Oligonucleotide analysis by capillary polymer sieving electrophoresis using acryloylaminoethoxyethanol-coated capillaries

Characterization of the Interaction of Polymeric Micelles with siRNA: A Combined Experimental and Molecular Dynamics Study

The simulation of large molecular systems remains a daunting challenge, which justifies the exploration of novel methodologies to keep computers as an ideal companion tool for everyday laboratory work. Whole micelles, bigger than 20 nm in size, formed by the self-assembly of hundreds of copolymers containing more than 50 repeating units, have until now rarely been simulated, due to a lack of computational power. Therefore, a flexible amphiphilic triblock copolymer (mPEG45-α-PLL10-PLA25) containing a total of 80 repeating units, has been emulated and synthesized to embody compactified nanoconstructs of over 900 assembled copolymers, sized between 80 and 100 nm, for siRNA complexing purposes. In this study, the tailored triblock copolymers containing a controlled number of amino groups, were used as a support model to address the binding behavior of STAT3-siRNA, in the formation of micelleplexes. Since increasingly complex drug delivery systems require an ever more optimized physicochemical characterization, a converging description has been implemented by a combination of experimentation and computational simulations. The computational data were advantageous in allowing for the assumption of an optimal N/P ratio favoring both conformational rigidifications of STAT3-siRNA with low competitive phenomena at the binding sites of the micellar carriers. These calculations were consistent with the experimental data showing that an N/P ratio of 1.5 resulted in a sufficient amount of complexed STAT3-siRNA with an electrical potential at the slipping plane of the nanopharmaceuticals, close to the charge neutralization.

Determination of the isoelectric point of proteins by capillary isoelectric focusing

Different ways of determining isoelectric points (pI) of proteins in capillary isoelectric focusing are reviewed here. Due to the impossibility of direct pH measurements in the liquid phase, such assessments have to rely on the use of pI markers. Different types of pI markers have been described: dyes, fluorescently labelled peptides, sets of proteins of known pI values. It appears that, perhaps, the best system is a set of 16 synthetic peptides, trimers to hexamers, made to contain each a Trp residue for easy detection at 280 nm. By a careful blend of acidic (Asp, Glu), mildly basic, with pK around neutrality (His), and basic (Lys, Arg) amino acids, it is possible to obtain a series of pI markers with pI values quite evenly distributed along the pH scale, possessing good buffering capacity and conductivity around their pI values and thus focusing as sharp peaks. Another approach to pI determination is the monitoring of the current during mobilization: this allows, with the aid of known pI markers, to calibrate the system with a pI/current graph. Pitfalls and common errors in pI determinations are reviewed here and guidelines given for minimizing such errors in pI estimation.

Polymer wall coatings for capillary electrophoresis

This review article describes the preparation of dynamic and static polymeric wall coatings for capillary electrophoresis. Properties of bare fused-silica surfaces and methods for the characterization of capillary coatings are summarized. The preparation and basic properties of neutral and charged wall coatings are considered. Finally, advantages and potential applications of various coatings are discussed.

Capillary electrophoresis analysis of orange juice pectinesterases

Pectinesterase (PE) was extracted from orange juice and pulp with 1 M NaCl, desalted, and separated using capillary electrophoresis (CE) gel procedures (CE-SDS-CGE) and isoelectric focusing (CE-IEF). PE resolved as a single peak using noncoated fused silica columns with CE-SDS-CGE. CE-IEF separation of PE required acryloylaminoethoxyethanol-coated columns, which had limited stability. Thermal stability of PE extracts before and after heating at 75 degrees C for 30 min and at 95 degrees C for 5 min established heat labile and heat stabile fractions with identical PE migration times by CE-SDS-CGE or CE-IEF. Peak magnitude decreased to a constant value as heating time increased at 75 degrees C. Regression analysis of CE-SDS-CGE peak migration times of molecular weight (MW) standards estimated both heat labile and heat stable PE at MW approximately 36 900. Traditional SDS-PAGE gel separation of MW standards and active PE isolated by IEF allowed estimation of MW approximately 36 000. CE-SDS-CGE allowed presumptive, but not quantitative, detection of active PE in fresh juice.

Detection of a mixed-backbone oligonucleotide (GEM 231) in liver and tumor tissues by capillary electrophoresis

A simple, rapid and sensitive method has been developed and validated for the analysis of a mixed-backbone oligonucleotide (GEM 231) in tumor tissues. The analysis was performed using a capillary electrophoresis (CE) system with UV detection. An extended light path (bubble cell) capillary column of 64.5 cm (effective length 56 cm) x 50 microm I.D. is used as the separation column. The optimized chromatographic conditions were background electrolyte: sodium borate buffer (60 mM, pH 9.1), electrokinetic injection: 10 s, applied voltage: 30 kV, detection at lambda = 210 nm. A linear relationship was observed between the peak area and the amount of GEM 231 in the range of 1.0-1000 microg/ml. The lower detection limit of the drug was 100 pg with an average recovery of about 75 +/- 5%. The inter-day and intra-day relative standard deviations were <10%. Assay validation studies revealed that CE method is reproducible and specific for the determination of GEM 231 in tissue homogenates with a run time of less than 5 min.

