Capillary electrophoresis of DNA for molecular diagnostics

Capillary electrophoresis for the detection of Fragile X expanded alleles

Capillary electrophoresis is an analytical technique that separates ions based on their electrophoresis mobility with the use of an applied voltage. Capillary electrophoresis is used most predominantly in nuclear acid fragment analysis as well as DNA sequencing because it gives faster results and provides high resolution separation. Here we describe an application using capillary electrophoreses for screening the Fragile X expanded alleles to demonstrate the application.

KRAS mutation testing in colorectal cancer

In the US, colorectal cancer is the third leading cause of cancer-related death. Approximately 20% of patients present with metastatic disease, and an additional 30% to 40% develop metastasis during the course of their disease. Patients with metastatic colon cancer have a 5-year survival rate of only 11%. Although surgery is the mainstay of treatment for early stage colon cancer, adjuvant treatment is usually used in patients advanced stage disease. In particular, epidermal growth factor receptor (EGFR) inhibitor therapies have emerged as effective treatments in a subset of patients with metastatic colorectal carcinoma. Two anti-EGFR biologics, cetuximab and panitumumab, have been approved by the Food and Drug Administrations for the treatment of refractory metastatic colorectal carcinoma. Mounting evidence has shown that these therapies are ineffective in tumors with mutations of codons 12 and 13 of exon 2 of the KRAS gene. Because of this compelling data, the National Comprehensive Cancer Network and the American Society of Clinical Oncology have recommended determination of KRAS mutation status in all patients with metastatic colorectal cancer who are candidates for anti-EGFR therapy. Anatomic pathologists play an integral role in coordinating the testing for KRAS mutations, as this assay is performed on tissue samples selected by the pathologist. Herein, the authors present an up-to-date review of the biologic, clinical, and laboratory aspects of KRAS mutation testing in colorectal cancer.

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.

Simultaneous analysis of microsatellite instability and loss of heterozygosity by capillary electrophoresis with a homemade kit

Microsatellite instability (MSI) and loss of heterozygosity (LOH), the alteration in length and strength of short tandem repeat sequences are an important molecular characteristic of many human tumors. MSI and LOH analysis has become an attractive method for diagnostic and tumor research purposes. A method for the simultaneous analysis of MSI and LOH at the five microsatellite loci (BAT-26, D17S261, D3S1283, D2S123 and D3S1611) was developed employing a cheap homemade kit to replace the expensive commercial kit on ABI 310 capillary genetic analyzer. After studying the effect of temperature and urea denaturant on microsatellite analysis, 8 mol/L urea and 60 degrees C were selected for assessing accurately fragment size of microsatellite alleles. Based on this method, 52 sporadic gastric cancers were screened, and MSI and LOH, at least one locus was observed in 15 of 52 (28.8%) patients. Moreover, it is found that a statistically significant association exists between MSI and LOH and tumor-differentiated level.

Glassy Carbon Electrode Modified with Gold Nanoparticles and DNA for the Simultaneous Determination of Uric Acid and Norepinephrine under Coexistence of Ascorbic Acid

A novel biochemical sensor was assembled on a glass carbon electrode by a electrodeposition process. Gold nanoparticles were deposited by potential +1.5 V on the glass carbon electrode. CT-DNA was deposited by potential +1.5 V on the gold nanoparticles array electrode. The properties of the modified electrode were characterized by electrochemical impedance spectroscopy (EIS), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). Our results showed that gold nanoparticles increase the DNA membrane capacitance and reduce the membrane resistance. This modified electrode can selectively determine uric acid and norepinephrine in the presence of a larger amount of ascorbic acid. The fabricated electrode showed good sensitivity, reproducibility, and stability.

Microsatellite analysis in Turner syndrome: parental origin of X chromosomes and possible mechanism of formation of abnormal chromosomes

Turner syndrome is a chromosomal disorder in which all or part of one X chromosome is missing. The meiotic or mitotic origin of most cases remains unknown due to the difficulty in detecting hidden mosaicism and to the lack of meiotic segregation studies. We analyzed 15 Turner patients, 10 with a 45,X whereas the rest had a second cell line with abnormal X-chromosomes: a pseudodicentric, an isochromosome, one large and one small ring, and the last with a long arm deletion. Our aims were: to detect X cryptic mosaicism in patients with a 45,X constitution; to determine the parental origin of the abnormality; to infer the zygotic origin of the karyotype and to suggest the timing and mechanism of the error(s) leading to the formation of abnormal X chromosomes from maternal origin. Molecular investigation did not revealed heterozygosity for any microsatellite, excluding X mosaicism in the 45,X cases. Parental origin of the single X chromosome was maternal in 90% of these patients. Three of the structurally abnormal Xs were maternally derived whereas the other two were paternal. These results allowed us to corroborate breakpoints in these abnormal X chromosomes and suggest that the pseudodicentric chromosome originated from post-zygotic sister chromatid exchange, whereas the Xq deleted chromosome probably arose after a recombination event during maternal meiosis.

