Capillary electrophoresis of polymerase chain reaction-amplified DNA using fluorescence detection with an intercalating dye

CGE-laser induced fluorescence of double-stranded DNA fragments using GelGreen dye

Nowadays, new solutions focused on the replacement of reagents hazardous to human health are highly demanded in laboratories and Green Chemistry. In the present work, GelGreen, a new nonhazardous DNA staining reagent, has been assayed for the first time to analyze double-stranded DNA by CGE with LIF detection. The effect of GelGreen concentration on S/N ratio and migration time of a wide concentration range of standard DNA mixtures was evaluated. Under optimum GelGreen concentration in the sieving buffer efficient and sensitive separations of DNA fragments with sizes from 100-500 base pairs (bp) were obtained. A comparison in terms of resolution, time of analysis, LOD, LOQ, reproducibility, sizing performance, and cost of analysis was established between two optimized CGE-LIF protocols for DNA analysis, one based on the dye YOPRO-1 (typically used for CGE-LIF of DNA fragments) and another one using the new GelGreen. Analyses using YOPRO-1 were faster than those using GelGreen (ca. 31 min versus 34 min for the analysis of 100-500 bp DNA fragments). On the other side, sensitivity using GelGreen was twofold higher than that using YOPRO-1. The cost of analysis was significantly cheaper (ninefold) using GelGreen than with YOPRO-1. The resolution values and sizing performance were not significantly different between the two dyes (e.g. both dyes allowed the separation of fragments differing in only 2 bp in the 100-200 bp range). The usefulness of the separation method using GelGreen is demonstrated by the characterization of different amplicons obtained by PCR.

An overview of DNA typing methods for human identification: past, present, and future

This chapter presents a brief introduction to the historical development of current technologies used in DNA analysis for human identification. The text describes the development of the PCR and short tandem repeats along with subsequent advances in instrumentation such as real-time PCR and capillary electrophoresis. These techniques have brought about a revolution in DNA typing methods through increased efficiency and the application of multiplex fluorescence detection. More recently the development of new STR based typing methods utilizing mini- and Y-STR PCR multiplexes has increased the flexibility of the investigator, permitting the analysis of inhibited and degraded DNA. Future directions for DNA typing are also discussed, including the development of methods for touch samples based on low copy DNA analysis and the determination of tissue/cell type.

Combining ligation reaction and capillary gel electrophoresis to obtain reliable long DNA probes

New DNA amplification methods are continuously developed for sensitive detection and quantification of specific DNA target sequences for, e.g. clinical, environmental or food applications. These new applications often require the use of long DNA oligonucleotides as probes for target sequences hybridization. Depending on the molecular technique, the length of DNA probes ranges from 40 to 450 nucleotides, solid-phase chemical synthesis being the strategy generally used for their production. However, the fidelity of chemical synthesis of DNA decreases for larger DNA probes. Defects in the oligonucleotide sequence result in the loss of hybridization efficiency, affecting the sensitivity and selectivity of the amplification method. In this work, an enzymatic procedure has been developed as an alternative to solid-phase chemical synthesis for the production of long oligonucleotides. The enzymatic procedure for probe production was based on ligation of short DNA sequences. Long DNA probes were obtained from smaller oligonucleotides together with a short sequence that acts as bridge stabilizing the molecular complex for DNA ligation. The ligation reactions were monitored by capillary gel electrophoresis with laser-induced fluorescence detection (CGE-LIF) using a bare fused-silica capillary. The capillary gel electrophoresis-LIF method demonstrated to be very useful and informative for the characterization of the ligation reaction, providing important information about the nature of some impurities, as well as for the fine optimization of the ligation conditions (i.e. ligation cycles, oligonucleotide and enzyme concentration). As a result, the yield and quality of the ligation product were highly improved. The in-lab prepared DNA probes were used in a novel multiplex ligation-dependent genome amplification (MLGA) method for the detection of genetically modified maize in samples. The great possibilities of the whole approach were demonstrated by the specific and sensitive detection of transgenic maize at percentages lower than 1%.

