The use of capillary electrophoresis for DNA polymorphism analysis

Capillary electrophoresis has advanced enormously over the last 10 yr as a tool for DNA sequencing, driven by the human and other major genome projects and by the need for rapid electrophoresis-based DNA diagnostic tests. The common need of these analyses is a platform providing very high throughput, high-quality data, and low process costs. These demands have led to capillary electrophoresis machines with multiple capillaries providing highly parallel analyses, to new electrophoresis matrices, to highly sensitive spectrofluorometers, and to brighter, spectrally distinct fluorescent dyes with which to label DNA. Capillary devices have also been engineered onto microchip formats, on which both the amount of sample required for analysis and the speed of analysis are increased by an order of magnitude. This review examines the advances made in capillary and chip-based microdevices and in the different DNA-based assays developed for mutation detection and genotype analysis using capillary electrophoresis. The automation of attendant processes such as for DNA sample preparation, PCR, and analyte purification are also reviewed. Together, these technological developments provide the throughput demanded by the large genome-sequencing projects.

[1]  P. McEwan,et al.  Eight hundred-base sequencing in a microfabricated electrophoretic device. , 2000, Analytical chemistry.

[2]  S. R. Park,et al.  Base stacking: pH-mediated on-column sample concentration for capillary DNA sequencing. , 1998, Analytical chemistry.

[3]  D. Schmalzing,et al.  Recent advances in DNA sequencing by capillary and microdevice electrophoresis , 2001, Electrophoresis.

[4]  X. Le,et al.  Fluorescence polarization detection for affinity capillary electrophoresis , 2002, Electrophoresis.

[5]  F. Regnier,et al.  Chromatography and electrophoresis on chips: critical elements of future integrated, microfluidic analytical systems for life science. , 1999, Trends in biotechnology.

[6]  William G. Thilly,et al.  Combination of Competitive Quantitative PCR and Constant-Denaturant Capillary Electrophoresis for High-Resolution Detection and Enumeration of Microbial Cells , 2001, Applied and Environmental Microbiology.

[7]  W. Kuhr,et al.  Capillary gel electrophoresis with sinusoidal voltammetric detection: a strategy to allow four-"color" DNA sequencing. , 2001, Analytical chemistry.

[8]  Enhanced throughput for DNA sequencing by capillary array electrophoresis with a gradient of electric field strength. , 2001, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.

[9]  J. Bashkin.  Determining dye-induced DNA mobility shifts for DNA sequencing fragments by capillary electrophoresis. , 2001, Methods in molecular biology.

[10]  Z. Rónai,et al.  DNA analysis on electrophoretic microchips: Effect of operational variables , 2001, Electrophoresis.

[11]  J. Butler,et al.  Detection of DNA polymorphisms using PCR-RFLP and capillary electrophoresis. , 2001, Methods in molecular biology.

[12]  H. Swerdlow,et al.  Capillary gel electrophoresis for DNA sequencing. Laser-induced fluorescence detection with the sheath flow cuvette. , 1990, Journal of chromatography.

[13]  D. J. Harrison,et al.  Red diode laser induced fluorescence detection with a confocal microscope on a microchip for capillary electrophoresis. , 2000, Biosensors & bioelectronics.

[14]  M. Uhlén,et al.  Single-nucleotide polymorphism analysis by pyrosequencing. , 2000, Analytical biochemistry.

[15]  A. Hatakka,et al.  Silver stained polyacrylamide gels and fluorescence-based automated capillary electrophoresis for detection of amplified fragment length polymorphism patterns obtained from white-rot fungi in the genus Trametes. , 2000, Journal of microbiological methods.

[16]  P. Williams,et al.  Quantitation of mRNA by competitive PCR using capillary electrophoresis. , 2001, Methods in molecular biology.

[17]  J. Landers,et al.  Effective capillary electrophoresis-based heteroduplex analysis through optimization of surface coating and polymer networks. , 2000, Analytical chemistry.

[18]  P. Boček,et al.  DNA analysis under highly denaturing conditions in bare fused silica capillaries. , 2001, Methods in molecular biology.

