Mechanism of sequence-based separation of single-stranded DNA in capillary zone electrophoresis

Separation of DNA by length using CGE is a mature field. Separation of DNA by sequence, in contrast, is a more difficult problem. Existing techniques generally rely upon changes in intrinsic or induced differences in conformation. Previous work in our group showed that sets of ssDNA of the same length differing in sequence by as little as a single base could be separated by CZE using simple buffers at high ionic strength. Here, we explore the basis of the separation using circular dichroism spectroscopy, fluorescence anisotropy, and small angle X-ray scattering. The results reveal sequence-dependent differences among the same length strands, but the trends in the differences are not correlated to the migration order of the strands in the CZE separation. They also indicate that the separation is based on intrinsic differences among the strands that do not change with increasing ionic strength; rather, increasing ionic strength has a greater effect on electroosmotic mobility in the normal direction than on electrophoretic mobility of the strands in the reverse direction. This increases the migration time of the strands in the normal direction, allowing more time for the same-length strands to be teased apart based on very small differences in the intrinsic properties of the strands of different sequence. Regression analysis was used to model the intrinsic differences among DNA strands in order to gain insight into the relationship between mobility and sequence that underlies the separation.     

毛细管区带电泳法拆分手性药物环扁桃酯

近年来,随着不同种类的手性添加剂[1]在毛细管电泳(CZE)中的使用,毛细管电泳越来越显示出其强有力的手性拆分性能。具有特殊笼状结构并含有多个手性中心的环糊精及其衍生物是毛细电泳手性分离研究中最常采用的手性添加添[2-4]。本文合成了环糊精衍生物单3 O 苯基胺甲酰基 β CD[2]并以之作为手性选择剂分离了β CD及手性药物环扁桃酯。1　实验部分932 3 HVPS高压电源(山东省化工研究院),DD 2000型可调波长紫外检测器(中国科学院大连化学物理研究所),XWT型记录仪(上海大华仪表厂),pHS 25型酸度计(上海雷磁仪器厂),石英毛细管45cm…     

DNA fragment separations by on‐line combination of capillary isotachophoresis–capillary zone electrophoresis with UV detection

A high‐speed DNA fragment separation system based on an on‐line combination of capillary ITP with CZE (CITP‐CZE) and using UV detection at 260 nm was developed. A novel CITP‐CZE buffer system of pH 6.1 was designed for the separation of ten DNA fragments with sizes ranging from 100 to 1000 bp. An effect of underivatized α‐, β‐ and γ‐cyclodextrins on the resolution of DNA fragments in the CZE step of the CITP‐CZE combination was systematically investigated. Methylhydroxyethylcellulose present in the BGE was used to eliminate the EOF. DNA ladder fragments were separated within 10 min with LODs in the range of 1–5 ng/μL (S/N = 3). The RSDs of the migration time and peak area of individual DNA fragments were in the range of 1–3 and 3–9%, respectively. The developed CITP‐CZE system was further applied to the analysis of digest plasmid DNA samples.     

Size separation of silica nanospheres by means of capillary zone electrophoresis

The electrophoretic mobility of silica nanospheres was shown to be a function of separation conditions such as pH and phosphate concentration of a carrier electrolyte. The separation selectivity can be controlled by the separation conditions and optimised depending on the sample composition. The effects of pH and phosphate concentration of buffer solutions on the nanosphere electrophoretic mobility are explained using the Overbeek-Booth electrokinetic theory taking into account both electrophoretic retardation and the relaxation effect.     

Separation of single‐base sequential isomers of single‐stranded DNA by capillary electrophoresis and its application in the discrimination of single‐base DNA mutations

Separation of single‐base substitution sequential DNA isomers remains one of the most challenging tasks in DNA separation by capillary electrophoresis. We developed a simple, versatile capillary electrophoresis technique for the separation of single‐base sequential isomers of DNA having the same chain length. This technique is based on charge differences resulting from the different protonation (acid dissociation) properties of the four DNA bases. A mixture of 13 single‐base sequential isomers of 12‐mer single‐stranded DNA was separated by using an electrophoretic buffer solution containing 20 mM phosphoric acid (pH 2.0) and 8 M urea. We demonstrated that our method could separate all possible mutation patterns under identical experimental conditions. In addition, application of our method to the separation of the polymerase chain reaction product of a 68‐mer gene fragment and its single‐base isomers indicates that in combination with the appropriate genomic DNA extraction techniques, the method can detect single‐base gene mutations.     

Isotopic separation of lithium ions by capillary zone electrophoresis

Separation of ⁶Li and ⁷Li isotopes by CZE was demonstrated. The BGE contained 5 mM 4‐aminopyridine, 0.9 mM oxalic acid, 0.25 mM CTAB, and 0.25% w/v Tween 20 (рН = 9.2). The running conditions were +25 kV at 30°C with indirect photometric detection at 261 nm. Under optimal experimental conditions, the analysis time was less than 21 min. Separation of Li preparations with mole fraction of ⁶Li ranging from 3.44 up to 90.38% was demonstrated.     

