DNA is negatively charged at a neutral pH, and its migration in an electrophoretic field is molecular weight dependent. When molecules <50 kb are subjected to an electric current in an agarose matrix, they migrate at a rate that is inversely proportional to its size (i.e., the larger the DNA fragments, the slower the rate of migration). However, when the molecular size exceeds the threshold of >50 kb, all fragments exhibit size-independent mobilities (Carle et al., 1986). This poses a major limitation to the use of conventional electrophoresis for microbial analysis because bacterial chromosomes are several mega base pairs in size.
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