Separation of DNA by capillary electrophoresis

This chapter reports an overview of the analytical techniques used to perform genetic analysis of polymerase chain reaction products using capillary electrophoresis. Three separate but related techniques are described: the separation of native DNA with detection using fluorescent intercalating dyes, the separation of denatured DNA using fluorescently labeled primers, and the detection of single-strand conformation polymorphisms using denatured DNA separated under native conditions. The various techniques involve electrokinetic injection of the DNA onto a narrow band at the head of the column, sieving the DNA through various entangled polymer matrices, and detection via single or multichannel laser-induced fluorescence. Analytical protocols are provided, and a series of representative electropherograms are included.

Microchip Laser-Induced Fluorescence Detection of Proteins at Submicrogram per Milliliter Levels Mediated by Dynamic Labeling under Pseudonative Conditions

We have previously demonstrated on-column dynamic labeling of protein-SDS complexes on capillaries and microchips for laser-induced fluorescence (LIF) detection using both a commercially available fluor and a protein separation buffer. Upon binding to hydrophobic moieties (of the analyte or separation buffer), the fluor undergoes a conformational change allowing fluorescence detection at 590 nm following excitation with 488-nm light. Our original work showed on-chip limits of detection (LOD) comparable with those using UV detection (1 x 10(-5) M) on capillaries-falling significantly short of the detection limits expected for LIF. This was largely a function of the physicochemical characteristics of the separation buffer components, which provided significant background fluorescence. Having defined the contributing factors involved, a new separation buffer was produced which reduced the background fluorescence and, consequently, increased the available dye for binding to protein-SDS complexes, improving the sensitivity in both capillaries and microchips by at least 2 orders of magnitude. The outcome is a rapid, sensitive method for protein sizing and quantitation applicable to both capillary and microchip separations with a LOD of 500 ng/mL for bovine serum albumin. Interestingly, sensitivity on microdevices was improved by inclusion of the dye in the sample matrix, while addition of dye to samples in conventional CE resulted in a drastic reduction in sensitivity and resolution. This can be explained by the differences in the injection schemes used in the two systems. The linear range for protein quantitation covered at least 2 orders of magnitude in microchip applications. On-chip analysis of human sera allowed abnormalities, specifically the presence of elevated levels of gamma-globulins, to be determined.

The Human Genome Project: the role of analytical chemists

The Human Genome Project (HGP) is the most ambitious and important effort in the history of biology. It has provided a complete genetic blueprint for human life, and will provide important insights into human health and development. HGP involves a huge amount of data that is stored on computers all over the world. More than just vast amounts of DNA sequences, the project is about developing sets of integrated maps that involve genetic, physical, and sequence data. The data can be sorted, annotated and organized in many different ways using different types of database software, different analysis algorithms and different forms of interfaces. The genomic sequences of the human and the substantial portions of the mouse genome are expected to be finished by 2005. Analytical chemists took the opportunity, addressing the problem of achieving a high throughput with good sensitivity. This paper discusses how analytical chemists saved the Human Genome Project or at least gave it a helping hand.

Dynamic labeling during capillary or microchip electrophoresis for laser-induced fluorescence detection of protein-SDS complexes without pre- or postcolumn labeling