Prediction of the separation of phenols by capillary zone electrophoresis

The effect of pH and ionic strength on the migration of neutral acids in capillary zone electrophoresis (CZE) has been studied for several phenols. The mobilities of the phenols and the efficiency of the capillary have been related to the studied factors. The mobility can be related to the pH of the running buffer through the mobility of the phenolate ion, and the conditional acidity pK value of the phenol at the working ionic strength. This allows prediction of the migration of the phenol, solely from its pK_a^′ value (literature pK_a corrected for the ionic strength of the solution) and mobility of the anion, which can be easily calculated from the mobility at a basic pH value and the pK_a^′ value. Combination of the predicted mobility with the efficiency allows estimation of the resolution of the consecutive peaks obtained for a mixture of phenols. This method has been tested for two groups of phenols of environmental interest.     

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.     

有机改性剂对氯代酚毛细管区带电泳分离的影响

在分离19种氯代酚的过程中,考察了不同的有机添加剂对其毛细管区带电泳分离的影响,发现除了缓冲溶液的pH值外,缓冲溶液添加剂对氯代酚的电泳分离也有较大影响。这种影响与添加剂和氯代酚形成氢键的能力有关。     

Characterization of single-stranded DNA separation by capillary gel electrophoresis

We have investigated the effect of polymer gel reconditioning, the shape of the capillary, the applied electric field, and the capillary length for single-stranded DNA. The polyethylene oxide gel had deformed under the high electric field causing the degradation of the separation power. By the reintroduction of the fresh polyethylene oxide gel for the next run, one-base resolution was recovered. It turned out that the tip of the capillary at the injection side needed to be clean and symmetric for much improved resolution. Changing DNA motion by the pulsed electric field resulted in the separation of DNA far more than 500 bases.     

Enhancing separation in short‐capillary electrophoresis via pressure‐driven backflow

We present a novel easy‐to‐operate and efficient method to improve the separation efficiency in short‐capillary electrophoresis by introducing steady backflow to counterbalance electro‐osmotic flow without the use of any external pressure. The backflow was easily generated by tapering the capillary end, which was achieved by heating a straight capillary and stretching it with a constant force. We investigated the net fluidic transport rate under different tip lengths and separation voltages. Good run‐to‐run repeatability and capillary‐to‐capillary reproducibility of the present method were obtained with RSD less than 1.5%, indicating the stability of the fluid transport rate in the tapered capillary, which ensures the quantification and repeatability of capillary zone electrophoresis (CZE) analysis. Enhanced separation of the tapered short capillary electrophoresis was demonstrated by CZE analyzing amino acids and positional isomers. Baseline separations were achieved in less than 60 s using a tapered capillary with the effective length of 5 cm, while no separation was achieved using a normal capillary without a tapered tip. The present study provides a promising method to use pressure‐driven backflow to enhance separation efficiency in short‐capillary electrophoresis, which would be of potential value in a wide application for fast analysis of complex samples.     

高效毛细管区带电泳法快速测定尿液中的肌酐

建立了一种快速测定尿中肌酐浓度的高效毛细管电泳方法。利用非涂层石英毛细管(64.5 cm×50μm i.d),以pH 2.5,0.1 mmol/L H3PO4作为电泳缓冲液,检测波长191 nm,用0.05 Pa压力进样4 s,在电压16 kV快速分离尿液中的肌酐,采用外标法定量。肌酐的迁移时间约为5.5 min,肌酐浓度在34.5~8840μmol/L范围内呈良好的线性(r2=0.999)。平均日内精密度为2.5%,日间精密度为3.0%。回收率94.1%~99.0%。与全自动生化分析仪碱性苦味酸速率法相比有良好的相关性(r=0.990,n=56)。高效毛细管电泳法测定尿肌酐可应用于临床样品的检测。     

Enantiomeric analysis of rivastigmine in pharmaceuticals by cyclodextrin-modified capillary zone electrophoresis

Chiral separation method development is usually very time-consuming due to the diversity in chemical structures of pharmaceutical drug substances as well as the suitable separation conditions and the problem to choose the appropriate chiral selector. This paper shows capillary zone electrophoresis (CZE) which was developed for chiral separation of a basic compound - rivastigmine (RIV) using 30 cm × 50 μm i.d. polyacrylamide (PAA)-coated fused-silica capillary (effective length 20 cm), amine-modified phosphate buffer of pH 2.5 and sulfated-β-CD (S-β-CD) as chiral selector. Other selected native or derivatized cyclodextrins (CDs) were also tested: β-CD (5, 30 mM), carboxymethyl-β-CD (5, 30 mM), dimethyl-β-CD (15 mM), hydroxypropyl-β-CD (5, 30 mM), hydroxypropyl-α-CD (5, 30 mM) and hydroxypropyl-γ-CD (5, 30 mM). Complete enantiomeric separation of RIV was achieved at 20 kV, 18 °C and detection at 200 nm within 8 min with R.S.D. for the absolute migration time reproducibility of less than 2.1%. Rectilinear calibration range was 5.0-500.0 μM of each enantiomer (r = 0.9994-0.9995). The CZE method proposed was used for the control of chiral purity of pharmaceutically active S-RIV and for the analysis of Exelon caps preparation.     

