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At least 811 records · Page 45Linked to original sources
PubMed1991

Analysis of limiting factors of DNA band separation by a DNA sequencer using fluorescence detection.

The factors affecting the electrophoretic separation of DNA bands in DNA base sequencing using fluorescence detection are analyzed. All the factors contributing to DNA band spacing and band width are evaluated; DNA diffusion and thermal effects on gels are the main considerations. The dependence of the gel's electrical resistivity on gel temperature and the variation of temperature over gel thickness are associated with a broadening of DNA band width. As a result of the analyses the maximum separable base number is represented as a function of various electrophoretic variables. The best separations are possible with an electric field strength corresponding to gel thickness. The maximum separable base number increases as the gel thickness decreases. It also increases as the migration distance increases, but it becomes saturated and has an upper limit when the migration distance is long. This upper limit increases as gel thickness decreases. DNA fragments with 600 and 601 bases can be completely separated from each other under optimum conditions for a 0.2 mm thick gel plate. Furthermore, using the band spacing information, under the same conditions, 750 bases could be assigned separately.

Base Sequence↗
PubMedDate not supplied

Two-dimensional separations of peptides and proteins by comprehensive liquid chromatography-capillary electrophoresis.

Analysis of biological samples is problematic because of their complex composition. Reversed phase liquid chromatography (RPLC), size exclusion chromatography (SEC), and, more recently, capillary zone electrophoresis (CZE) are routinely used for the analysis of these samples, but are eventually limited because they are one-dimensional (1-D) methods. As sample complexity increases, the separation efficiency necessary to resolve a large number of sample components in one dimension becomes prohibitively high. A solution to this problem has been to use a two-dimensional (2-D) approach. Each dimension in a 2-D separation relies on a different separating mechanism. By expanding the separation into two dimensions, sample components unresolved in the first dimension can often be separated in the second. This circumvents the requirement for extremely high efficiencies in either dimension. Two-dimensional slab gel electrophoresis has been used successfully in this area, but a more instrumental approach is desired. In this paper we describe three coupled-column approaches to 2-D separations. First, microcolumn SEC-CZE is explored as a means of 2-D protein analysis. Next, RPLC-CZE is investigated for analysis of peptides in tryptic maps. Finally, RPLC is coupled with fast CZE (FCZE), a unique form of CZE analysis, for fast 2-D analysis of peptides. Details of the instrumentation used in these 2-D systems will be presented along with the results of some typical 2-D analyses.

Chromatography, Gel↗
PubMed1994

Size-dependent separation of proteins in the presence of sodium dodecyl sulfate and dextran in capillary electrophoresis: effect of molecular weight of dextran.

Dextran solutions are widely used as sieving medium in protein analysis by capillary electrophoresis in the presence of sodium dodecyl sulfate. We studied the effect of dextran molecular weight on the separation efficiency using different dextran preparations with wide and very narrow molecular weight distributions, in the range between 1270 and 2,000,000. Migration times and band broadening of proteins were significantly affected by the molecular weight of dextran. Migration times of proteins decreased as molecular weights of the dextrans decreased. Satisfactory separation of all the proteins was possible with all dextrans except those with molecular weights of 70,000 and 23,800 where bovine serum albumin and phosphorylase b failed to be separated. Unexpectedly rapid separation of all the proteins with enhanced resolution could be observed using two dextrans with a narrow molecular weight distribution, with molecular weights of 1270 and 5220. Clearly the use of dextran with higher molecular weight is not the only way to achieve efficient separation of proteins. The separation mechanism in the presence of the low molecular weight dextrans remains to be made clear in a future study.

Carbonic Anhydrases↗
PubMed1995

Electrophoretic size separation of proteins treated with sodium dodecyl sulfate in 1% agarose gels.