The analysis of proteins under denaturing conditions is routinely performed with SDS-polyacrylamide gel electrophoresis. The automated capabilities of CE, use of nongel sieving matrixes, and on-line optical detection by either ultraviolet (UV) absorption or laser-induced fluorescence (LF) promise to revolutionize this method. While direct on-line detection of proteins is possible as a result of their intrinsic ability to absorb light in the UV part of the spectrum (detection sensitivity comparable to Coomassie Blue staining of gels), LIF provides more powerful detection but requires pre- or postcolumn fluorescence labeling of the proteins. The development of a protocol analogous to that used for double-stranded DNA analysis, where fluorescent intercalating dyes are simply included in the separation medium, would simplify size-based protein analysis immensely. This would avoid the complications associated with covalent modification of the proteins but still exploit the sensitivity of LIF detection. We demonstrate that this is possible with CE and microchip detection by incorporating, into the run buffer, a fluorescent dye that interacts hydrophobically with protein-SDS complexes. Key to this is a dye that fluoresces significantly when bound to protein-SDS complexes but not when bound to SDS micelles. Comparison of electropherograms from CE-based denaturing protein analysis with UV and LIF detection indicates that the presence of the fluor does not alter separation of the proteins. Moreover, comparison with electropherograms generated from microchip electrophoresis with LIF detection shows that equivalent patterns can be obtained. Despite the unoptimized nature of this separation system, a dynamic labeling protocol that allows for LIF detection for proteins is attractive and has the potential to circumvent the tedious labeling steps typically required.

Genetic fingerprinting of grape plant (Vitis vinifera) using random amplified polymorphic DNA (RAPD) analysis and dynamic size-sieving capillary electrophoresis

Dynamic size-sieving capillary electrophoresis with laser-induced fluorescence detection (DSCE-LIF) was combined with random amplified polymorphic DNA (RAPD) analysis to demonstrate the feasibility of the genetic analysis of grape plant varieties and clones within a variety. Parameters of the genomic DNA extraction process, as well as those of the RAPD analysis, were optimized specifically for this application. Polymorphic DNA fragments were generated for four different grape plant varieties including Cabernet Franc, Cabernet Sauvignon, Merlot, and Chardonnay. Relative to slab gel electrophoresis (SGE) with ethidium bromide staining, DSCE-LIF provided superior separation efficiency and detection limits in the analysis of DNA polymorphic bands. Optimal DSCE-LIF analyses were achieved using a 10-fold RAPD sample dilution, hydrodynamic sample injection, and 100 ng/mL of YO-PRO-1 DNA intercalator in the dynamic size-sieving buffer solution. In addition, the reproducibility of both the DSCE-LIF and RAPD analyses were demonstrated.

Separation of polymerase chain reaction amplified bird genes by capillary electrophoresis

Female birds possess one Z and one W chromosome, whereas male birds possess two identical Z chromosomes. Thus, the presence of a W genetic marker is diagnostic of the female sex. Capillary electrophoresis with buffer containing an entangled solution of hydroxyethylcellulose was used to separate the polymerase chain reaction (PCR) amplified bird sexing genes CHD-Z and CHD-W. The relative standard deviations (RSD) were less than 0.6% for the male genes and less than 0.4% for the female genes for six runs and detection limits of 0.1 ng/microL were obtained with laser-induced fluorescence (LIF) detection. Using a DNA ladder and theoretical models for DNA separation in sieving media, the sizes of the two bird genes were determined.

Optimization of intercalation dye concentration for short tandem repeat allele genotyping using capillary electrophoresis with laser-induced fluorescence detection

DNA analysis using capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection requires that polymerase chain reaction products either be prepared using primers with fluorescent molecules covalently bonded to them, or stained with a fluorescent intercalation dye following amplification. The intercalation technique has the advantage of allowing fluorescence detection of any double-stranded DNA (dsDNA) product regardless of the amplification primers used. The increased sensitivity of LIF detection is sometimes compromised by the intercalation dye changing the mass to charge ratio of the DNA. The purpose of this study was to evaluate the changes of migration rate, resolution and fluorescent intensity of dye-DNA complexes during electrophoretic separations, and to establish the optimal parameters for short tandem repeats alleles profiling. The alleles of three STR loci THO1, F13A01 and vWFA31 were intercalated with the monomeric dyes TOPRO-1 and YOPRO-1, and their corresponding dimers, TOTO-1 and YOYO-1 (Molecular Probes, Eugene, OR, USA). Alleles intercalated before injection onto the CE column resulted in loss of resolution and sensitivity when compared to the on-column labeling technique. The results of this experimentation were then applied to a STR typing assay using a commercially available polymer and buffer matrix. This assay included development of a unique internal standard used for migration time normalization assignment of alleles. Consequently, the 9 allele and the 9.3 microvariant of the THOI locus were separated and typed correctly with a resolution of 0.49 in less than 20 min, and the only sample preparation necessary after amplification was a dilution step.