A well-defined diblock copolymer of poly-(ethylene oxide)-block-poly (4-vinylpyridine) for separation of basic proteins by capillary zone electrophoresis

A series of well-defined diblock copolymers, poly(ethylene oxide)-block-poly(4-vinylpyridine) (PEO-b-P4VP) used as physical coating of capillaries, were synthesized by atom transfer radical polymerization (ATRP). EOF measurement results showed that all synthesized PEO-b-P4VP diblock copolymer-coated capillaries in this report could suppress EOF effectively compared to the bare fused-silica capillaries, and efficient separations of basic proteins were achieved. The effects of the molecular weight of P4VP block in PEO-b-P4VP and buffer pH on the separation of basic proteins for CE were investigated in detail. Moreover, the relationships between morphologies of PEO-b-P4VP diblock copolymers in buffer, which were studied by transmission electron microscopy, and the separation efficiencies of basic protein with PEO-b-P4VP diblock copolymers coatings were discussed.     

Separation of diastereomers of phosphinic pseudopeptides by capillary zone electrophoresis and reverse phase high‐performance liquid chromatography

Capillary zone electrophoresis (CZE) and reverse phase high‐performance liquid chromatography (RP‐HPLC) were used for separation of diastereomers of phosphinic pseudopeptides in achiral separation media. A set of phosphinic pseudopeptides, i. e. peptides with one peptide bond substituted by phosphinic acid moiety ‐PO₂^–‐CH₂‐ derived from the structure N‐Ac‐Val‐AlaB(‐CH₂)Leu‐His‐NH₂ synthesized as a mixture of four diastereomers was used. Separations of diastereomers by CZE were carried out in Tris‐phosphate background electrolytes in the pH range 1.1–3.2 and at least partial separation of the four diastereomers of each pseudopeptide was achieved. A routinely used RP‐HPLC method (C₁₈‐silica column and water/acetonitrile/trifluoroacetic acid mobile phase) was also capable of resolving the diastereomers. In addition, since individual diastereomers of majority of the pseudopeptides were isolated by RP‐HPLC it was possible to check the purity of these RP‐HPLC separated diastereomers and to compare the migration order of the diastereomers in CZE with their elution order in RP‐HPLC. The results obtained by CZE and RP‐HPLC demonstrate a complementarity of both methods in analysis and separation of phosphinic pseudopeptides including their diastereomers.     

Use of zwitterionic buffer additives to improve the separation of proteins in capillary zone electrophoresis

In CZE, the adsorption of the proteins on the capillary wall is a common problem. This paper describes the simple method of utilizing zwitterionic buffer additives to improve the separation of proteins in untreated fused silica capillaries at neutral pH. Three kinds of zwitterion are evaluated in the separation of acidic, neutral, and basic proteins, including their effect on protein efficiency, mobility, separation, and resolution; the difference between the effects of the different additives are also highlighted. The method has proved to be a possible means of reducing protein adsorption, especially for basic proteins.     

A new quantitative method for circulating DNA level in human serum by capillary zone electrophoresis with laser-induced fluorescence detection

We present a method for the quantification of circulating DNA in serum by capillary zone electrophoresis (CZE) with laser-induced fluorescence detection (LIF). The serum was digested by proteinase to release free DNA. SYBR Gold was utilized as DNA intercalating dye, fluorescein as internal standard (ISTD). CZE-LIF was applied for the separation and quantification of total circulating DNA. Good linearity (R = 0.9992) in the low range of DNA concentrations (0.5-40 ng/mL) and a detection limit of 0.5 ng/mL for DNA (S/N = 3) were obtained. Our data demonstrated that CZE-LIF system has a good linearity with excellent sensitivity and satisfactory reproducibility in the quantification of circulating DNA in serum. This method was successfully used for the quantification of circulating DNA levels in serum. We observed that the circulating DNA levels in certain cancer patients were significantly higher than that in healthy individuals. Compared to current methods, our protocol does not need the extraction of DNA from serum. Our preliminary results have illustrated that CZE-LIF system is simple, rapid, and sensitive, and it is well suitable for large-scale quantification of circulating DNA levels in clinical diagnosis.