[19]  J. G. Chirikjian,et al.  Mutation identification DNA analysis system (MIDAS) for detection of known mutations , 1999, Electrophoresis.

[20]  G. Mátyás,et al.  Quantification of single nucleotide polymorphisms: A novel method that combines primer extension assay and capillary electrophoresis , 2002, Human mutation.

[21]  Andersen,et al.  Mutation Detection by Cleavase in Combination With Capillary Electrophoresis Analysis: Application to Mutations Causing Hypertrophic Cardiomyopathy and Long-QT Syndrome. , 1998, Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology.

[22]  Bruce P. Neri,et al.  Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes , 1999, Nature Biotechnology.

[23]  M. Vaneechoutte,et al.  Application and Evaluation of the Interlaboratory Reproducibility of tRNA Intergenic Length Polymorphism Analysis (tDNA-PCR) for Identification of StreptococcusSpecies , 2001, Journal of Clinical Microbiology.

[24]  S. Lillard,et al.  Measurement of single-cell gene expression using capillary electrophoresis. , 2001, Analytical chemistry.

[25]  A. Pingoud,et al.  Influence of fluorophor dye labels on the migration behavior of polymerase chain reaction – amplified short tandem repeats during denaturing capillary electrophoresis , 2001, Electrophoresis.

[26]  J L Viovy,et al.  New block‐copolymer thermoassociating matrices for DNA sequencing: Effect of molecular structure on rheology and resolution , 2001, Electrophoresis.

[27]  J. Landers,et al.  Direct quantitation of RNA transcripts by competitive single-tube RT-PCR and capillary electrophoresis. , 1998, BioTechniques.

[28]  D. Fang,et al.  Separation of double‐stranded DNA fragments by capillary electrophoresis in interpenetrating networks of polyacrylamide and polyvinylpyrrolidone , 2001, Electrophoresis.

[29]  N. Dovichi,et al.  A multiple-capillary electrophoresis system for small-scale DNA sequencing and analysis. , 1999, Nucleic acids research.

[30]  D. Fang,et al.  Fast DNA sequencing up to 1000 bases by capillary electrophoresis using poly(N,N‐dimethylacrylamide) as a separation medium , 2001, Electrophoresis.

[31]  B. Gaš,et al.  Effect of temperature on the separation of long DNA fragments in polymer solution. , 2001, Journal of chromatography. A.

[32]  X. Zhao,et al.  Differential display analysis by capillary electrophoresis. , 2001, Methods in molecular biology.

[33]  P. Righetti,et al.  An isoelectrically trapped enzyme reactor operating in an electric field , 1998, Electrophoresis.

[34]  C. Koertje,et al.  Capillary electrophoresis-mass spectrometric analysis of DNA adducts. , 2001, Methods in molecular biology.

[35]  M. Metzker,et al.  Electrophoretically Uniform Fluorescent Dyes for Automated DNA Sequencing , 1996, Science.

[36]  J. Landers,et al.  Exploiting sensitive laser-induced fluorescence detection on electrophoretic microchips for executing rapid clinical diagnostics. , 2001, Luminescence : the journal of biological and chemical luminescence.

[37]  Piero Carninci,et al.  RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer. , 2000, Genome research.

[38]  Gregor Ocvirk,et al.  Integrated microfluidic electrophoresis system for analysis of genetic materials using signal amplification methods. , 2002, Analytical chemistry.

[39]  J. Viovy,et al.  Robust field inversion capillary electrophoretic separation of long DNA fragments. , 2001, Methods in molecular biology.

[40]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[41]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.

[42]  W. Xie,et al.  Microchip-based capillary electrophoresis systems. , 2001, Methods in molecular biology.

[43]  J. Xian.  Capillary DNA-protein mobility shift assay. , 2001, Methods in molecular biology.

[44]  S. Soper,et al.  Near‐infrared laser‐induced fluorescence detection in capillary electrophoresis , 2000, Electrophoresis.

[45]  P. Grodzinski,et al.  Microfabricated polycarbonate CE devices for DNA analysis. , 2001, Analytical chemistry.