Spectral measurements of intercalated PCR-amplified short tandem repeat alleles

Short tandem repeat (STR) alleles are popular for use as forensic markers due to their highly polymorphic nature. Commonly they are separated by gel electrophoresis and visualized using intercalation dyes. The purpose of this study was to determine the changes in absorbance and fluorescence of DNA-intercalation dye complexes as a function of base pair (bp)-to-dye ratio. The DNA samples consisted of STR alleles from loci THO1, F13A01, and vWFA31. The alleles were PCR amplified and HPLC purified to ensure that only the desired DNA fragment was present in each sample. Alleles ranged in size from 151 bp for locus vWFA (allele 17) to 199 bp for the locus F13A01 (allele 8). The adenine and thymine (AT) content varied from 48% for the THO1 locus to 69% for F13A01 and vWFA31 loci. The homozygous alleles of each locus were mixed individually with the bis-intercalators TOTO-1 and YOYO-1 and their corresponding monomeric dyes TOPRO-1 and YOPRO-1. The absorbance of the DNA-dye complex at 260 nm increased with addition of each intercalation dye. Subtraction of the dye absorbance rendered the DNA absorbance constant at 260 nm. Fluorescence emission increased dramatically upon intercalation of both the monomeric and dimeric dyes into the DNA helix. A plateau of fluorescence intensity was observed at base pair-to-dye ratios of 10/1 for the bis-intercalator TOTO-1 and 5/1 for YOYO-1 for all three loci. The greatest fluorescence intensity response was obtained with the intercalator YOYO-1 using allele 8 of the F13A01 locus, which had the greatest AT concentration.

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.

Advances in capillary electrophoresis

This review summarizes the advancement in operational modes and selected applications of the title technique over the past five years. Regarding operational modes particular emphasis is put upon increasing selectivity and resolution, hyphenation of capillary electrophoresis with techniques based on other than electromigration principles, the so-called chip technology and new ways of detection. In applications selected examples of chiral separation and separation of biopolymers (proteins, nucleic acids) are emphasized. It is demonstrated that capillary electrophoresis represents a complementary technique to high-performance column chromatography and in a number of cases it offers better separations than standard chromatographic procedures.

Analysis of multiplexed short tandem repeat (STR) systems using capillary array electrophoresis

The profiling of polymorphic short tandem repeat (STR) markers is being applied to human identification, parentage testing and genetic mapping. Reliable genotyping of these markers is facilitated by polymerase chain reaction (PCR) amplification and high-resolution electrophoretic separation. Capillary array electrophoresis (CAE) offers very rapid, high-resolution separation of the amplified DNA and potential for automated sample processing not realized employing conventional slab-gel electrophoresis. The use of CAE to type DNA samples amplified at 11 genetic loci in multiplex profiles is presented. Two sets totaling 208 samples were amplified in a multiplex fashion using AmpFlSTR-Blue or AmpFlSTR-Green I and analyzed in a blind study using CAE. With the exception of one sample, the CAE genotyping results were in complete agreement with results obtained using a single-capillary system or two slab-gel electrophoresis systems. The sample, genotype TH01 7/10, migrated similar to TH01 6.3/9.3 allele sizes, which suggested a potential band migration shift. The recommended approach to such an observation is to analyze the sample again. The sample was rerun and correct genotype verified. Allelic ladder samples were analyzed multiple times by CAE to determine sizing accuracy and precision. The sizing of over 240 allelic ladder samples yielded an average within-run precision of +/- 0.13 bp and between-run precision of +/- 0.21 bp for fragments up to 350 bp. The CAE protocols permit processing of up to 96 multiplex STR samples in under 70 min.

