Characterization of DNA standards by capillary electrophoresis

High-throughput DNA diagnostic measurements using capillary electrophoresis: p53, fragile X and telomerase

Capillary electrophoresis (CE) has become recognized as a powerful tool for the characterization of DNA. It has numerous advantages over slab-gel electrophoresis in that it is fast, highly reproducible and easy to automate. It is well known for its contribution to success in sequencing the human genome, but it is equally important in a wide range of forensic and pharmaceutical applications. Of these applications, CE plays a large and important role in mutation scanning and DNA sizing. From the author's laboratory, three previously published examples are given of clinical applications in this area that have benefited from the use of capillary electrophoresis: the detection of p53 mutations by single strand conformational polymorphism, the analysis of fragile X syndrome and the measurement of telomerase activity. There are many examples from other laboratories where CE has played an important role in this field. For acceptance by the medical community, there must be a clear demonstration that capillary electrophoresis can replace and improve previous slab-gel methods. In this regard, the examples given in this review help to demonstrate that CE can replace previous slab-gel methods and show that CE can improve a wide range of applications in the medical field.

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).

Comparison of the separation of large DNA fragments in the presence and absence of electroosmotic flow at high pH

This paper describes the analysis of large DNA fragments at pH > 10.0 by capillary electrophoresis (CE) in the presence of electroosmotic flow (EOF) using hydroxyethylcellulose (HEC) solution. HEC solution in the anodic reservoir enters the capillaries filled with high-pH buffer by EOF after sample injection. With respect to resolution, sensitivity, and speed, separation conducted under discontinuous conditions (different pH values of HEC solutions and buffer filling the capillary) is appropriate. Using HEC solution at concentrations higher than its entanglement threshold ensures a good separation of large DNA fragments in the presence of EOF at high pH. In addition to pH and HEC, the electrolyte species, dimethylamine, methylamine, and piperidine, play different roles in determining the resolution. The separation of DNA fragments ranging in size from 5 to 40 kilo base pairs was completed in 6 min using 1.5% HEC prepared in 20 mM methylamine-borate, pH 12.0, and the capillary filled with 40 mM dimethylamine-borate, pH 10.0. In comparison, this method allows faster separations of large DNA fragments compared with that conducted in the absence of EOF using dilute HEC solutions.

Analysis of leptin gene expression in chickens using reverse transcription polymerase chain reaction and capillary electrophoresis with laser-induced fluorescence detection

Leptin is a peptide hormone product of the obese (ob) gene that functions in the regulation of appetite, energy expenditure and reproduction in animals and humans. We have developed a technique using capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) for the analysis of chicken leptin (261 base pairs, bp) and beta-actin (612 bp) double-stranded DNA products from reverse transcription polymerase chain reaction (RT-PCR) assays. Amplicons were separated using a DB-1 coated capillary (27 cm x 100 microns I.D.) at a field strength of 300 V/cm in a replaceable sieving matrix consisting of 0.5% hydroxypropylmethylcellulose (HPMC) in 1X TBE (89 mM Tris-base, 89 mM boric acid, 2 mM EDTA, pH 8.3) buffer with 0.5 microgram/ml EnhanCE fluorescent intercalating dye. RT-PCR samples (1-2 microliters) were diluted 1:100 with deionized water and introduced into the capillary by electrokinetic injection. Separations were completed in less than 6 min and the total time required per sample, including capillary conditioning, was 8 min. We have applied RT-PCR-CE-LIF to determine the effects of insulin and estrogen treatment on leptin gene expression relative to that of beta-actin in chicken liver and adipose tissue. In addition, we have constructed a chicken leptin mRNA competitor (234 bp amplicon) and evaluated it for use as an internal standard in the development of a quantitative-competitive RT-PCR assay. Our findings represent the first reported application of capillary electrophoresis to the analysis of leptin gene expression by RT-PCR.

Capillary electrophoretic separation of 1 to 10 kbp sized dsDNA using poly(ethylene oxide) solutions in the presence of electroosmotic counterflow

DNA fragments of 1 to 10 kbp in length were separated by capillary electrophoresis (CE), using poly(ethylene oxide) (PEO) solutions in the presence of electroosmotic flow. The technique requires filling the capillary with the polymer solution by means of electroosmotic flow (EOF). Separation times of 6-7 min in PEO solutions ranging from 0.3 to 8 x 10(6) Mr at 375 V/cm were sufficient to separate the 11 components of the dsDNA ladder (0.5 to 10 kbp) by size. The migration behavior of the double-stranded (ds)DNA fragments, interpreted by "Ferguson plot analysis", in the system is indistinguishable from that previously reported for capillary zone electrophoresis (CZE) in a polyacrylamide solution without EOF. Potential advantages of conducting CZE using polymer solutions in the presence of EOF are: (i) Possibility of long migration times on short columns; (ii) possibility of introducing relatively viscous, high Mr polymer solutions into narrow capillaries; (iii) possibility of establishing polymer concentration gradients in capillaries; (iv) possibility of concentrating the starting zone by balancing electrophoretic migration and electroosmotic transport.