Separation of proteins treated with sodium dodecyl sulfate (SDS) according to molecular size was achieved by discontinuous electrophoresis in vertical low-concentration agarose gels. A linear relationship was found between the migration distance and the square root of the molecular weight. This holds for proteins in the range of 7-200 kDa separated in 1.25% w/v agarose gel slabs (7 x 7 x 0.15 cm) with 0.1% w/v SDS and sulfate as leading ion. The linear regression coefficient was 0.998. The molecular weight and charge of coions influenced the separation. Small ions with low pKa values were found suitable as coions. The migration distance of proteins treated with SDS varied linearly with the agarose concentration of the gel. The agarose type and quality affected the resolution of the SDS-protein bands. We conclude that agarose gels can substitute polyacrylamide gels for the separation of proteins treated with SDS. A homogeneous agarose gel at a concentration of about 1% is a nonsieving support for electrophoresis. Therefore, the separation described here cannot be explained by the pore size of the gel. The results suggest that the separation is mainly due to the relative migration velocities of the coion and the proteins treated with SDS.

Blood Proteins↗
PubMed1995

Novel separation scheme for capillary electrophoresis of enantiomers.

A systematic approach is described for methods development of chiral separations of weak acidic and basic compounds by capillary electrophoresis, using several natural and derivatized neutral cyclodextrins as chiral selectors. Following the methods development scheme suggested here, the appropriate pH of the running buffer as well as the type and concentration of the cyclodextrin is established for the separation of enantiomers. Preselected chiral selectors of beta-cyclodextrin, gamma-cyclodextrin, hydroxypropyl-beta-cyclodextrin and dimethyl-beta-cyclodextrin in low and high concentrations, dissolved in low pH, high pH or pH = pK buffers, are employed during the separation method development and optimization. Depending on the type of separation, introduced by Vigh (desionoselective: only the nondissociated; ionoselective: only the dissociated; duo-selective: both enantiomers complex selectively), in most instances at least one of the pH/cyclodextrin combinations results in acceptable separation of the solute enantiomers. The viability of the approach is demonstrated through step by step development of chiral separation for several basic and acidic enantiomers.

Aspartic Acid↗
PubMed1995

Theory of zone separation in isotachophoresis: a diffusional approach.

The qualitative characteristics of isotachophoresis differ substantially from "classical" separation methods such as chromatography or zone electrophoresis. Self-sharpening zone boundaries and step-like concentration profiles are the most specific features of this method, which does not allow the description of the isotachophoretic separation in usual "chromatographic" terms, such as resolution or number of theoretical plates. A theory is presented in this paper, combining the usual isotachophoretic separation characteristics with the theory of isotachoporetic zone boundary, which is the only element of the isotachophoretic system with dispersional properties. This allows us to consider situations near the limits of the isotachophoretic method as far as both selectivity and sample amount (i.e., zone size) are concerned. Based on a simplified expression of the concentration profiles across the isotachophoretic zone boundary, separation and separation limits are described and discussed in terms of resolution, selectivity and zone capacity. Equations are derived showing the relationships between resolution, boundary width, selectivity, sample amount, and column and electrolyte conditions. A simple phenomenological equation is presented, expressing isotachophoretic resolution as a function of only sample amount (or sample zone length) and boundary width. A thermodynamic form of this equation is derived, which is shown to be similar to such an expression for resolution in zone electrophoresis. In both cases resolution is a function of sample selectivity, electric field strength and column length. A simple theoretical model for zone capacity is presented, making it possible to estimate the separation performance of isotachophoretic systems. Based on the presented theory, parallels between isotachophoresis and zone electrophoresis are discussed and both methods are compared.

Diffusion↗
PubMed1995

Performance of amino-silylated fused-silica capillaries for the separation of enkephalin-related peptides by capillary zone electrophoresis and micellar electrokinetic chromatography.

Enkephalin-related peptides were separated at low pH in a capillary with covalently bonded aminopropyl groups. The peptides are electrostatically repelled from the capillary surface and much higher efficiencies and faster separations were achieved compared to separations using uncoated capillaries. At low pH the amino groups are protonated, which results in reversed electroosmosis. The influence of voltage and ionic strength on the mobility and the separation efficiency was studied. The repeatability of migration times within one day was very good with relative standard deviations of 0.3-0.7%. Increasing the pH decreased the electroosmosis, eventually turning towards the cathode in the pH range 5-6; the separation performance, however, was lower at higher pH. Neutral and anionic micellar agents were added to the background electrolyte at different concentrations; the enkephalins had weak association with the neutral micellar agents but were distributed to the anionic taurodeoxycholic acid (TDC) micelles, giving rise to changes in separation selectivities. Very high efficiencies were obtained for peptides with a low distribution to the TDC micelles, while the efficiencies were impaired for those with a strong association with the micelles, which may indicate a slow mass transfer in the association process.