Sex determination of forensic samples by polymerase chain reaction of the amelogenin gene and analysis by capillary electrophoresis with polymer matrix

The aim of this study was to validate an application of GenePrint Sex Determination System based on amplification of a section of the X-Y homologous gene amelogenin followed by capillary electrophoresis (CE) separation of polymerase chain reaction (PCR) products for gender testing of forensic DNA. It was found that subnanogram quantities of male and female DNA were correctly detected by this system. Experiments were performed to investigate the possibility of quantitating the X-Y chromosome-specific PCR products to disclose sex-mixed DNA samples. It was found that observed electrophoretic profiles correctly reflected an X-Y chromosome proportion of the DNA sample which was introduced into the PCR mix. The tested amelogenin PCR-CE system was successfully used for gender testing of a wide range of biological evidence including sex-mixed DNA samples from rape cases. These results demonstrate that the tested amelogenin PCR-CE system is a useful tool for gender determination of forensic DNA.

The use of capillary electrophoresis for point-mutation screening

Advances in capillary electrophoresis technology over the past three years have been rapid. Capillary electrophoresis offers high-throughput, high-resolution, automatic operation and on-line detection with automatic data acquisition, and this has stimulated its application to the analysis of DNA mutations. Many different PCR-based DNA-mutation assays have been developed for unknown and known mutations. This article compares conventional PCR-based mutation-detection assays with the methods developed for use with capillary electrophoresis. Future trends for mutation detection using capillary electrophoresis are also assessed, with a special emphasis on totally integrated, microchip capillary-electrophoresis-based mutation-detection systems.

The characterization of composite agarose/hydroxyethylcellulose matrices for the separation of DNA fragments using capillary electrophoresis

Mixtures of the polysaccharide derivatives, 19% hydroxyethylated SeaPrep agarose (SP-AG) and hydroxyethylcellulose (HEC), in aqueous buffer solutions are applied for the first time to the separation of DNA fragments using capillary electrophoresis (CE). These matrices form unique size-sieving networks that allow the separation of a wide size range of DNA fragments in a single analysis. Relative to their homogeneous counterparts, the composite separation matrices provide enhanced selectivity properties of DNA fragments, especially for fragments greater than 1000 base pairs (bp) in length. Additionally, the effects on separation performance of capillary temperature, the incorporation of a DNA intercalator, and applied field strength are demonstrated. Solution viscosity measurements of the homogeneous and composite matrix solutions were made in order to establish the entanglement threshold concentrations for the unique size-sieving solutions. The relatively low solution viscosities of the composite separation matrices allow reproducible replacement of the separation matrix between analyses. The mechanism of separation of DNA fragments for the composite matrices is proposed.

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.

New approaches in clinical chemistry: on-line analyte concentration and microreaction capillary electrophoresis for the determination of drugs, metabolic intermediates, and biopolymers in biological fluids

The use of capillary electrophoresis (CE) for clinically relevant assays is attractive since it often presents many advantages over contemporary methods. The small-diameter tubing that holds the separation medium has led to the development of multicapillary instruments, and simultaneous sample analysis. Furthermore, CE is compatible with a wide range of detectors, including UV-Vis, fluorescence, laser-induced fluorescence, electrochemistry, mass spectrometry, radiometric, and more recently nuclear magnetic resonance, and laser-induced circular dichroism systems. Selection of an appropriate detector can yield highly specific analyte detection with good mass sensitivity. Another attractive feature of CE is the low consumption of sample and reagents. However, it is paradoxical that this advantage also leads to severe limitation, namely poor concentration sensitivity. Often high analyte concentrations are required in order to have injection of sufficient material for detection. In this regard, a series of devices that are broadly termed 'analyte concentrators' have been developed for analyte preconcentration on-line with the CE capillary. These devices have been used primarily for non-specific analyte preconcentration using packing material of the C18 type. Alternatively, the use of very specific antibody-containing cartridges and enzyme-immobilized microreactors have been demonstrated. In the current report, we review the likely impact of the technology of capillary electrophoresis and the role of the CE analyte concentrator-microreactor on the analysis of biomolecules, present on complex matrices, in a clinical laboratory. Specific examples of the direct analysis of physiologically-derived fluids and microdialysates are presented, and a personal view of the future of CE in the clinical environment is given.

