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

Detection and differentiation of Entamoeba histolytica and Entamoeba dispar in clinical samples through PCR-denaturing gradient gel electrophoresis

Amebiasis is one of the twenty major causes of disease in Mexico; however, the diagnosis is difficult due to limitations of conventional microscopy-based techniques. In this study, we analyzed stool samples using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to differentiate between Entamoeba histolytica (pathogenic) and E. dispar (non-pathogenic). The target for the PCR amplification was a small region (228 bp) of the adh112 gene selected to increase the sensitivity of the test. The study involved 62 stool samples that were collected from individuals with complaints of gastrointestinal discomfort. Of the 62 samples, 10 (16.1%) were positive for E. histolytica while 52 (83.9%) were negative. No sample was positive for E. dispar. These results were validated by nested PCR-RFLP (restriction fragment length polymorphism) and suggest that PCR-DGGE is a promising tool to differentiate among Entamoeba infections, contributing to determine the specific treatment for patients infected with E. histolytica, and therefore, avoiding unnecessary treatment of patients infected with the non-pathogenic E. dispar.

DNA diagnosis by capillary electrophoresis and microfabricated electrophoretic devices

DNA diagnosis is experiencing an impressive progression towards the development of novel technology to identify various clinically relevant categories of genetic changes and to meet the exponential growth of genomics. The introduction of capillary electrophoresis has dramatically accelerated the completion of the first draft of the human DNA sequence in the Human Genome Project, and thus, has become the method of choice for analysis of various genetic variants. The recent development of microfabricated electrophoretic devices has led to the possibility of integrating multiple sample handling with the actual measurement steps required for automation of molecular diagnostics. This review highlights the most recent progress in capillary electrophoresis and electrophoretic microdevices for DNA-based diagnostics, including the important areas of genotyping for point mutation, single nucleotide polymorphisms, short tandem repeats and organism identification. The application of these techniques for infectious and genetic disease diagnosis, as well as forensic identification purpose, are covered. The promising development and the challenges for techinical problems are also discussed.

Perspectives on analyses of nucleic acid constituents: the basis of genomics

The recent mapping of the human genome was a tremendous achievement made possible to a large degree by the development of analytical methods for sequencing purine and pyrimidine bases in nucleic acids. In the last 3 decades, the number of analyses of nucleic acids and their constituents by HPLC and capillary electrophoresis (CE) has exploded. These techniques have been used not only for genomics, but also for the determination of free nucleotides, nucleosides and their bases in body fluids and tissues. Although a large number of HPLC and CE papers have been published on nucleic acid constituent applications, relatively little has been written on the mechanisms of the separations. However, to optimize analytical conditions knowledgeably and rapidly, it is important to know why and how these separations occur and the factors that affect them. The HPLC methods for the analysis of nucleic acid constituents and the information available on some of the mechanisms of separation of nucleotides, nucleosides and their bases, as well as the analysis of these compounds by CE and the factors that affect these separations are discussed.

A separation carrier in high-speed proteome analysis by capillary electrophoresis

We obtained a high-efficiency separation carrier for proteome analysis by capillary electrophoresis. The addition of curdlan or laminaran to the run buffer hastened the migration time without any degradation in resolution. We propose that for the development of the separation carrier it is necessary to synthetically analyze each of the following mobility factors of electroosmotic flow: buffer ionic strength, additional disturbance and adsorption. The total analysis for buffer and additive will be useful for designing high-throughput screening (HTS) systems for proteome analysis without annoying adsorption.

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.

Capillary affinity gel electrophoresis: new technique for specific recognition of DNA sequence and the mutation detection on DNA

The present state of studies on capillary affinity gel electrophoresis, which is a new technique for the specific recognition of a target DNA sequence, is reviewed. This article includes the principle, theory, methods, and applications of this technology. The great potential of capillary affinity gel electrophoresis for the sequence-specific recognition of DNA and the detection of mutations in specific genes is illustrated.

Capillary electrophoresis of DNA in the 20-500 bp range: recent developments

The present mini-review summarizes recent developments in the field of DNA separations by capillary zone electrophoresis (CZE), as developed by our group. Separation of antisense oligonucleotides in sieving liquid polymers in isoelectric buffers is first discussed. It is shown that the use of isoelectric buffers (notably His) permits very high voltage gradients (up to 1,000 V/cm) with much reduced transit times and increased resolution of all truncated and failed sequences. Oligonucleotides can also be analyzed by zone electrophoresis against a stationary pH gradient (typically a pH 6.5-10 range): if injected at the alkaline end, the sample components experience stacking and zone sharpening due to modulation of charge as the oligonucleotides move along the pH gradient. Oligonucleotides having the same length, but differing by one single nucleotide in the chain, can be separated in free solution (i.e., in the absence of a sieving matrix) at strongly acidic pH values (pH 3.0-3.3) where charge differences due to base protonation are maximized. By working in free solution, it has also been possible to measure accurately the free mobility of DNAs, shown to reach a constant value of 3.75+/-0.04 10(-4) cm2 V(-1) s(-1) at 25 degrees C and in Tris-acetate-EDTA buffer, pH 8.3, above a critical length of ca. 400 bp. However, when double-stranded, rather than single-stranded, DNA is analyzed in isoelectric His buffer, some peculiar phenomena are observed: improved resolution for smaller DNA fragments (up to ca. 150 bp) and a rapid deterioration of resolution above this critical length. Direct binding of His to the DNA helix is hypothesized, via a bidentate salt bridge of the two charged amino groups of His on the negatively charged oxygen of the phosphate group. Upon extensive binding, occupying every available phosphate site, pi-pi interactions could occur among the stacks of bound His residues, thus further stabilizing the complex.

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.