Rapid typing of variable number of tandem repeat locus in the human apolipoprotein B gene for DNA diagnosis of heart disease by polymerase chain reaction and capillary electrophoresis

Migration mechanism of bases and nucleosides in oil-in-water microemulsion capillary electrophoresis

The electrophoretic behaviors of five bases and corresponding nucleosides in the oil in water (o/w) microemulsion capillary electrophoresis, microemulsion electrokinetic chromatography (MEEKC), were examined in comparison with those in normal capillary zone electrophoresis (CZE). The microemulsion systems were composed of heptane, sodium dodecyl sulfate (SDS), 1-butanol and 10 mM phosphate buffer (pH 7.0) or toluene, SDS, 1-butanol and 5 mM carbonate buffer (pH 10.0). CZE was carried out in the range of pH 9.7-10.9, and the dissociation constants, pKa, of the bases and nucleosides and the electrophoretic mobilities of the anionic forms were determined. The electrophoretic behaviors of the solutes in the microemulsion systems were analyzed from their pKa, the electrophoretic mobilities of the anions determined by CZE, and the distribution constants, K(D), of the neutral forms between the microemulsion droplets and the outer aqueous phase. The importance of adsorption mechanism in MEEKC system was suggested from the correlation between log K(D) and log P.

Evaluation of chimerism in DNA samples by PCR amplification of D1S80 with detection by capillary electrophoresis

BACKGROUND

Analysis of the relative amounts of donor and recipient DNA in bone marrow after bone marrow transplantation is frequently used to determine the status of the transplant. We studied the performance of an assay to quantify chimerism based on amplification of the D1S80 variable number tandem repeat marker by PCR with detection of PCR products by capillary electrophoresis (CE).

METHODS AND RESULTS

Samples from potential bone marrow donors and recipients were analyzed separately and in mixtures to simulate various degrees of chimerism from 10% to 90% and subjected to PCR/CE analysis. There was excellent agreement between the measured and known relative proportions of DNA components in chimeric samples. The lower limit of sensitivity for detection of chimerism was 1%; between-runs coefficients of variation were <5%.

CONCLUSIONS

Amplification of the D1S80 minisatellite by PCR with CE detection is a reliable method for determination of the relative contribution of different DNAs in mixed samples. This method is fast, quantitative, and extremely reproducible.

Genetic typing and HIV-1 diagnosis by using 96 capillary array electrophoresis and ultraviolet absorption detection

Current high-throughput approaches to the analysis of PCR products are based primarily on electrophoretic separation and laser-excited fluorescence detection. We show that capillary array electrophoresis can be applied to HIV-1 diagnosis and D1S80 VNTR genetic typing based simply on UV absorption detection. The additive contribution of each base pair to the total absorption signal provides adequate detection sensitivity for analyzing most PCR products. Not only is the use of specialized and potentially toxic fluorescent labels eliminated, but also the complexity and cost of the instrumentation are greatly reduced.

Ultrafast detection of microsatellite repeat polymorphism in endothelin 1 gene by electrophoresis in short capillaries

The methodology and instrumentation for fast denaturing electrophoresis in short capillaries was developed and exemplified by detection of short tandem repeat polymorphism in the endothelin 1 gene. The resolution of two nucleotides, which is required for the detection of a dinucleotide repeat polymorphism, was achieved in a capillary of an effective length of 2.5 cm at a temperature of 600C and an electric field strength of 600 V/cm in 42 s. Thus, the use of denaturing electrophoresis in short capillaries with laser-induced fluorescence detection resulted in a reduction of analysis time by a factor of 200 when compared to the conventional slab gel electrophoresis. The developed methodology and instrumentation is advantageous for an implementation in clinical diagnostics and genetic population screening where fast analytical instrumentation amenable to automation is of paramount importance.