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.

Ultrathin slab gel separations of DNA using a single capillary sample introduction system

We demonstrate here a novel method for DNA separations which combines the parallel processing capabilities of slab gels with the advantages of sample introduction obtained with a single capillary. This sample introduction format allows rapid sequential separations or continuous analysis to be carried out on ultrathin slab gels with efficient heat dissipation. Ultrathin slab gels have been fabricated by using 57-micron spacers between quartz plates, and a single capillary has been used to introduce plugs of dsDNA fragments into the ultrathin gel. These fragment plugs were deposited along the entrance to the ultrathin gel at spatially discrete locations by micromanipulation of the capillary. Spatially resolved detection has been accomplished with an argon ion laser focused to a line for excitation and a CCD for collection of fluorescence. Double-stranded DNA separations are demonstrated in a plug injection format. This approach allows multiple unique samples to be rapidly deposited on the ultrathin slab gels for separation.

Short tandem repeat typing by capillary array electrophoresis: comparison of sizing accuracy and precision using different buffer systems

Polymorphic microsatellite markers are widely used in gene discovery and mapping, human identification, agricultural genetics, and diagnosis of triplet-repeat expansion disorders. Reliable genotyping of these markers requires polymerase chain reaction (PCR) amplification and very-high-resolution electrophoresis. Capillary array electrophoresis offers extremely fast, high-resolution separation of DNA and more automated sample processing because labor-intensive slab-gel pouring and sample loading are eliminated. We report a simple, reliable procedure for preparing PCR samples for electrokinetic injection into capillaries using a 96-well tray and float dialysis. We developed an improved sizing standard for genotyping and used it to evaluate systematically the sizing accuracy and precision of low-viscosity, replaceable matrix formulations. Our study sizing over 28,000 alleles yielded an average precision of +/- 0.12 bp for fragments up to 350 bp. Low-viscosity formulations permit low-pressure matrix injection (40 psi) and a turnaround time of 70 min for 48-96 samples.

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.

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.

Characterization of mitochondrial DNA using low-stringency single specific primer amplification analyzed by laser induced fluorescence--capillary electrophoresis

Polymerase chain reaction (PCR)-based DNA typing is routinely used in forensics for identity testing. Those assays that distinguish single nucleotide polymorphisms (SNPs) require other biochemical reactions in addition to PCR to identify the sequence polymorphisms. Low-stringency sequence-specific PCR (LSSP-PCR) is an example of a recent method that does not require additional biochemical treatments. The analysis of LSSP-PCR by capillary electrophoresis (CE) to discriminate the highly polymorphic mitochondrial DNA (mtDNA) D-loop region is described. The DNA from five individuals were amplified (first step) using sequence-specific primers to produce 1021 bp fragments containing the D-loop region. Each fragment was isolated by electroelution using CE and UV detection, and subjected to a second amplification (second step) using a single primer annealed under low stringency conditions. This generated a range or profile of PCR products for each sample, which were resolved and analyzed by CE with the intercalator TOTO-1 and laser-induced fluorescence (LIF) detection. The LSSP-PCR profiles were unique for each individual, indicating that this technique may be applicable for forensic identity testing.