[46]  M. Sepaniak,et al.  Evaluation of a sheath flow cuvette for postcolumn fluorescence derivatization of DNA fragments separated by capillary electrophoresis. , 1998, Analytical chemistry.

[47]  E. Yeung,et al.  Side-entry excitation and detection of square capillary array electrophoresis for DNA sequencing. , 1999, Journal of chromatography. A.

[48]  M. Uhlén,et al.  Cooperative oligonucleotides in purification of cycle sequencing products. , 2000, BioTechniques.

[49]  N. Dovichi,et al.  Instrumentation for chemical cytometry. , 2000, Analytical chemistry.

[50]  Q Gao,et al.  Multiple-channel microchips for high-throughput DNA analysis by capillary electrophoresis , 2001, Fresenius' journal of analytical chemistry.

[51]  X. Le,et al.  Immunofluorescence detection of radiation-induced DNA base damage. , 2002, Military medicine.

[52]  D. Rank,et al.  Sub-microliter DNA sequencing for capillary array electrophoresis. , 2000, Journal of chromatography. A.

[53]  Christian M. Ruitberg,et al.  Capillary electrophoresis as a tool for optimization of multiplex PCR reactions , 2001, Fresenius' journal of analytical chemistry.

[54]  S. Lassiter,et al.  Sanger DNA-sequencing reactions performed in a solid-phase nanoreactor directly coupled to capillary gel electrophoresis. , 1998, Analytical chemistry.

[55]  R. Zhu,et al.  Post-column derivatization for fluorescence and chemiluminescence detection in capillary electrophoresis. , 1998, Journal of pharmaceutical and biomedical analysis.

[56]  B. McCord,et al.  Temperature and pH studies of short tandem repeat systems using capillary electrophoresis at elevated pH , 2001, Electrophoresis.

[57]  S S Chan,et al.  Sorting biomolecules with microdevices , 2000, Electrophoresis.

[58]  W. Thilly,et al.  Two-point fluorescence detection and automated fraction collection applied to constant denaturant capillary electrophoresis. , 2000, BioTechniques.

[59]  Synchronized cyclic capillary electrophoresis using channels arranged in a triangle and low voltages , 2001, Fresenius' journal of analytical chemistry.

[60]  M. Cretich,et al.  Capillary coatings. Choices for capillary electrophoresis of DNA. , 2001, Methods in molecular biology.

[61]  F. Kramer,et al.  Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. , 1998, Nucleic acids research.

[62]  B. Lin,et al.  Spatial temperature gradient capillary electrophoresis for DNA mutation detection , 2001, Electrophoresis.

[63]  M. Quesada,et al.  Formation of concentration gradient and its application to DNA capillary electrophoresis , 2000, Electrophoresis.

[64]  T. Tahira,et al.  SSCP analysis of point mutations by multicolor capillary electrophoresis. , 1999, Methods in molecular biology.

[65]  P. Nilsson,et al.  Mutational scanning of PCR products by subtractive oligonucleotide hybridization analysis. , 1999, BioTechniques.

[66]  E. Yeung,et al.  DNA capillary electrophoresis in entangled dynamic polymers of surfactant molecules. , 2001, Analytical chemistry.

[67]  P. Boček,et al.  Fast separation of DNA sequencing fragments in highly alkaline solutions of linear polyacrylamide using electrophoresis in bare silica capillaries , 2001, Electrophoresis.

[68]  R Madabhushi,et al.  DNA sequencing in noncovalently coated capillaries using low viscosity polymer solutions. , 2001, Methods in molecular biology.

[69]  M. Heller,et al.  Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips , 1998, Nature Biotechnology.

[70]  B Budowle,et al.  Validation of STR typing by capillary electrophoresis. , 2001, Journal of forensic sciences.

[71]  G. S. Wilson,et al.  MicroITIES detection of nitrate by facilitated ion transfer. , 2001, Analytical chemistry.

[72]  P. Wilding,et al.  Microchip module for blood sample preparation and nucleic acid amplification reactions. , 2001, Genome research.

[73]  D C Ward,et al.  Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[74]  T Fujii,et al.  Microfabricated Polymer Chip for Capillary Gel Electrophoresis , 2001, Biotechnology progress.

