In article <Pine.SOL.3.91.951212122819.20606A-100000 at tin>, "Mr. I.S.
Viney" <iviney at hgmp.mrc.ac.uk> wrote:
> I think this is an expected anomaly, the forms which migrate slightly
> differently are topoisomers. Pretreatment with EtBr destroys the
> differences in mobility, maybe someone else (better versed in DNa
> topology!) can explain this clearly.
EtdBr is an intercalating dye and in the process of intercalating it leads
to "positive" supercoiling in contrast to the normal negative
supercoiling. The bulk and positive charge of EtdBr slows down the DNA on
gel and drowns out the difference between different topoisomers at high
concentrations. At very low concentrations the differe may actually be
increased. Then of course linear and nicked DNA can bind more EtdBr than
covalently closed ds DNA circles, that's why nicked and linearized
plasmids run slower than intact ones on gel. That about summarizes it.
For more take a look at:
Keller, W. (1975) PNAS 72:1787-1791 or
Foglesong, P.D. and C. Reckord (1992) BioTechniques 13:402-404
or if you are really into it
Bauer, W and J. Vinograd (1968) J.Mol.Biol. 33:141-171
Zophonias O. Jonsson
Institut fur Veterinarbiochemie Tel: (41-1)-257-54-75
Universitat Zurich-Irchel Fax: (41-1)-362-05-01