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Computer simulation of pulsed field gel runs allows the quantitation of radiation‐induced double‐strand breaks in yeast
Author(s) -
Kraxenberger Alfred,
Friedl Anna A.,
Kellerer Albrecht M.
Publication year - 1994
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.1150150122
Subject(s) - breakage , gel electrophoresis , pulsed field gel electrophoresis , calibration , dna , molecular mass , physics , chemistry , materials science , biology , genetics , quantum mechanics , gene , genotype , composite material , nuclear magnetic resonance , enzyme
A procedure for the quantification of double‐strand breaks in yeast is presented that utilizes pulsed field gel electrophoresis (PFGE) and a comparison of the observed DNA mass distribution in the gel lanes with calculated distributions. Calculation of profiles is performed as follows. If double‐strand breaks are produced by sparsely ionizing radiation, one can assume that they are distributed randomly in the genome, and the resulting DNA mass distribution in molecular length can be predicted by means of a random breakage model. The input data for the computation of molecular length profiles are the breakage frequency per unit length, α, as adjustable parameter, and the molecular lengths of the intact chromosomes. The obtained DNA mass distributions in molecular length must then be transformed into distributions of DNA mass in migration distance. This requires a calibration of molecular length vs. migration distance that is specific for the gel lane in question. The computed profiles are then folded with a Lorentz distribution with adjusted spread parameter Γ to account for and broadening. The DNA profiles are calculated for different breakage frequencies α and for different values of Γ, and the parameters resulting in the best fit of the calculated to the observed profile are determined.