[75]  D. Ehrlich,et al.  Optimization of high-performance DNA sequencing on short microfabricated electrophoretic devices. , 2000, Analytical chemistry.

[76]  H. Coller,et al.  High resolution analysis of point mutations by constant denaturant capillary electrophoresis (CDCE). , 2001, Methods in molecular biology.

[77]  S S Chan,et al.  Separation of 100-kilobase DNA molecules in 10 seconds. , 2001, Analytical chemistry.

[78]  On-line nanoliter cycle sequencing reaction with capillary zone electrophoresis purification for DNA sequencing. , 2001, Journal of chromatography. A.

[79]  E. Yeung,et al.  High-throughput single-molecule DNA screening based on electrophoresis. , 2000 .

[80]  Christoph Heller,et al.  Principles of DNA separation with capillary electrophoresis , 2001, Electrophoresis.

[81]  J P Landers,et al.  Polymerase chain reaction in polymeric microchips: DNA amplification in less than 240 seconds. , 2001, Analytical biochemistry.

[82]  S J Lillard,et al.  Continuous cell introduction for the analysis of individual cells by capillary electrophoresis. , 2001, Analytical chemistry.

[83]  E. Yeung,et al.  Single‐molecule immunoassay and DNA diagnosis , 2001, Electrophoresis.

[84]  F. Oaks,et al.  Separating DNA sequencing fragments without a sieving matrix , 1999, Electrophoresis.

[85]  W. Krzyzosiak,et al.  Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection. , 2001, Nucleic acids research.

[86]  Z. Rónai,et al.  Rapid single nucleotide polymorphism analysis by primer extension and capillary electrophoresis using polyvinyl pyrrolidone matrix , 2001, Electrophoresis.

[87]  P. Righetti,et al.  The state of the art of dynamic coatings , 2001, Electrophoresis.

[88]  R A Mathies,et al.  Capillary electrophoresis chips with integrated electrochemical detection. , 1998, Analytical chemistry.

[89]  Q. Fang,et al.  A high-throughput continuous sample introduction interface for microfluidic chip-based capillary electrophoresis systems. , 2002, Analytical chemistry.

[90]  H Nakanishi,et al.  Field‐inversion electrophoresis on a microchip device , 2001, Electrophoresis.

[91]  Yongseong Kim,et al.  DNA sequencing with pulsed‐field capillary electrophoresis in poly(ethylene oxide) matrix , 1997, Electrophoresis.

[92]  D. J. Lecaptain,et al.  Characterization of DNA-protein complexes by capillary electrophoresis-single molecule fluorescence correlation spectroscopy. , 2001, The Analyst.

[93]  Brian N. Johnson,et al.  An integrated nanoliter DNA analysis device. , 1998, Science.

[94]  R. Kennedy,et al.  Aptamers as ligands in affinity probe capillary electrophoresis. , 1998, Analytical chemistry.

[95]  A Paulus,et al.  Rapid, parallel separations of d1S80 alleles in a plastic microchannel chip. , 2000, Journal of chromatography. A.

[96]  L J Kricka,et al.  Analysis of ligase chain reaction products amplified in a silicon-glass chip using capillary electrophoresis. , 1996, Journal of chromatography. A.

[97]  J. Zahn,et al.  Microchannel DNA sequencing matrices with a thermally controlled "viscosity switch". , 2001, Analytical chemistry.

[98]  H. John Crabtree,et al.  Construction and evaluation of a capillary array DNA sequencer based on a micromachined sheath‐flow cuvette , 2000, Electrophoresis.

[99]  L J Kricka,et al.  Degenerate oligonucleotide primed-polymerase chain reaction and capillary electrophoretic analysis of human DNA on microchip-based devices. , 1998, Analytical biochemistry.

[100]  DNA sequencing by capillary electrophoresis using mixtures of polyacrylamide and poly(N,N-dimethylacrylamide). , 2001, Journal of chromatography. A.

[101]  M. Ferrari,et al.  Amplification refractory mutation system analysis of point mutations by capillary electrophoresis. , 2001, Methods in molecular biology.

