[RASMB] AUC of RNA and RNA-proteins complexes

[Jacob Lebowitz]

Pascal,

You can determine the vbar of your RNA using a sedimentation equilibrium 
experiment to determine the buoyant molar mass. Since you know the Mw of 
the RNA you can solve for the vbar.  A sedimentation velocity titration 
should be easily  performed since the RNA has a signal approximately 20X 
the protein signal. Consequently, by monitoring 260 or 250nm you can follow 
the changes in the s value of the RNA as it binds protein with minimal 
optical contribution from the protein. We did this using both band and 
boundary velocity for a regulatory protein binding to operator/promoter DNA 
(Biochemistry 40, 13378-13389, 2001).  I submitted error corrections 
for  eqns. 1 and 2 but they have not appeared yet. This gives me an 
opportunity to correct the errors.  Eq.1: M should be to the 2/3 power and 
in eq.2: the hydration friction term should be [(vbar2+vbar1xdelta)/vbar2] 
raised to the 1/3 power.
         Good luck with your future experiments.


Jacob Lebowitz, PhD
Molecular Interactions Resource
Division of Bioengineering and Physical Science, ORS
National Institutes of Health
Mail: Bldg. 13 Rm. 3N17
Office Bldg. 13 Rm. 3E49
13 South Drive
Bethesda, MD 20892 - 5766
Tel: (301) 435-1955
Fax: (301) 480-1242
email: lebowitz at helix.nih.gov
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