Miniaturized ultrathin slab gel electrophoresis with thermal lens microscope detection and its application to fast genetic diagnosis

A miniaturized ultrathin slab gel electrophoresis (MUSGE) apparatus was developed, and fast separation of DNA fragments was obtained using it. To obtain sufficient separation efficiency in a limited space, a discontinuous buffer system was used. In general, it is difficult to cast a discontinuous ultrathin slab gel of adequate quality. However, the miniaturized resolving gel could be cast by taking advantage of the "capillary phenomenon" of the ultrathin channel. A gradient plate was used to control the height of the resolving gel and to form a clear interface between the concentrating gel and the resolving gel. This method was used to cast multiple gels simultaneously and reproducibly. The gradient plate also facilitated sample introduction, which was carried out by using a micropipet. A 25-mm-long and 80-micron thick-resolving gel was used to separate the 100-base pair ladder DNA within 10 min. Bandwidth was reduced to 100-200 microns, thus improving the number of theoretical plates to 22,000, which was comparable to that in conventional slab gel electrophoresis even though the migration distance was reduced to 1/10. Satisfactory lane-to-lane reproducibility (RSD < 1.0%, n = 6) and gel-to-gel reproducibility (RSD < 2.7%, n = 4) were obtained. Finally, the MUSGE apparatus was successfully applied to get a rapid genetic diagnosis.

On-line coupling of polymerase chain reaction and capillary electrophoresis for automatic DNA typing and HIV-1 diagnosis

We demonstrate an integrated on-line system with a fused-silica capillary as the microreactor for PCR and capillary gel electrophoresis with laser-induced fluorescence detection for DNA typing and disease diagnosis. Two applications have been investigated: the four short tandem repeat (STR) loci vWA, THO1, TPOX and CSF1PO (CTTv) for DNA typing, and DNA probe for human immunodeficiency virus (HIV-1) diagnosis. The CTTv are important loci in forensic and genetic linkage analysis. The PCR technique is a powerful tool in HIV research because it can detect the presence of the virus before any antibody response in the infected person. Thus it is important for early diagnosis. Multiplexed PCR in a fused-silica capillary, on-line injection, DNA denaturation and calibration based on a standard ladder have been successfully combined. Also, on-line liquid flow management, DNA separation and detection have been completely integrated.

Analysis of clinically relevant, diagnostic DNA by capillary zone and double-gradient gel slab electrophoresis

A number of applications of capillary zone electrophoresis (CZE) in sieving liquid polymers (notably linear polyacrylamides and cellulose) for the analysis of polymerase chain reaction products of clinically relevant, diagnostic DNA, are reviewed here. The fields covered are human genetics, quantitative gene dosage, microbiology and virology, forensic medicine and therapeutic DNA (notably antisense nucleotides). Some unique, novel developments are highlighted, such as (a) non-isocratic CZE, i.e., temperature-programmed CZE for detection of DNA point mutations and (b) the synthesis of novel N-substituted acrylamides, offering extreme resistance to alkaline hydrolysis, coupled with high hydrophilicity. In the field of denaturing gradient gel electrophoresis (DGGE), as routinely performed in gel slabs, a novel methodology is described, i.e., double-gradient DGGE. In this technique, two gradients are simultaneously applied along the migration direction; a chemical denaturing gradient, for partially unwinding homo- and hetero-duplexes of DNA and a porosity gradient, for re-compacting diffuse bands melting over a broader range of denaturing conditions. Both the CZE and the slab gel methodologies, with the latest developments described in this review, appear to be promising tools for screening diagnostic DNA.

Polymeric separation media for capillary electrophoresis of nucleic acids

The choice of polymer matrix for separating nucleic acids by capillary electrophoresis has often been arbitrary. However, considerable research in the area has led to a wealth of data exploring the key parameters of the polymer matrix that affect nucleic acid separations: polymer type, polymer molecular mass, polymer concentration, temperature, and buffer components and additives. Using this information, it is possible to use rational methods of choosing a good polymer matrix for a particular application. Further research into the properties of the mechanism of separation in polymer solutions, as well as the polymer matrix and other solution components will lead to even more efficient separations.