[102]  M. Burns,et al.  Electrophoretic separations using sweeping fields , 1998, Electrophoresis.

[103]  X. Le,et al.  Studies of protein--DNA interactions by capillary electrophoresis/laser-induced fluorescence polarization. , 2000, Analytical chemistry.

[104]  S. Lillard,et al.  In-situ sampling and separation of RNA from individual mammalian cells. , 2000, Analytical chemistry.

[105]  T Fujii,et al.  Integration of gene amplification and capillary gel electrophoresis on a polydimethylsiloxane‐glass hybrid microchip , 2001, Electrophoresis.

[106]  R A Mathies,et al.  Loss of heterozygosity assay for molecular detection of cancer using energy-transfer primers and capillary array electrophoresis. , 2000, Genome research.

[107]  P. Vouros,et al.  Capillary electrochromatography-mass spectrometry for the separation and identification of isomeric polyaromatic hydrocarbon DNA adducts derived from in vitro reactions. , 2000, Journal of chromatography. A.

[108]  E. Yeung,et al.  Automated and integrated system for high-throughput DNA genotyping directly from blood. , 1999, Analytical chemistry.

[109]  G. Whitesides,et al.  A prototype two-dimensional capillary electrophoresis system fabricated in poly(dimethylsiloxane). , 2002, Analytical chemistry.

[110]  R. Pal,et al.  Microfabricated reaction and separation systems. , 2001, Current Opinion in Biotechnology.

[111]  J. Roeraade,et al.  DNA sequencing at elevated temperature by capillary electrophoresis. , 2001, Methods in molecular biology.

[112]  M. Sauer,et al.  Single molecule DNA sequencing in submicrometer channels: state of the art and future prospects. , 2001, Journal of biotechnology.

[113]  M. Stratton,et al.  Rapid detection of DNA sequence variants by conformation-sensitive capillary electrophoresis. , 2000, Genomics.

[114]  Determination of the protooncogene ets-2 gene transcript in human brain at the atto-gram-level by the use of competitive RT/PCR , 2005, Amino Acids.

[115]  B. Chu,et al.  Spatial open‐network formed by mixed triblock copolymers as a new medium for double‐stranded DNA separation by capillary electrophoresis , 2001, Electrophoresis.

[116]  Igor L. Medintz,et al.  Genotyping energy-transfer-cassette-labeled short-tandem-repeat amplicons with capillary array electrophoresis microchannel plates. , 2001, Clinical chemistry.

[117]  Igor L. Medintz,et al.  Single-molecule DNA amplification and analysis in an integrated microfluidic device. , 2001, Analytical chemistry.

[118]  M. Ferrari,et al.  Point mutation detection by temperature-programmed capillary electrophoresis. , 2001, Methods in molecular biology.

[119]  M. Chiari,et al.  Use of peptide nucleic acid probes for detecting DNA single‐base mutations by capillary electrophoresis , 2002, Electrophoresis.

[120]  D. Deforce,et al.  Analysis of DNA damage using capillary zone electrophoresis and electrospray mass spectrometry. , 2001, Methods in molecular biology.

[121]  J. Roeraade,et al.  Laser-induced fluorescence detection by liquid core waveguiding applied to DNA sequencing by capillary electrophoresis. , 2000, Analytical chemistry.

[122]  J P Landers,et al.  Capillary and microchip electrophoresis for rapid detection of known mutations by combining allele-specific DNA amplification with heteroduplex analysis. , 2001, Clinical chemistry.

[123]  G. Sayler,et al.  Capillary Electrophoresis as a Method to Study DNA Reassociation , 2001, Biotechnology progress.

[124]  R A Mathies,et al.  Turn geometry for minimizing band broadening in microfabricated capillary electrophoresis channels. , 2000, Analytical chemistry.

[125]  K. Klepárník,et al.  Ultra-fast DNA separations using capillary electrophoresis. , 2001, Methods in molecular biology.

[126]  Genotyping by microdevice electrophoresis. , 2001, Methods in molecular biology.

[127]  M. Schell,et al.  Footprinting with an automated capillary DNA sequencer. , 2000, BioTechniques.