Evaluation of capillary electrophoresis in polymer solutions with laser-induced fluorescence detection for the automated detection of T-cell gene rearrangements in lymphoproliferative disorders

The rapid increase in the number of DNA-based clinical diagnostic procedures, particularly polymerase chain reaction (PCR)-based assays, has generated interest in analytical techniques that are less time-consuming and labor-intensive than traditional procedures such as polyacrylamide gel electrophoresis (PAGE). Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection, which allows for rapid and sensitive detection of DNA fragments in an automated format, is well-suited for DNA-based clinical assays. In this study, we demonstrate the potential of CE-LIF for the detection of PCR products from T-cell receptor gamma (TCR gamma) gene rearrangements present in monoclonal populations of lymphocytes. The presence of monoclonal populations of T-cells is associated (but not always synonymous) with lymphocytic malignancies. Analysis of 31 patient samples, as well as sensitivity controls, demonstrated that CE-LIF detection of monoclonal lymphocytic populations is comparable to that of PAGE-SYBR Green I staining, and that CE-LIF detection can be accomplished in less than 20 min. These preliminary results illustrate the potential feasibility of a CE-based diagnostic assay for the detection of T-cell gene rearrangements.

DNA typing of a polymerase chain reaction amplified D1S80/amelogenin multiplex using capillary electrophoresis and a mixed entangled polymer matrix

In this study, a technique was developed to separate by capillary electrophoresis (CE) the widely varying DNA fragment sizes produced by a multiplex polymerase chain reaction (PCR) amplification of the loci D1S80 and amelogenin. Experiments were performed to analyze different buffer systems and obtain optimal resolution for the separation. A matrix composed of two different molecular weights of the same polymer was constructed to separate the DNA fragments with baseline resolution, and a cubic spline fit was used to estimate the size of DNA fragments over 350 base pairs. Over 100 samples were examined to demonstrate the rapid, robust and precise characteristics of this CE system. An average relative standard deviation of 0.3% was obtained for the sizing of the D1S80 alleles in these samples. DNA from mixed body fluid samples, samples subjected to environmental insult, and D1S80 sequence variants were also typed successfully. These results demonstrate that CE is a viable method for analysis of D1S80 and amelogenin forensic DNA samples.

Sensitivity, reproducibility, and accuracy in short tandem repeat genotyping using capillary array electrophoresis

The Human Genome Initiative has increased significantly the rate at which disease-causing genes are being mapped and sequenced. New cost-effective methods to locate the genes and to characterize disease-causing mutations require robust, reproducible, and accurate protocols for measuring DNA fragment lengths. Capillary array electrophoresis (CAE) offers rapid, high-resolution separations, high throughput, and sensitive detection. To assess the utility of CAE for the accumulation of genetic information, we tested both sizing accuracy and reproducibility using 48-capillary prototype systems. Two multiplex PCR allelic ladder standards and several CA-repeat markers were analyzed in > 100 runs. Reproducibility in typing > 8000 genotypes reveals a standard deviation of less than 0.2 bp on these systems under optimized conditions. However, sequence-dependent migration anomalies were observed at most simple sequence loci even when analyzed under denaturing conditions, resulting in a systematic bias in estimated fragment sizes. We show here that, by normalizing results to known typing controls, one can obtain locus-averaged accuracies of < 0.06 bp and normalized results within 1 bp of actual. We detect as little as a 1:30,000 dilution of a DNA quantitation standard stained with highly sensitive intercalating dyes, indicating an 80-zeptomole sensitivity limit. However, to obtain reproducible electrokinetic injection, approximately 200 attomoles of fluorescein-labeled DNA is required. These sensitivity limits, sizing precision, and accuracy, together with the 1-hr run times for 48-96 samples, indicate that CAE is a viable method for high-throughput genetic analysis of simple sequence repeat polymorphisms.

Automated polymerase chain reaction product sample preparation for capillary electrophoresis analysis

The analysis of crude polymerase chain reaction (PCR) products by capillary electrophoresis (CE) is often compromised due to the presence of a high concentration of salt. Salt interferes with the electrokinetic injection and induces localized heating within the column; hence, PCR products must be desalted or cleaned-up prior to CE analysis. A variety of commercial clean-up systems are available that have been traditionally used to prepare PCR products for cloning, sequencing and digestion with restriction enzymes. These systems were tested for their effectiveness in preparing PCR products for CE analysis and were evaluated based on CE resolution, salt removal, DNA recovery, processing time and cost. One particularly effective clean-up system, membrane dialysis, was automated using a robotic workstation.