Mobility shift assay

Wed Dec 20 11:05:06 EST 1995

In article <v01510109acfc8d0de7d6@[]>, rxr21 at PSU.EDU
(Ramesh Raina) writes:

> I am having some trobule with mobility shift assays.
> [stuff deleted]
> I would
> expect the DNA-protein complex with 47 KD protein to migrate faster than
> the complex with 70 KD because the DNA fragment used in both the cases is
> same but protein sizes are significantly different.

Fellow Arabidians,

I posted this reply to Ramesh yesterday, but it may be of general 
information, so I am posting it to the entire group.  The molecular 
weight of the entire complex (250 bp of DNA plus 70kD of protein) is 
236,500 for the full length protein and 213,500 for the complex with 
the truncated protein.  This is a difference of less than 10%.  
Between the resolution of the gels commonly used for mobility shift 
assays and the difuse bands that are usually seen, I doubt that such 
a small difference would be detected.  The previous comments about 
charge distribution in the protein are correct, but because 
there are 500 negative charges on a 250 bp DNA probe, any effect would 
be small also.

Tom McKnight
Dept. of Biology
Texas A&M University

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