Capillary electrophoresis in clinical chemistry

Since its introduction, capillary electrophoresis has diversified, spreading out into different specialized fields covering solutions for almost any analytical questions arising in research laboratories. In the context of clinical chemistry, results must be provided at low costs and in a clinically relevant time frame; however, the attributes which have made capillary electrophoresis such a successful tool in basic research are identical to those attracting clinical laboratories: speed (more efficient, less labor-intensive), low costs (minimal buffer consumption), small sample volume (reduced blood collection volume from patient), increased selectivity (determination of multiple solutes in one run), and versatility (detection of analytes over the wide range of molecular masses and chemical composition). Nevertheless, it should be mentioned that there are still some drawbacks at this stage to be solved in the near future, such as lack of sensitivity for many clinical applications or the constraint to measure in a sequential mode. The aim of this survey is to familiarize clinical chemists, as well as chemists, with a short introduction to capillary electrophoresis, followed by chapters reviewing prominent fields of applications and the latest developments in clinical chemistry.

Capillary electrophoresis of DNA for molecular diagnostics

A number of applications of capillary zone electrophoresis (CZE) in sieving liquid polymers (notably linear polyacrylamides and cellulose) for the analysis of polymerase chain reaction (PCR) products of clinically relevant, diagnostic DNA, are reviewed. The fields covered are: human genetics, quantitative gene dosage, microbiology and virology, forensic medicine and therapeutic DNA (notably, antisense nucleotides). Some unique, novel developments are highlighted, such as: (i) nonisocratic CZE, i.e., temperature-programmed CZE for detection of DNA point mutations; (ii) the synthesis of novel N-substituted acrylamides, offering extreme resistance to alkaline hydrolysis coupled to high hydrophilicity. In the field of denaturing gradient gel electrophoresis (DGGE), as routinely performed in gel slabs, a novel methodology is described in CZE: double-gradient DGGE. In this technique, two gradients are simultaneously applied along the migration direction: a chemical (or thermal) denaturing gradient, for partially unwinding homo- and hetero-duplexes of DNA, and a porosity gradient, for recompacting diffuse bands melting over a broader range of denaturing conditions. It is thus demonstrated that chemical gradients, in addition to temperature gradients, can be easily implemented even in a capillary format.

Analysis of disease-causing genes and DNA-based drugs by capillary electrophoresis. Towards DNA diagnosis and gene therapy for human diseases

Rapid progress in the Human Genome Project has stimulated investigations for gene therapy and DNA diagnosis of human diseases through mutation or polymorphism analysis of disease-causing genes and has resulted in a new class of drugs, i.e., DNA-based drugs, including human gene, disease-causing gene, antisense DNA, DNA vaccine, triplex-forming oligonucleotide, protein-binding oligonucleotides, and ribozyme. The recent development of capillary electrophoresis technologies has facilitated the application of capillary electrophoresis to the analysis of DNA-based drugs and the detection of mutations and polymorphism on human genes towards DNA diagnosis and gene therapy for human diseases. In this article the present state of studies on the analysis of DNA-based drugs and disease-causing genes by capillary electrophoresis is reviewed. The paper gives an overview of recent progress in the Human Genome Project and the fundamental aspects of polymerase chain reaction-based technologies for the detection of mutations and polymorphism on human genes and capillary electrophoresis techniques. Attention is mainly pad to the application of capillary electrophoresis to polymerase chain reaction analysis, restriction fragment length polymorphism, single strand conformational polymorphism, variable number of tandem repeat, microsatellite analysis, hybridization technique, and monitoring of DNA-based drugs. Possible future trends are also discussed.