[128]  R. Mathies,et al.  Single-molecule detection of DNA separations in microfabricated capillary electrophoresis chips employing focused molecular streams. , 1999, Analytical chemistry.

[129]  K. Mitchelson,et al.  Using MF-PCR to diagnose multiple defects from single cells: implications for PGD , 2001, Molecular and Cellular Endocrinology.

[130]  D. J. Harrison,et al.  A multireflection cell for enhanced absorbance detection in microchip‐based capillary electrophoresis devices , 2000, Electrophoresis.

[131]  A. Barron,et al.  Impact of polymer hydrophobicity on the properties and performance of DNA sequencing matrices for capillary electrophoresis , 2001, Electrophoresis.

[132]  M. Fox,et al.  Genetic fingerprinting of grape plant (Vitis vinifera) using random amplified polymorphic DNA (RAPD) analysis and dynamic size-sieving capillary electrophoresis. , 2000, Journal of agricultural and food chemistry.

[133]  J. Viovy,et al.  Collection of capillary electrophoresis fractions on a moving membrane. , 2001, Methods in molecular biology.

[134]  G. Whitesides,et al.  Microfabrication inside capillaries using multiphase laminar flow patterning , 1999, Science.

[135]  P. Wilding,et al.  Agilent 2100 Bioanalyzer for Restriction Fragment Length Polymorphism Analysis of the Campylobacter jejuni Flagellin Gene , 2001, Journal of Clinical Microbiology.

[136]  E. Yeung,et al.  Integrated electroosmotically-driven on-line sample purification system for nanoliter DNA sequencing by capillary electrophoresis. , 2000, Journal of chromatography. A.

[137]  Performances of new sugar‐bearing poly(acrylamide) copolymers as DNA sieving matrices and capillary coatings for electrophoresis , 2001, Electrophoresis.

[138]  J. Korlach,et al.  DNA fragment sizing by single molecule detection in submicrometer-sized closed fluidic channels. , 2002, Analytical chemistry.

[139]  R A Mathies,et al.  Optimization of high-speed DNA sequencing on microfabricated capillary electrophoresis channels. , 1999, Analytical chemistry.

[140]  G. Bruin,et al.  Recent developments in electrokinetically driven analysis on microfabricated devices , 2000, Electrophoresis.

[141]  Harrison Dj,et al.  Chemiluminescence detection in integrated post‐separation reactors for microchip‐based capillary electrophoresis and affinity electrophoresis , 1998 .

[142]  S. Soper,et al.  Nanoliter-scale sample preparation methods directly coupled to polymethylmethacrylate-based microchips and gel-filled capillaries for the analysis of oligonucleotides. , 1999, Journal of chromatography. A.

[143]  P. Fortina,et al.  Analysis of short tandem repeat markers by capillary array electrophoresis. , 2001, Methods in molecular biology.

[144]  B. Karger,et al.  Fraction collection in micropreparative capillary zone electrophoresis and capillary isoelectric focusing , 2000, Electrophoresis.

[145]  A. Ewing,et al.  Electrophoresis in nanometer inner diameter capillaries with electrochemical detection. , 2001, Analytical chemistry.

[146]  L. Kotler,et al.  DNA sequencing up to 1300 bases in two hours by capillary electrophoresis with mixed replaceable linear polyacrylamide solutions. , 2000, Analytical chemistry.

[147]  D. Hsiang,et al.  Automated DNA mutation analysis by single-strand conformation polymorphism using capillary electrophoresis with laser-induced fluorescence detection , 2000, Molecular biotechnology.

[148]  N. Dovichi,et al.  Two-dimensional direct-reading fluorescence spectrograph for DNA sequencing by capillary array electrophoresis. , 2001, Analytical chemistry.

[149]  B. Chu,et al.  Clay‐enhanced DNA separation in low‐molecular‐weight poly(N,N‐dimethylacrylamide) solution by capillary electrophoresis , 2001, Electrophoresis.

[150]  N. Dovichi,et al.  The effect of temperature oscillations on DNA sequencing by capillary electrophoresis. , 2001, Analytical chemistry.