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Circular DNA & EthBr in electrophoresis

Zophonias O. Jonsson zjons at vetbio.unizh.ch
Wed Dec 13 04:41:10 EST 1995

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

Have fun


Zophonias O. Jonsson
Institut fur Veterinarbiochemie               Tel: (41-1)-257-54-75
Universitat Zurich-Irchel                     Fax: (41-1)-362-05-01
Winterthurerstrasse 190
CH-8057 Zurich

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