Fast capillary electrophoresis-laser induced fluorescence analysis of ligase chain reaction products: human mitochondrial DNA point mutations causing Leber's hereditary optic neuropathy

High speed capillary electrophoresis-laser-induced fluorescence (CE-LIF) has been used to separate and detect point mutations using the ligase chain reaction (LCR). The method utilizes short capillary columns (7.5 cm effective length) and fields of 400 V/cm to analyze DNA-ethidium bromide complexes using an He/Ne laser. The method was first demonstrated with a commercially available kit for LCR based on a lacI gene fragment inserted in a Bluescript II phagemid. LCR-CE-LIF was then applied to detect point mutations in human mitochondrial DNA, resulting in Leber's hereditary optic neuropathy (LHON). Three severe mutations were analyzed in which the original base is substituted by a thymidine base at positions 3460, 11778 and 14459. Appropriate primers were designed with polyT tails for length discrimination of pooled samples. Successful detection of mutated samples was achieved, with appropriate correction for small amounts of nonspecific ligated product. The method is rapid, easy to implement, and automatable.

Application of capillary gel electrophoresis to the diagnosis of the aldehyde dehydrogenase 2 genotype

This study dealt with the application of capillary gel electrophoresis (CGE) to diagnosis of the aldehyde dehydrogenase 2 (ALDH-2) genotype. Electrophoresis was performed on a low cross-linked polyacrylamide gel ¿3% T [g acrylamide+g Bis (N,N'-methylenebisacrylamide)], 0.5% C (g Bis/% T)¿ in 100 mM Tris-borate buffer (pH 8.3) at -10 kV with on-column UV detection (260 nm). During the PCR reaction, DNA from the wild-type allele generated a MboII restriction site, which is an amplification created restriction site. This did not occur, however, with DNA fragments from the mutant allele. Therefore, determination of the heterozygous genotype, the coexistence of wild-type and mutant alleles, was easily possible. Analysis of the MboII restriction digests of the PCR products was completed in less than 20 min, showing two peaks corresponding to fragments of 125 (cleaved) and 135 (uncleaved) base pairs (bp), respectively. On the other hand, determination of the homozygous genotype, wild-type or mutant, was difficult in one electrophoresis run. The CGE of the MboII restriction digests gave a single peak and the identification, cleaved or uncleaved, was difficult under our experimental conditions. However, the addition of aliquots of the PCR reaction mixture to the restriction digests, followed by re-electrophoresis, allowed successful diagnosis, yielding two peaks (cleaved and uncleaved) for the wild-type and one peak (uncleaved) for the mutant allele. This study demonstrated that CGE offers a high-speed, high-resolution analytical tool for determining genetic types, as compared with the conventional slab gel methodologies.

Screening and identification of familial defective apolipoprotein B-100 in clinical samples by capillary gel electrophoresis

Familial defective apolipoprotein B-100 (FDB) is a dominantly inherited disorder. It is characterized by a decreased affinity of low density lipoprotein (LDL) for the LDL receptor, as a consequence of a substitution of adenine by guanine in exon 26 of the apolipoprotein B-100 gene, coding for the putative LDL receptor-binding domain of the mature protein. This disorder is associated with a strikingly high incidence of arteriosclerosis and tends to cause disease and premature death. In this communication we describe a rapid capillary gel electrophoretic method in combination with molecular biology techniques to facilitate the diagnosis of FDB. Mutation screening for FDB is performed by an allele-specific amplification followed by capillary gel electrophoresis (CGE). For the combined polymerase chain reaction (PCR)-CGE method, a total analysis time of only 3 h is needed, a period that is normally necessary for the run and for staining of the gel only, not including the time for PCR, gel casting, etc. In our pilot study 4 of 43 hypercholesterolemic patients were found to have the predominant apoB 3500 codon mutation. The verification is demonstrated by DNA-sequencing. This pilot study will be followed by a large cohort analysis of the south-west German population to determine the frequency of FDB in this area. The PCR-CGE method on the Dionex capillary electrophoresis system (CES I) allows rapid, fully automated detection of the mutation resulting in the unequivocal diagnosis of FDB.