Moderation of the electroosmotic flow in capillary electrophoresis by chemical modification of the capillary surface with tentacle-like oligourethanes

The surface chemistry of the inner wall of fused-silica capillaries is one important means to control the magnitude as well as the direction of the electroosmotic flow and the adsorption activity. A method was developed to change the surface characteristics of fused-silica capillaries by binding tentacle-like oligourethane groups onto the inner surface. The electroosmotic flow at a buffer pH of 6-9 was reduced by 15 to 40% compared to that in a bare fused-silica tubing, dependent on the type of coating. Sample adsorption is diminished at the same time resulting in a separation of proteins with higher resolution and good migration time precision. At a pH below 4.5 the electroosmotic flow is reversed into the anodic direction, which offers further possibilities for the separation of positively charged analytes as demonstrated for the separation of aromatic and biogenic amines.

Applications of capillary electrophoresis in biotechnology

Capillary electrophoresis (CE)-related techniques are increasingly being used as a matter of routine practice in the biotechnology discipline. Since recombinant DNA-derived proteins and the antisense oligonucleotides constitute a large portion of the applications of these techniques, they have been emphasized in this review. Analyses by CE of Escherichia coli-derived proteins and glycosylated proteins derived from mammalian cell cultures are summarized, as well as those of the carbohydrate chains that have been enzymatically removed from the protein. Applications of CE in the analysis of the antisense oligonucleotides for the determination of purity and the analytical studies on the metabolism of these modified oligonucleotides, by CE are reviewed. The literature mainly covers the period from 1996.

Application of capillary nongel sieving electrophoresis for gene analysis

Capillary electrophoresis (CE) has proved to be a strong tool for DNA analysis and has found abundant applications in the fields of restriction fragment sizing, mutation screening, polymerase chain reaction (PCR) product characterizing and forensic identifying. CE may be the main alternative to slab gel electrophoresis. Capillary nongel electrophoresis is the most favorable mode when aiming for this purpose because of its advantages of long lifetime, easy operation, good reproducibility, and low expense. In this paper, a new kind of sieving matrix, with mannitol as the additive for capillary electrophoresis, as well as related methods and their application for gene analysis were reported. Nine DNA fragments amplified by multiplex PCR from a normal dystrophin gene were well separated by this system. Three different deletions were found in Duchenne muscular dystrophy (DMD) patients. Three to four copies of the sex-determination region of the Y chromosome (SRY) gene, as well as the phenylalanine hydroxylase (PAH) gene, could be detected in mixed samples. The frequencies of short tandem repeats (STR) in PAH genes was analyzed in 61 normal Chinese individuals and 6 phenylketonuria families. One case of prenatal gene diagnosis was performed. By using this matrix, CE coupled with reverse transcription PCR (RT-PCR), the analysis of the alternative splicing expression pattern of the fragile X mental retardation 1 (FMR1) gene in adult lung tissue was achieved.

Electrophoretic separation of small DNA fragments in the presence of electroosmotic flow using poly(ethylene oxide) solutions

A new and simple method was demonstrated for separating phi X-174/Hae III DNA restriction fragments and DNA markers V and VI, respectively, without filling capillaries with polymer solutions prior to analysis. Using this novel method, poly(ethylene oxide) (PEO) solutions containing ethidium bromide migrated into capillaries by electroosmotic flow (EOF) during the separation. Two DNA fragments (123 and 124 bp) in markers V and VI were well-resolved. RSD values for the separation of phi X-174/Hae III DNA restriction fragments were less than 0.52% for 3 runs using a single 75-micron capillary and less than 3.96% using three different 75-micron capillaries. A highly viscous polymer solution prepared from 3% PEO was also used for separation of DNA markers V and VI. Theoretical plates up to 11.91 million/m and separation times of less than 7 min were achieved in the separation of phi X-174/Hae III DNA restriction fragments using a 10-micron capillary and a 2% PEO solution. Advantages of this method include simplicity, short separation times, the ability to use highly viscous polymer solutions for separating small DNA fragments, and the possibility of introducing several different polymer solutions into capillaries to extend the DNA separation range.

Capillary electrophoretic analysis of synthetic short-chain oligoribonucleotides

Thirty synthetic oligoribonucleotides, 3 to 18 nucleotides (nt) long, were analyzed by capillary electrophoresis, under nondenaturing conditions, using a commercial kit. The migration time t(m) was dependent on nt length and composition, capillary length, operating temperature, and type of sieving polymer. Under fixed experimental conditions, the t(m) proved predictable by the equation: t(m) = [0.22(n-1) + 6.14A/n + 6.86G/n + 3.61 (C+U)/n] min, for n>3, where A/n, G/n, C/n, U/n is the frequency of each type of nt within the oligonucleotide (ONT). The equation accounts for the influence of charge-to-mass ratio on t(m), but not for structural effects, if present. This approximation is acceptable for short ONTs. The possibility of detecting n+1, n-1, n-2 impurities, having predicted the t(m), is of crucial importance in assessing the purity of synthetic ONTs dedicated to structural studies. This appears to be feasible. High resolution was shown among homologous series of ONTs of increasing length, and in some cases, even within groups of ONTs of the same length but different composition. The addition of 7 M urea to the buffer, as denaturing agent, accelerates the t(m) and significantly lowers the resolution for the shortest ONTs. It was also possible to monitor the state of association of mixtures of RNA and DNA sequence-complementary strands.