Identifying the orientation of DNA fragment in recombinant plasmid by capillary electrophoresis with a non-gel sieving solution

It was demonstrated that a capillary electrophoresis (CE) method with a non-gel sieving solution has been developed to identify the orientation of DNA fragments in recombinant plasmids in molecular biology. The influences of the concentration of sieving polymer HEC, the applied electric field strength and sampling on CE separation were analyzed concerning the optimization of separation. YO-PRO-1 was used as a DNA intercalating reagent to facilitate fluorescence detection. Under the chosen conditions (buffer, 1 x TBE containing 1 microM YO-PRO-1 and 1.2% HEC; applied electric field strength, 200 V/cm; electrokinetic sampling: time, 5 s; voltage, -6 kV), three DNA markers (phi 174/HaeIII, pBR322/HaeIII and lambda DNA/HindIII) were tested for further evaluating the relationship between the DNA size and the mobility. The established CE method conjugated with the enzymatic approach was successfully applied to identifying the DNA orientation of recombinant plasmid in transgene operations of a newly cloned gene from Arabidopsis Thaliana.

Miniaturization Technologies for Molecular Diagnostics

Background: Molecular diagnostics devices are becoming smaller. With the advancement of miniaturization technologies, microchip-based systems will soon be available for genetic testing. The purpose of this review is to highlight the underlying principles in miniaturization, the strategies being developed for bioanalysis, and the potential impact on the practice of this rapidly growing medical discipline.

Approach: The author discusses DNA microchips and their practical importation into the clinical laboratory, based on his background in medical device and microchip design and development. His discussion is supported by a body of literature covering both biomedical and electrical engineering and more recent publications in the field of molecular genetics and pathology.

Content: This review is descriptive and intended to outline the technologic and methodologic approaches to the creation of an integrated genetic analysis instrument based on miniature components. The review draws on published scientific evaluations of these devices without regard to the companies involved in their development.

Summary: The intent of this review is that the reader will better understand the variety of technical approaches toward the miniaturization of molecular genetic testing for the clinical laboratory. With insight into the principles underlying the operation of these chips and the integrated systems, the end user can better evaluate the value to the field in terms of making molecular genetics testing simpler, faster, and less expensive.

Single-strand conformation polymorphism analysis to detect the p53 mutation in colon tumor samples by capillary electrophoresis

The polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) technique is developed for the detection of point mutations in DNA samples, and is very useful in the research of tumors. The traditional SSCP was carried out with slab gel electrophoresis (SGE), but this is time-consuming and labor-intensive, particularly for clinical diagnoses. We have developed a capillary electrophoresis (CE) method for SSCP detection with a linear polyacrylamide gel solution as the sieving matrix. Twenty colon tumor samples were detected with SSCP-CE and the point mutation in exon 7 of the p53 gene was found in six of the samples. Based on the sequencing results, the accuracy of SSCP-CE was better than that of SSCP-SGE. We hope this rapid and convenient method could be applied in the clinical diagnosis of tumors soon.

Capillary electrophoresis coupled to biosensor detection

The present review highlights some modern aspects of biosensor revelation, a detection method which has already found a large number of applications in healthcare, food industry and environmental analysis. First, the concept of bio-recognition, which is at the heart of biosensor technology, is discussed, with emphasis on host-guest-like recognition mechanisms. This detection device has been successfully coupled, in its first applications, to chromatographic columns, which allow a high resolution of complex mixtures of analytes prior to interaction with the biosensing unit. The properties of the transducing elements, which should generate a signal (e.g., electrochemical, thermal, acoustic, optical) of proper intensity and of relative fast rise, are additionally evaluated and discussed. The review then focuses on potential applications of biosensing units in capillary electrophoresis (CE) devices. CE appears to be an excellent separation methodology to be coupled to biosensor detection, since it is based on miniaturized electrophoretic chambers, fast analysis times, complete automation in sample handling and data treatment and requires extremely small sample volumes. Although only a few applications of CE-based biosensors have been described up to the present, it is anticipated that this hyphenated technique could have a considerable expansion in the coming years.

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.

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.

