prepared from aqueous alkali-urea solution. As the synthetic polymer, polystyrene (PS) and poly(methyl methacrylate) (PMMA) were used. The polymer content could be changed between 10 and 80% by changing polymer concentration of immersing solution. While the mechanical properties of the cellulose-PMMA composite films showed a nearly linear dependence on PMMA content, those of cellulose-PS composites showed an anomalous behavior; both tensile strength and Young’s modulus showed prominent maxima at 15–30 wt% PS contents. This anomaly may have resulted from the specific interaction between the aromatic ring of PS and the hydrophobic plane of the glucopyranoside. Both PMMA and PS composite films showed significant improvements in dimensional thermal stability; up to 25 wt% synthetic polymer content, the coefficient of thermal expansion (CTE) was as low as ca. 30 ppm/K, about 1/3 of the pure polymers. This indicates that the regenerated cellulose network is effective in suppressing thermal expansion of the synthetic polymers.     

Separation of living and dead polymers in synthetic polypeptide mixtures by nonaqueous capillary electrophoresis using differences in ionization states

The complexity in the mechanisms of polymerization of N-carboxyanhydrides requires the development of new analytical techniques able to separate mixtures of synthetic polypeptides. This work focuses on the separation of poly(N(epsilon)-trifluoroacetyl-L-lysine) (PTLL) mixtures by nonaqueous capillary electrophoresis (CE). The main goal of this work was to find electrophoretic conditions that permit the separation and the quantification of the dead polymer families that were previously identified in the samples. The influence of the pH of the electrolyte on the selectivity of the separation was carefully investigated. The mechanisms of separation of the PTTLs are discussed as a function of their ionization state. The separations obtained on a noncovalently coated capillary were compared with those obtained on a fused-silica capillary. Finally, using two different electrolytes, it is possible to quantify the three families of PTLLs, namely, the living PTLLs, the dead PTLLs with N-formyl end group and the dead PTLLs with a carboxylic end group. These results confirm the importance of CE for the separation of synthetic organic polymers in nonaqueous electrolytes.     

Evaluation of carrier ampholyte-based capillary electrophoresis for separation of peptides and peptide mimetics

Carrier ampholyte-based capillary electrophoresis (CABCE) has recently been introduced as an alternative to CE (CZE) in the classical buffers. In this study, isoelectric BGEs were obtained by fractionation of Servalyt pH 4-9 carrier ampholytes to cuts of typical width of 0.2 pH unit. CABCE feasibility was examined on a series of insect oostatic peptides, i.e. proline-rich di- to decapeptides, and phosphinic pseudopeptides--tetrapeptide mimetics synthesized as a mixture of four diastereomers having the -P(O)(OH)-CH(2)- moiety embedded into the peptide backbone. With identical selectivity, the separation efficiency of CABCE proved to be as good as classical CE for the insect oostatic peptides and better for diastereomers of the phosphinic pseudopeptides. In addition, despite the numerous species present in the narrow pH cuts of carrier ampholytes, CABCE seems to be free of system zones that could hamper the analysis. Peak symmetry was good for moderately to low mobile peptides, whereas some peak distortion due to electromigration dispersion, was observed for short peptides of rather high mobility.     

Evaluation of sieving matrices used to separate alleles by cycling temperature capillary electrophoresis

Denaturing CE (DCE) is a powerful tool for analysis of DNA variation. The development of commercial multi-CE instruments allows large-scale studies of DNA variation (many samples and many fragments). However, the cost of consumables like capillary arrays and sieving matrix might limit the use of DCE in such studies. Thus, we have tested 72 different in-house formulated sieving matrices' ability to suppress EOF and separate PCR-amplified alleles with the DCE variant, cycling temperature CE (CTCE). The data herein demonstrate that alleles can be baseline-separated by use of PVP and poly(N,N-dimethyl acrylamide) polymers at various percentages and pH. Allele separation by CTCE is matrix-independent and consequently applicable to any capillary instrument used for DNA separation. Formulation of sieving matrix for CTCE was done by dissolving appropriate amount of polymer powder into the running buffers. Allele separation was observed at different pH (7.5-8.5), concentrations and molecular size of the polymer, without compromising the separation and reproducibility. Finally, the cost reduction of homemade matrices is more than 1000-fold as compared to commercial sieving matrices.     