Study of phosphorothioate-modified oligonucleotide resistance to 3'-exonuclease using capillary electrophoresis

The effect of phosphorothioate (PS) internucleotide linkages on the stability of phosphodiester oligodeoxyribonucleotides (ODNs) was investigated using 25-mer ODNs containing single or multiple PS backbone modifications. The in vitro stability of the oligomers was measured both in 3'-exonuclease solution and in plasma. For the separation of ODNs, capillary electrophoresis with a replaceable polymer separation matrix was used. As expected, DNA fragments with PS linkages at the 3'-end were found to be more resistant to 3'-exonuclease hydrolysis. Also increasing exonuclease resistance was the non-specific adsorption of phosphorothioate ODNs to enzyme.

Interfacing of CE in a PVP matrix to ion trap mass spectrometry: analysis of isomeric and structurally related (N-acetylamino)fluorene-modified oligonucleotides

This work demonstrates the interfacing of capillary electrophoresis in a poly(N-vinylpyrrolidone) (PVP) solution to electrospray ionization ion trap mass spectrometry (ESI-ITMS). This methodology was used for on-line analysis of modified and unmodified oligonucleotides. Oligonucleotides were covalently modified using the model carcinogen 2-(N-acetoxy-N-acetylamino)fluorene. In the presence of PVP, separation was achieved for a set of isomeric (N-acetylamino)fluorene (AAF)-modified oligonucleotides differing only in their base sequences, while open-tube control experiments showed no separation between these compounds. The resolved analytes were identified by ESI-ITMS with negative ion detection. Online acquisition of MS and MS/MS data allowed unambiguous identification of all structural isomers. Baseline separation was also accomplished for a 10-compound mixture containing a series of five nonisomeric AAF-modified oligonucleotides and their unmodified parent oligonucleotides.

Preconcentration and separation of antisense oligonucleotides by on-column isotachophoresis and capillary electrophoresis in polymer-filled capillaries

Small, single-stranded, chemically modified oligonucleotides, complementary to a specific gene section, commonly referred to as antisense compounds, are being investigated as potential therapeutic drugs. A number of modified oligonucleotides, in particular phosphorothioates, are in clinical development. Shorter fragments are found as metabolic products. Isotachophoresis (ITP) allows the introduction of large, diluted sample plugs into the separation capillary. In this work, ITP and capillary electrophoresis (CE) in polymer solutions were successfully coupled in a single capillary in a commercial instrument to increase sensitivity with UV detection and to shorten the time for sample pretreatment. It was shown that ITP-CE can be used as a preconcentration and clean-up method for phosphodiester- and phosphorothioate-containing samples. Up to 3 microL sample could be injected into the capillary without significantly disturbing the separation performance. ITP-CE of phosphodiesters directly out of salt- and protein-containing samples could be demonstrated. For phosphorothioates in serum samples an additional sample clean-up was necessary, due to oligonucleotide-protein binding. An optimized replaceable polymer solution was developed to increase the separation performance for heterogeneous phosphorothioates. A dextran-based sieving medium showed a good separation performance in ITP-CE of phosphorothioates. A concentration detection limit of 8.10(-9) mol/L for the 20-mer phosphorothioate ISIS5132, isolated from rat serum, was found.

Application of capillary electrophoresis to the measurement of oligonucleotide concentration and purity over a wide dynamic range

Synthetic oligonucleotides rarely contain 100% of the full-length sequence due, in part, to the failure sequences produced during synthesis. In this paper, a method is described for the determination of both the concentration and the purity of oligonucleotides, utilizing capillary electrophoresis with a deoxyribo-nucleoside triphosphate as an internal standard. This method is advantageous for several reasons: (a) the wide dynamic range allows for the analysis of samples without the need for dilutions; (b) a small sample size is used for analysis; (c) capillary electrophoresis is automatable which allows for high throughput; and (d) all of the samples are analyzed at the same run temperature which aids in reproducibility and consistency between runs performed at different times.

Capillary isoelectric focusing

Capillary isoelectric focusing (CIEF) provides excellent resolution of proteins with the advantage that separations are carried out in a capillary format with on-tube detection and automated analysis. Recent advances in the technique provide improved resolution, reproducibility and reliability. This review summarizes improvements in sample preparation, capillary selection, and focusing and zone mobilization procedures which have helped CIEF become a more robust analytical method. New applications are reviewed, in particular the use of CIEF in analysis of biopharmaceutical products.