Amino Acid Sequence↗
PubMed1996

The influence of buffer composition on separation efficiency and resolution in capillary electrophoresis of 8-aminonaphthalene-1,3,6-trisulfonic acid labeled monosaccharides and complex carbohydrates.

The effect of buffer conditions -- varying in salt type, pH, and concentration -- on the separation of 8-aminonaphthalene-1,3,6-trisulfonic acid (ANTS)-labeled monosaccharides and complex-type carbohydrates was investigated. Different buffer systems for high and low electroosmotic flow conditions were chosen: a phosphate and a citrate background electrolyte, each at pH 2.5, a phosphate buffer, pH 9.0, and a borate buffer at pH 9.5. All buffer systems displayed differences in resolution and selectivity. Phosphate and borate buffer demonstrated the greatest selectivity changes for ANTS-labeled carbohydrates. While separation in the phosphate system relies mainly on differences in the charge-to-mass-ratio, additional selectivity can be achieved with borate complexation of glycoconjugates. The use of borate buffers improved monosaccharide separations whereas complex carbohydrates showed a loss in resolution. The citrate background electrolyte at low pH caused no significant changes in the separation performance. The pH 9.0 phosphate buffer showed a reversed migration order of the ANTS conjugates with a decreased resolution, compared to the pH 2.5 phosphate buffer, due to the strong electroosmotic flow generated under high pH conditions. An ovalbumin-derived oligosaccharide library demonstrates the significance of buffer selectivity for complex carbohydrate separations. The separation in the acidic phosphate and the alkaline borate buffer generates a different pattern and only the combination of both buffer systems allows an appropriate assessment of sample complexity.

Acids↗
PubMed1996

Separation of 1-aminopyrene-3,6,8-trisulfonate-labeled asparagine-linked fetuin glycans by capillary gel electrophoresis.

Asparagine-linked glycans of bovine fetuin were separated by capillary gel electrophoresis after enzymatic release (peptide-N-glycosidase F) and labeling via reductive amination by a fluorescent dye, 1-aminopyrene-3,6-8-trisulfonate (APTS). At low separation pH (2.5) only two dominant peaks were observed. Increasing the separation buffer pH to 4.75 resulted in complete separation of two primary doublets and several minor peaks from the fetuin N-linked glycan pool. Two of the four major peaks were spiked with purified individual standards and were identified as trisialylated triantennary structures with different sialylation linkages. The other two larger peaks were postulated to be tetrasialylated triantennary structures, based on calculations considering their corresponding glucose unit (GU) values. Effects of the electrophoretic separation parameters, such as gel concentration, electric field strength and temperature on the migration behavior of the two major doublets of the fetuin glycan pool were also thoroughly examined. Our data suggest that the capillary gel electrophoresis separation of the multisialylated branched oligosaccharides with different linkage isomers, released from bovine fetuin, is fundamentally based on their degree of sialylation and hydrodynamic volumes.

Asparagine↗
PubMed1996

Electrokinetic chromatography in suppressed electroosmotic flow environment: use of a charged cyclodextrin for the separation of enantiomers and geometric isomers.

