DNA analysis, by capillary electrophoresis

Muller, O., Minarik, M., and Foret, F., Ultrafast DNA analysis by capillary Electrophoresis/laser-induced fluorescence detection, Electrophoresis, 19,1436, 1998. 

Fasco MJ, Treanor CP, Spivack S, Figge HL, Kaminsky LS (1995) Quantitative RNA-polymerase chain reaction—DNA analysis by capillary electrophoresis and laser induced fluorescence. Anal Biochem 224 140-147. 

Righetti PG, Gelfi C, DWcunto MR. Recent progress in DNA analysis by capillary electrophoresis. Electrophoresis 2002 23 1361-74. 

Gao, Q., Shi, Y., and Liu, S., Multiple-channel microchips for high-throughput DNA analysis by capillary electrophoresis, Fresenius J. Anal. Chem., 371, 137, 2001. 

The limitations of microtechnology are invariably related to the concentration of the analyte or type of cell under study. If the device is only capable, of receiving microliter quantities, then the final signal strength being measured will depend on the inclusion of an amplification process (e.g., PCR) or the ability to detect extremely low levels of analyte concentration or type of cell identification. For example, only O.SpL of whole blood are necessary to ahow for isolation of 500 WBCs, more than sufficient to provide genomic DNA for mutation detection by PCR. Similarly, submicroliter quantities of protein or DNA solutions provide adequate material for analysis by capillary electrophoresis (see Chapter 5). However, if the aim is to identify and isolate an infected WBC m whole blood that is present at an incidence of only 1 in 10 million, then quantities in excess of 10 mL of whole blood may be required just to encounter 5 cells. This does not provide the ideal situation for a microdevice. Another key limitation, namely the impact of surface chemistry, has been addressed in a previous section. 

Giovannoli, C., Anfossi, L., Tozzi C., Giraudi, G, and Vanni, A. DNA separation by capillary electrophoresis with hydrophilic substituted celluloses as coating and sieving polymers. Apphcation to the analysis of genetically modified meals, J. Sep. ScL, 27, 1551, 2004. 

Wang, Y, et al.. Quasi-interpenetrating network formed by polyacrylamide and poly(lV,lV-dimethylacrylamide) used in high-performance DNA sequencing analysis by capillary electrophoresis, Electrophoresis, 26, 126, 2005. 

Salas-Solano, O., Ruiz-Martinez, M.C., Carrilho, E., Kotler, L., and Karger, B.L., A sample purification method for ragged and high-performance DNA sequencing by capillary electrophoresis using replaceable polymer solutions. B. Quantitative determination of the role of sample matrix components on sequencing analysis, AnoZ. Chem., 70, 1528, 1998. 

Atha, D., Kasprzak, W., O Connell, C., etal.. Prediction of DNA single-strand conformation polymorphism Analysis by capillary electrophoresis and computerized DNA modeling. Nucleic Acids Res, 29, 4643, 2001. 

Fasco, M. J. Analysis of amplified DNA molecules by capillary electrophoresis and laser induced fluorescence. Methods Mol. Med. 1999,26,131-146. 

Arakawa, H., Nakashiro, S., Maeda, M., and Tsuji, A., Analysis of single-strand DNA conformation polymorphism by capillary electrophoresis, /. Chromatogr. A, 722, 359, 1996. 

SNP arrays result useful to detect DNA rearrangements by an indirect approach. In this case, the result will be measured as a loss of heterozygosity, a statistical value which measures DNA deletions due to statistical deviations from the expected rate in the different alleles. Loss of heterozygosity can also be measured at a shorter scale by capillary electrophoresis, in this case restricted to individual gene analysis (92). 

J. M. Butler, Separation of DNA restriction fragments and PCR products, m Analysis of Nucleic Acids by Capillary Electrophoresis (C. Heller, ed.), Verlag Vieweg, Wiesbaden, 1997, pp. 195-217. 

Baba, Y. Analysis of disease-causing genes and DNA-based drugs by capillary electrophoresis— towards DNA diagnosis and gene therapy for human diseases. J. Chromatogr. B 687 271-302, 1996. 

In this chapter we summarize the complex issues that are involved in the analysis of sizing DNA by capillary electrophoresis (CE), and how chemomet-ric methods can help to optimize a high number of interrelated variables. It is impressive to observe how diverse is the obtainable biological information despite the size of the double-stranded DNA molecule. We also briefly introduce some typical genetic assays that rely on sizing DNA molecules, and how some chemometric approaches are used to correlate sizes of DNA with population and or evolution of species. 

One of the most important fields in which the rapidity of the analytical process is necessary is in vivo clinical analysis. The use of chemical sensors (amperometric or potentiometric) as array sensors has solved the problem of time, sensitivity, and selectivity. Because of the selectivity and sensitivity assured by capillary electrophoresis, it can be successfully used for highspeed DNA genotyping, as in microfabricated capillary array electrophoresis chips.237 Its capacity to analyze 12 different samples in parallel in less than 160 s has made it the method of choice for this type of analysis. 

Lin, Y. W. and Chang, H. T. Analysis of double-stranded DNA by capillary electrophoresis using polyfethylene oxide) in the presence of hexadecyltrimethylammonium bromide. J. Chromatogr. A, 1130, 206, 2006. 

Figure 2 A schematic view of multiplex PCR analysis of STRs. In a test tube, some STRs from the sample s DNA (A) are amplified by PCR (B) using fluorescent-labeled primers. After the addition of an internal standard (red-labeled fragments) (C) the DNA fragments obtained at the end of the PCR are separated by capillary electrophoresis according to their size (D) and detected at the end of the capillary. Each peak (E) is then electronically labeled with the name of the corresponding allele. The profiles in blue, green, and black present the alleles detected for the STRs VWA, D21S11, andTHOI, respectively. The red profile displays two peaks from the internal standard.

Cohen, A.S. Najarian, D.R. Karger, B.L. Separation and analysis of DNA sequence reaction products by capillary electrophoresis. J. Chromatogr. 1990, 516,49-60. 

Heller, C. The separation matrix. In Analysis of Nucleic Acids by Capillary Electrophoresis Heller, C., Ed. Vieweg VerlagsgeseUschaft Wiesbaden, 1997 9. Madabhushi, R.S. Vainer, M. Dolnik, V. Enad, S. Barker, Di. Harris, D.W. Mansfield, E.S. Versatile low-viscosity sieving matrices for nondenaturing DNA separations using capdlary array electrophoresis. Electrophoresis 1997, 18 (1), 104-111. 

SkeidsvoU, J. Ueland, M. Analysis of double-stranded DNA by capillary electrophoresis with laser-induced fluorescence detection using the monomeric dye SYBR Green 1. Anal. Biochem. 1995, 231, 359-365. 

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