[RASMB] 3mm vs 12 mm

[Borries Demeler]

Hi Michael,

My feeling is that for complexes of this size and composition you want
to run at the lowest concentration possible to minimize concentration
dependent nonideality effects. Especially when DNA or extended/charged
molecules are involved, the lower concentration will help to obtain
results that are easier to interpret. Also make sure you have enough ionic
strength in your buffer to neutralize charges on the DNA (if they aren't
balanced by the protein). So the upshot is that you want to use the 12 mm
centerpieces, since they will allow you to get the same absorbance/fringes
at lower concentration than in the 3 mm cells. 

Another thought: Also check where the absorbance maximum is,
dependending on the length of the DNA it may be at 260 or below 230. If
your buffer allows it, you may be able to measure at 230 or below and
take advantage of a higher extinction coefficient.

Good luck with the experiment, -Borries

> 
> Hi, I am wondering if there is any advantage to using 12 mm cells  vs. the 3 mm cells for velocity experiments with a protein-DNA complex that is ~ 1Mda.
> 
> Michael S. Cosgrove, Ph.D.
> Assistant Professor
> Syracuse University
> Department of Biology
> 406D Lyman Hall
> 108 College Place
> Syracuse, NY 13244
> 
> Phone: (315) 443-2964
> Fax: (315) 443-2156
> Email: mscosgro at syr.edu
> 
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