Electrokinetic chromatography (EKC), with negatively-charged cyclodextrins (NCDs) added to the buffer, was conducted in polyacrylamide-coated columns under suppression of electroosmotic flow. The equations of migration and resolution for neutral solutes in this mode of chromatography, which for brevity we term NCD-EKC, are presented. The chiral sulfated cyclodextrin, beta-CD-SBE (IV), used in this study is anionic over the entire pH range accessible to capillary electrophoresis, and the coated columns are stable and provide reproducible performance in the pH range 2.5-8.8. Optimum separation was obtained in the pH range where the solutes are neutral. The incorporation of an alkyl spacer between the sulfate ion and the rim of the cyclodextrin allows an unhindered approach and inclusion of neutral solutes in the cyclodextrin cavity. Solute migration time is inversely proportional to the concentration of the chiral selector. Separation (relative migration time difference) increases with decreasing chiral selector concentration and approaches a maximum, beyond which further decreases in chiral selector concentration result in broad peaks and loss of resolution. A chiral selector concentration of 1% in a 10 mM phosphate buffer produced excellent separation of amino acids and dipeptide enantiomers. In addition to being chiral selectors, cyclodextrins are also known as shape selectors. NCD-EKC is particularly suited for the separation of positional isomers of hydrophobic solutes. The separation of aflatoxin isomers and chlorophenol congeners is presented. In the separation of chlorophenols the more hydrophobic trichlorophenols eluted first and the least hydrophobic, phenol, eluted last.

Amino Acids↗
PubMed1997

Chiral separation of DL-peptides and enantioselective interactions between teicoplanin and D-peptides in capillary electrophoresis.

Teicoplanin has been evaluated as a selector for enantioseparation of di- and tripeptide derivatives in capillary electrophoresis. Separation variables such as type of buffer, pH, concentrations of teicoplanin and organic modifier were examined. Optimal separation conditions were obtained by means of factorial design experiments. The effects of teicoplanin concentrations below and above its critical micellar concentration (CMC) and of acetonitrile (ACN) on the separation were demonstrated. The use of a high concentration of ACN resulted not only in increased selectivity, but also in improved separation efficiency. Electroosmotic flow was observed to be largely independent of the concentrations of teicoplanin under the optimized conditions. Good repeatability of migration times was obtained. The interactions between teicoplanin and D and L peptides were studied, and it was found that, for some peptides, teicoplanin exhibited enantioselective interaction only with the D-form. Somewhat lower separation efficiencies were thus observed for the strongest interacting (D-form) peptides. Chiral separation of 15 DL-peptide derivatives was achieved in less than 10 min.

Adsorption↗
PubMed1998

Capillary sample introduction of polymerase chain reaction (PCR) products separated in ultrathin slab gels.

Polymerase chain reaction (PCR) amplified short tandem repeat (STR) samples from the HUMVWF locus have been analyzed using a unique sample introduction and separation technique. A single capillary is used to transfer samples onto an ultrathin slab gel (57 microm thin). This ultrathin nondenaturing polyacrylamide gel is used to separate the amplified fragments, and laser-induced fluorescence with ethidium bromide is used for detection. The feasibility of performing STR analysis using this system has been investigated by examining the reproducibility for repeated samples. Reproducibility is examined by comparing the migration of the 14 and 17 HUMVWF alleles on three consecutive separations on the ultrathin slab gel. Using one locus, separations match in migration time with the two alleles 42 s apart for each of the three consecutive separations. This technique shows potential to increase sample throughput in STR analysis techniques although separation resolution still needs to be improved.

Acrylamide↗
PubMed1998

Sequencing using capillary electrophoresis of short tandem repeat alleles separated and purified by high performance liquid chromatography.