Separation and quantification of viral double-stranded RNA fragments by capillary electrophoresis in hydroxyethylcellulose polymer solutions

Capillary electrophoresis (CE) is an analytical technique widely utilized to resolve complex mixtures of nucleic acids. CE uses a variety of polymers in solution that act as a molecular sieve to separate nucleic acid fragments according to size. It has been shown previously that purified dsDNA can be resolved efficiently by solutions of hydroxyethylcellulose (HEC) polymer, providing a rapid and high resolution method of separation. We have applied this separation technique to viral double-stranded (ds) RNA segments derived from rotavirus process samples. HEC polymers of various molecular masses and concentrations were identified and compared for their ability to separate dsRNA based on the extent of expected polymer network formation. The HEC polymer exhibiting the most desirable separation characteristics was then used for subsequent optimization of various method parameters, such as, injection time, electric field strength, dye concentration and capillary equilibration. The optimized method was then applied to the quantification of genome concentration based on a representative segment of the rotavirus genome. This study demonstrated that purified viral dsRNA material of known concentration could be used to generate an external standard curve relating concentration to peak area. This standard curve was used to determine the concentration of unknown samples by interpolation. This novel RNA quantification assay is likely to be applicable to other types of virus, including those containing dsDNA.     

Nanomaterials and chip-based nanostructures for capillary electrophoretic separations of DNA

Capillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) using polymer solutions are two of the most powerful techniques for the analysis of DNA. Problems, such as the difficulty of filling polymer solution to small separation channels, recovering DNA, and narrow separation size ranges, have put a pressure on developing new techniques for DNA analysis. In this review, we deal with DNA separation using chip-based nanostructures and nanomaterials in CE and MCE. On the basis of the dependence of the mobility of DNA molecules on the size and shape of nanostructures, several unique chip-based devices have been developed for the separation of DNA, particularly for long DNA molecules. Unlike conventional CE and MCE methods, sieving matrices are not required when using nanostructures. Filling extremely low-viscosity nanomaterials in the presence and absence of polymer solutions to small separation channels is an alternative for the separations of DNA from several base pairs (bp) to tens kbp. The advantages and shortages of the use of nanostructured devices and nanomaterials for DNA separation are carefully addressed with respect to speed, resolution, reproducibility, costs, and operation.     

Protein polymer drag-tags for DNA separations by end-labeled free-solution electrophoresis

We demonstrate the feasibility of end-labeled free-solution electrophoresis (ELFSE) separation of DNA using genetically engineered protein polymers as drag-tags. Protein polymers are promising candidates for ELFSE drag-tags because their sequences and lengths are controllable not only to generate monodisperse polymers with high frictional drag, but also to meet other drag-tag requirements for high-resolution separations by microchannel electrophoresis. A series of repetitive polypeptides was designed, expressed in Escherichia coli, and purified. By performing an end-on conjugation of the protein polymers to a fluorescently labeled DNA oligomer (22 bases) and analyzing the electrophoretic mobilities of the conjugate molecules by free-solution capillary electrophoresis (CE), effects of the size and charge of the protein polymer drag-tags were investigated. In addition, the electrophoretic behavior of bioconjugates comprising relatively long DNA fragments (108 and 208 bases) and attached to uncharged drag-tags was observed, by conjugating fluorescently labeled polymerase chain reaction (PCR) products to charge-neutral protein polymers, and analyzing via CE. We calculated the amount of friction generated by the various drag-tags, and estimated the potential read-lengths that could be obtained if these drag-tags were used for DNA sequencing in our current system. The results of these studies indicate that larger and uncharged drag-tags will have the best DNA-resolving capability for ELFSE separations, and that theoretically, up to 233 DNA bases could be sequenced using one of the protein polymer drag-tags we produced, which is electrostatically neutral with a chain length of 337 amino acids. We also show that denatured (unfolded) polypeptide chains impose much greater frictional drag per unit molecular weight than folded proteins, such as streptavidin, which has been used as a drag-tag before.     

Poly(trialkoxysilyltricyclononenes): A New Type of Polymers for Membrane Gas Separation

New metathesis and addition polymers containing Si–O–C groups were synthesized from 3-tri(n-propoxy) silyltricyclo[4.2.1.0^2.5]non-7-ene. It was shown for the first time that metathesis polymer was more permeable than the addition polymer. The prepared polymers showed high selectivity in the butane/methane separation controlled by solubility; therefore, they are promising for membrane separation of hydrocarbon mixtures.