Capillary electrophoresis in clinical and forensic analysis: recent advances and breakthrough to routine applications

This paper is a comprehensive review article on capillary electrophoresis (CE) in clinical and forensic analysis. It is based upon the literature of 1997 and 1998, presents CE examples in major fields of application, and provides an overview of the key achievements encountered, including those associated with the analysis of drugs, serum proteins, hemoglobin variants, and nucleic acids. For CE in clinical and forensic analysis, the past two years witnessed a breakthrough to routine applications. As most coauthors of this review are associated with diagnostic or forensic laboratories now using CE on a routine basis, this review also contains data from routine applications in drug, protein, and DNA analysis. With the first-hand experience of providing analytical service under stringent quality control conditions, aspects of quality assurance, assay specifications for clinical and forensic CE and the pros and cons of this maturing, cost-and pollution-controlled age technology are also discussed.

Application of capillary electrophoresis at low pH to oligonucleotides quality control

A method for oligonucleotides analysis by using capillary electrophoresis at low pH in free solution is described. It may be considered an alternative to classical analytical techniques which use basic buffers and require the presence of sieving media to separate oligonucleotides as a function of their length. On the contrary, at low pH oligo nucleotides can be separated only depending on their base composition. A large set of samples consisting of 72 synthetic oligonucleotides bearing a 5'-alkylamine moiety and designed for HLA genotyping were analysed. The quality of these synthetic oligos was easily assessed, and a single base difference in oligonucleotides of equal sequence was detected. The results suggest the application of this method to the emerging field of mutation detection and single nucleotide polymorfism analysis.

Strategies for capillary electrophoresis: method development and validation for pharmaceutical and biological applications

This review is in support of the development of selective, reproducible and validated capillary electrophoretis (CE) methods. Focusing on pharmaceutical and biological applications, the successful use of CE is demonstrated by more than 800 references, mainly from 1994 until 1998. Approximately 80 recent reviews have been catalogued. These articles sum up the existing strategies for method development in CE, especially in the search for generally accepted concepts, but also looking for new, promising reagents and ideas. General strategies for method development were derived not only with regard to selectivity and efficiency, but also with regard to precision, short analysis time, limit of detection, sample pretreatment requirements and validation. Standard buffer recipes, surfactants used in micellar electrokinetic capillary chromatography (MEKC), chiral selectors, useful buffer additives, polymeric separation media, electroosmotic flow (EOF) modifiers, dynamic and permanent coatings, actions to deal with complex matrices and aspects of validation are collected in 20 tables. Detailed schemes for the development of MEKC methods and chiral separations, for optimizing separation efficiency, means of troubleshooting, and other important information for key decisions during method development are given in 19 diagrams. Method development for peptide and protein separations, possibilities to influence the EOF and how to stabilize it, as well as indirect detection are considered in special sections.

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.

Capillary zone electrophoresis of ds-DNA in isoelectric buffers: effect of adding of competing, nonamphoteric ions

When separating ds-DNA in isoelectric His buffer (pH=pI=7.6), in the 50-250 mM concentration range, some unique phenomena were observed: improved resolution for smaller DNA fragments, up to ca. 150 bp, and a rapid deterioration of resolution above this critical length (which corresponds to the persistence length). Such phenomenon depended also on voltage and concentration of sieving liquid polymer. Direct binding of His to the DNA helix was hypothesized, with resultant stiffening and an increment of diameter of the DNA fragments, thus inducing an early onset of reptation at the applied voltage in the 100-300 V/cm range. In order to prove this hypothesis, "competing ions" (notably NaCl and KBr) were added to the His background electrolyte: a partial reversal of the His effect was already apparent at low concentrations of such ions (10 mM) and was complete at higher concentrations (30 and 50 mM). By molecular modeling, it was found that His could be docking on the negatively charged oxygen (bound to the phosphate) by offering both charged (primary and tertiary amino) groups to simultaneous binding, thus forming a salt and neutralizing the negative charge borne by the oxygen. The following characteristic bond distances were found: 0.34 nm between the N (imidazolic) and O; 0.32 nm between the primary N and O; 0.36 nm between the two nitrogens engaged in salt formation with the oxygen. In addition, for complexation to occur, the distance between the noncharged nitrogen in the imidazole ring and the nearest phosphate oxygen (engaged in the phosphodiester bridge) should be 0.44 nm. Under these conditions, the two rings present (a six-membered, ideal one, salt-linked with the oxygen and rather highly elongated, and the imidazole) will not be precisely coplanar, since the primary and tertiary nitrogens will be one slightly above and one slightly below the plane of the drawing. 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.