Polymerase chain reaction (PCR) amplified alleles need to be isolated and purified before carrying out additional analysis to confirm sequence, number of repeats and microvariants within a short tandem repeat (STR) locus. Also, PCR amplification of tetranucleotide repeat loci, used in DNA typing assays, often result in heteroduplex formation, adding to the complexity of analysis. Sequencing reactions require single specific target DNA for reliable sequencing analysis. Alkylated poly(styrene-divinylbenzene) columns at elevated temperature and gradient elution conditions increase the efficiency of separation to allow for the purification of PCR products. Using the separation technique of ion-pairing reverse-phase (IPRP) high performance liquid chromatography (HPLC), molecular biologists can separate and purify DNA fragments without alteration to the double-stranded DNA sequencing properties. In this study, the IP-RP chromatography technique has been demonstrated by separation of alleles of the short tandem repeat loci of TH01, vWA31, F13A01 and FES/ FPS. Alleles differing in size range of 12 to 4 base pairs were separated by IPRP/HPLC and individual alleles were peak-captured, then cycle-sequenced. These HPLC fractions required no additional steps prior to cycle sequencing. Capillary electrophoresis (CE) was used to sequence the alleles. Furthermore, CE offers advantages over traditional slab methods via automation and higher applied voltages. Interestingly, unlike traditional gel electrophoresis, samples were introduced into the sieving matrix by electrokinetic injection, which allows for multiple injections from a single sample, a key feature for method development. Applied voltage was 320 V per centimeter using a nonderivatized fused silica capillary with an interior diameter of 50 microm and a total length of 47 centimeters. The total analysis time including capillary filling and pre-electrophoresis was less than 30 min for a 220-bp fragment. A sequencing rate of 530 bp/h was achieved using these conditions. By combining the techniques of HPLC separation and CE sequencing, the results confirmed the sequence and number of nucleotide repeats for each STR loci. An average sequencing efficiency of 97% was achieved. Additionally, this method defined the absence of a 9.3 microvariant for a TH01 heterozygous individual previously typed as a 9, 9.3/10 using slab gel electrophoresis. The techniques described can be applied to other DNA purification and isolation problems.

Alleles↗
PubMed1998

Enantiomeric separation of methadone by cyclodextrin-based capillary and recycling isotachophoresis.

The separation of methadone enantiomers by cationic capillary isotachophoresis (CITP) and recycling isotachophoresis (RITP) having (2-hydroxypropyl)-beta-cyclodextrin (OHP-beta-CD) as chiral selector in the leading electrolyte is described. Sodium acetate/acetic acid (pH between 4 and 5) served as leading electrolyte (catholyte) and acetic acid as terminator (anolyte). Complete separation of the enantiomers was obtained by CITP in a 50 microm internal diameter (ID) fused-silica capillary and in a 500 microm ID Teflon capillary. In the first approach, enantiomeric separation could be monitored via UV absorbance detection at low wavelength. With the second instrumental setup, an additional conductivity sensor permitted the visualization of the enantiomeric separation and the characterization of the buffer system employed. A 10 mM sodium acetate/acetic acid leading buffer of pH 4.3, containing 5 mM OHP-beta-CD, was found to provide best enantiomeric separation and was thus chosen for RITP. With RITP processing of a few mg of racemic methadone, partial separation of methadone enantiomers was obtained. R-(-)-methadone and S-(+)-methadone were found to be significantly (up to about 80%) enriched at the front and back side, respectively, of the isotachophoretic zone. The enantiomeric composition of methadone in the collected fractions was assessed by chiral capillary zone electrophoresis (CZE) and circular dichroism spectroscopy. CZE was found to represent a simple and efficient method for the determination of the enantiomeric excess, whereas the latter technology was noted to be the superior approach for properly characterizing fractions that contain similar amounts of the two enantiomers. Furthermore, chiral RITP and analysis of the collected fractions by circular dichroism spectroscopy is shown to be potentially useful for identification of single enantiomers in absence of pure chiral standards.

Circular Dichroism↗
PubMed1998

The effect of blob size and network dynamics on the size-based separation of polystyrenesulfonates by capillary electrophoresis in the presence of entangled polymer solutions.

This work focuses on the separation of standard polystyrenesulfonates (PSS), with molecular masses (Mr) between 16 and 990 x 10(3) in capillaries filled with semidilute (entangled) linear hydrophilic polymers. Contrary to cross-linked chemical gels, which produce permanent networks, solutions of linear polymers lead to dynamic networks. The analytical performances and migration mechanisms are discussed on the basis of experiments performed in solutions of linear polyethyleneoxides and derivatized celluloses of various molecular masses. The influence of the mesh size and of the lifetime of the obstacles of the separating network has been investigated in detail. The mesh size is assimilated to the blob size of the separating polymer and is a decreasing function of its concentration. The lifetime of the obstacles of the network, identified with the reptation time of the polymer chain, characterizes its dynamics. This characteristic time increases with both the molecular weight of the separating polymer and its concentration. Its impact was first examined at fixed blob size. Then, the influence of the blob size was studied while keeping the reptation time of the network constant. By doing so, the existence of interactions between the solute and the separating polymer or between the solute and capillary wall can be more safely assessed. It appears that the reptation time of the mesh has a large influence on the electrophoretic mobility of the PSSs under a threshold value, which is of the order of magnitude of the time taken by the PSS to migrate on the blob size. Also shown are separations using networks made up with mixtures of polyethyleneoxides of the same nature and same mass concentration, but of very different molecular masses. This latter approach allows one to adapt the viscosity of the solution and the dynamics of the network, keeping the blob size constant.

