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Nucleic Acids Research, Vol 26, Issue 20 4787-4789, Copyright © 1998 by Oxford University Press

ARTICLES

Quantitative hybridization to genomic DNA fractionated by pulsed-field gel electrophoresis

TJ Leach and RL Glaser
Laboratory of Developmental Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA.

Hybridization to genomic DNA fractionated by CHEF electrophoresis can vary >100-fold if the DNA is acid depurinated prior to Southern blotting. The level of hybridization is high or low depending on whether the molecule being analyzed migrates at a size coincident with or different from the size of the majority of genomic DNA in the sample, respectively. Techniques that avoid acid depurination including in-gel hybridizations and UV irradiation of DNA prior to blotting provide more accurate quantitative results. CHEF analysis of DNA molecules containing repetitive satellite sequences is particularly prone to this effect.
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