Gel electrophoresis applications

Ferguson, KA, Starch-Gel Electrophoresis— Application to the Classification of Pituitary Proteins and Polypeptides, Metabohsm 13, 985, 1964. 

Just as gel electrophoresis methodology is commonly used to determine homogeneity, as well as molecular weights of proteins these techniques may be used similarly for dendrimer analysis. Other uses have included the assessment of DNA/dendrimer binding constants which have been studied using gel electrophoresis. Application of gel electrophoresis in dendritic science will be discussed from these three aspects. 

Ferguson, K. A. (1964). Starch-gel electrophoresis—Application to the classification of pituitary proteins and polypeptides. Metabolism 13(Suppl.), 985—1002. 

H8. Hardman, D. A., and Kane, J. P., Improved separation of high molecular weight proteins by preparative SDS gel electrophoresis Application to apolipopiotein B. Anal. Biochem. 105, 174-180 (1980). 

B. Fiszer-Szafarz. Hyaluronidase polymorphism detected by polyacrylamide gel electrophoresis. Application to hyaluronidases from bacteria, slime molds, bee and snake venoms, bovine testes, rat liver lysosomes and human serum. Anal. Biochem. 143 16 (1984). 

Advances in experimental techniques, including pulsed-field gradient NMR, and theoretical methods, including volume averaging, macrotransport, and variational methods, that may lead to the resolution of a number of the fundamental issues in gel electrophoresis and to improvements in the practical application of electrotransport in polymeric media... 

Butterman, M Tietz, D Orban, L Chrambach, A, Ferguson Plots Based on Absolute Mobilities in Polyarcylamide Gel Electrophoresis Dependence of Linearity of Polymerization Conditions and Application on the Determination of Free Mobility, Electrophoresis 9, 293, 1988. Caglio, S Chiari, M Righetti, PG, Gel Polymerization in Detergents Conversion Efficiency of Methylene Blue vs. Persulfate Catalysis, as Investigated by Capillary Zone Electrophoresis, Electrophoresis 15, 209, 1994. 

G. Muyzer and K. Smalla, Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73 127 (1998). 

A variety of formats and options for different types of applications are possible in CE, such as micellar electrokinetic chromatography (MEKC), isotachophoresis (ITP), and capillary gel electrophoresis (CGE). The main applications for CE concern biochemical applications, but CE can also be useful in pesticide methods. The main problem with CE for residue analysis of small molecules has been the low sensitivity of detection in the narrow capillary used in the separation. With the development of extended detection pathlengths and special optics, absorbance detection can give reasonably low detection limits in clean samples. However, complex samples can be very difficult to analyze using capillary electrophoresis/ultraviolet detection (CE/UV). CE with laser-induced fluorescence detection can provide an extraordinarily low LOQ, but the analytes must be fluorescent with excitation peaks at common laser wavelengths for this approach to work. Derivatization of the analytes with appropriate fluorescent labels may be possible, as is done in biochemical applications, but pesticide analysis has not been such an important application to utilize such an approach. 

Western blot A method to detect protein in a given sample of tissue homogenate or extract. It uses gel electrophoresis to separate denatured proteins by mass. Some diagnostic applications for the Western blot include Lyme disease, bovine spongiform encephalopathy, and human immunodeficiency virus (HIV) (it is considered the gold standard for HIV diagnostic testing). 

The utility of protein expression mapping using 2D gel electrophoresis and mass spectrometry has been demonstrated for several experimental systems. One application has been to assess the differences in protein expression between normal and cancerous cells. For example, expression mapping has been used to identify protein markers for bladder cancer (Ostergaard et al., 1999). This was accomplished by identifying proteins released into the urine of patients with and without bladder cancer using 2D electrophoresis and mass spectrometry. 

First Dimension Optimization After the second-dimension separation has been developed, the first-dimension flow rate is determined. This includes selecting a first-dimension column diameter to work at the flow rate selected. We illustrate the selection process with an application that addresses a column method for proteins that functions as a replacement for planar 2D gel electrophoresis (2DGE) within a narrow molecular weight and p/range. In the planar experiment, isoelectric focusing is performed in the first dimension and sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS/PAGE) in the second dimension. 

Although classic two-dimensional gel electrophoresis provides exquisite peak capacity, it suffers from several limitations. First, the technology is labor-intensive and difficult to automate, which hampers applications to large-scale proteomics analyses (Hanash, 2000). 

Capillary gel electrophoresis is becoming very widely used in the biotechnology field for the high resolution separation of DNA and peptides according to molecular weight, but it has limited application for the analysis of surfactants (Wallingford, 1996). CGE does result in an increase in the resolution per unit time over SEC for charged polymers (Poli and Schure,1992). 

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

In paper or gel electrophoresis, the sample may be applied with a syringe or a micropipette similar to the application of samples to thin-layer plates. In some cases, there may be wells in the gel that accept the solution containing the species to be separated. In CE, samples may be applied using electromigration, hydrostatic, or pneumatic injection. In all cases, the ions to be separated must be soluble in and compatible with the stationary phases and buffers used. 

Packed capillaries with a larger inner diameter may be useful in preparative separations. These will find an application in proteome research as a part of multidimensional separation systems that will replace 2-D gel electrophoresis. The preparative CEC will require solving of the problems related to heat dissipation since the radial temperature gradient negatively affects the separations, and sample injection. The fabrication of sintered frits in larger bore capillaries is also very difficult. However, in situ polymerized monolithic frits can be fabricated in capillaries of virtually any diameter [190]. 

The various types of capillary electrophoresis are performed either in free solution or in gels. The choice of method depends on the nature of the sample and the analytical objective but capillary gel electrophoresis, including iso-electric focusing and SDS electrophoresis, is particularly useful for protein applications. 

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