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Estimation of polyacrylamide gel pore size from Ferguson plots of normal and anomalously migrating DNA fragments. I. Gels containing 3 % N, N′‐methylenebisacrylamide
Author(s) -
Holmes Diana L.,
Stellwagen Nancy C.
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.1150120405
Subject(s) - polyacrylamide , radius of gyration , dna , acrylamide , chemistry , monomer , polyacrylamide gel electrophoresis , radius , analytical chemistry (journal) , gel electrophoresis , molecule , materials science , polymer , polymer chemistry , chromatography , organic chemistry , biochemistry , computer security , computer science , enzyme
The mobilities of normal and anomalously migrating DNA fragments were determined in polyacrylamide gels of different acrylamide concentrations, polymerized with 3 % N , N ′‐methylenebisacrylamide as the crosslinker. The DNA samples were a commercially available 123‐bp ladder and two molecular weight ladders containing multiple copies of two 147‐base pair (bp) restriction fragments, obtained from the MspI digestion of plasmid pBR322. One of the 147 bp fragments is known to migrate anomalously slowly in polyacrylamide gels. Ferguson plots were constructed for all multimer ladders, using both absolute mobilities and relative mobilities with respect to the smallest DNA molecule in each data set. If the retardation coefficients were calculated from the relative mobilities, and the rms radius of gyration was used as the measure of DNA size, the Ogston equations were obeyed and the gel fiber parameters could be calculated. The effective pore sizes of the gels were estimated from the gel concentration at which the mobility of a given DNA molecule was reduced to one‐half its mobility at zero gel concentration. The estimated pore radii ranged from ∼ 130 nm for 3.5 % gels to ∼ 70 nm for 10.5 % gels. These values are much larger than the pore sizes previously determined for the polyacrylamide matrix.