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Analysis of limiting factors of DNA band separation by a DNA sequencer using fluorescence detection
Author(s) -
Nishikawa Tetsuo,
Kambara Hideki
Publication year - 1991
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.1150120905
Subject(s) - electrophoresis , analytical chemistry (journal) , dna , materials science , gel electrophoresis , diffusion , electric field , limiting , fluorescence , base (topology) , chemistry , chromatography , optics , physics , thermodynamics , mechanical engineering , mathematical analysis , biochemistry , mathematics , quantum mechanics , engineering
The factors affecting the electrophoretic separation of DNA bands in DNA base sequencing using fluorescence detection are analyzed. All the factors contributing to DNA band spacing and band width are evaluated; DNA diffusion and thermal effects on gels are the main considerations. The dependence of the gel's electrical resistivity on gel temperature and the variation of temperature over gel thickness are associated with a broadening of DNA band width. As a result of the analyses the maximum separable base number is represented as a function of various electrophoretic variables. The best separations are possible with an electric field strength corresponding to gel thickness. The maximum separable base number increases as the gel thickness decreases. It also increases as the migration distance increases, but it becomes saturated and has an upper limit when the migration distance is long. This upper limit increases as gel thickness decreases. DNA fragments with 600 and 601 bases can be completely separated from each other under optimum conditions for a 0.2 mm thick gel plate. Furthermore, using the band spacing information, under the same conditions, 750 bases could be assigned separately.