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Electrophoretic mobility of partially denatured DNA in a gel: Qualitative and semiquantitative differences between bubbles and split ends
Author(s) -
Sean David,
Slater Gary W.
Publication year - 2012
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.201200097
Subject(s) - electrophoresis , gel electrophoresis , gel electrophoresis of nucleic acids , temperature gradient gel electrophoresis , pulsed field gel electrophoresis , dna , chemistry , langevin dynamics , biophysics , chromatography , chemical physics , biology , biochemistry , physics , gene , statistical physics , 16s ribosomal rna , genotype
Partially melted DNA is known to exhibit an abrupt decrease of electrophoretic mobility in a gel. Although this is the main phenomenon exploited in TGGE/DGGE (temperature gradient gel electrophoresis/denaturing gradient gel electrophoresis), not much is known about the physical processes responsible for the blocking. While there is a commonly used formula for the reduced mobility based on the theory of branched polymers, it does not discriminate between denatured domains bounded on one (split end) or two sides (bubble). To better understand how the blocking occurs in both of these cases, a coarse‐grained model of DNA gel electrophoresis is simulated using Langevin Dynamics. The simulations reveal that the low‐field mobility is much more sensitive to denatured domains located at the ends of a DNA fragment. A denatured domain occurring at the center of a fragment indeed reduces the mobility, but at a much lower rate.