Electrophoresis, Capillary↗
PubMed1998

Preparative separation of plasmid and bacterial artificial chromosome DNA by density gradient electrophoresis in the presence of linear polymers.

A density gradient apparatus was used to examine the separation of different physical forms and sizes of DNA. A gradient of sucrose was used to stabilize thermal convection during electrophoresis in the column (2.2 cm in diameter). Linear polymers were added to the density gradient and screened for their ability to separate the supercoiled, nicked circular, and linear forms of the plasmid pBR 322. The influence of different concentrations and molecular weights of the polymers was examined on the separation. Polyethylene oxide with a molecular weight of 5,000,000 and a concentration of 0.2% w/v achieved the best separation results for the different physical forms of the plasmid. The order of separation of the different physical forms of the plasmid were linear (fastest), supercoiled, and nicked circular (slowest). These conditions were also used to separate a preparation of bacterial artificial chromosome (BAC) DNA. A rapidly moving form, presumably the supercoiled form, was resolved from a large amount of E. coli genomic DNA and from sheared forms of the BAC DNA.

Cellulose↗
PubMed2003

Effects of organic solvents on sample pretreatment and separation performances in capillary electrophoresis.

A review of recent developments in theoretical as well as application studies concerning the use of organic solvents, either as purely nonaqueous solvents, hydro-organic mixtures, or a combination of an organic solvent with another organic modifier(s), in the sample matrix and/or separation buffer for effecting sample pretreatment and/or improving separation performances in capillary electrophoresis (CE) is presented. In particular, recent advances made in furthering the basic understanding of selectivity changes that occur in capillary zone electrophoresis due the presence of organic solvents in the separation medium, based on in-depth studies of fundamental processes, such as acid-base chemistry, ion-ion and ion-solvent interactions, were discussed in detail. The utilization of organic solvents for improving the resolution of highly challenging and important separations, i.e., those involving the separation of positional and optical isomers, was also critically reviewed. Furthermore, a comprehensive survey of the use of organic solvents for on-line sample pretreatment, e.g., minimizing aggregation and maximizing solubilization of hydrophobic analytes, improving concentration detection sensitivity for analytes via the use of sample stacking, was presented and discussed. Moreover, recent applications involving the use of organic solvents for improving the CE separations of a variety of molecular species with significance in various disciplines, including biological, environmental and pharmaceutical areas, were summarized and tabulated.

Electrophoresis, Capillary↗
PubMed2003

High-speed chiral separations on a microchip with UV detection.

Fast chiral separations of a variety of basic and acidic compounds could be realized on microfluidic quartz chips. A microchip electrophoresis instrument equipped with a linear imaging UV-detector was used. The usually applied but troublesome fluorescence tagging in order to enable fluorescence detection could be omitted. Using sulfated cyclodextrins as chiral selectors baseline separation of 19 compounds could be achieved in less than 1 min with high reproducibility. The relative standard deviation of migration time was below 7%. The fastest separation could be performed in 2.5 s which is to date the fastest separation of enantiomers reported. It was possible to apply microchip electrophoresis (MCE) for the determination of high enantiomeric excess (ee) values, as exemplarily shown for pseudoephedrin where 2% of the minor enantiomer could reliably be determined beside high amount of the other isomer. Successful separation of a mixture of 3 chiral drugs could be performed in a single run in less than 11 s utilizing a separation length of only 12 mm. These results show that MCE has great potential for fast chiral analysis and high-throughput screening.

Buffers↗