[RASMB] nucleic acid vbar

[Tom Laue]

Hi-
Be aware that nucleic acid bound to protein may have a different vbar 
than free nucleic acid in a salt solution. In such a case, the protein 
becomes a major fraction of the counterions. Counterion concentration 
matters to vbar in addition to counterion type, especially at low (< 10 
mM) counterion concentrations. It should be noted, too, that the Stokes 
radius determined for any of these conditions is the correct value. The 
variation in vbar is a reflection of the changes in solvation.
Depending on the question being asked, you may not need to measure vbar. 
In particular, the Stokes radius may be determined without knowing vbar 
by substituting the buoyant mass from equilibrium data in the velocity 
equation: S = Mb/f. The accuracy of this method is ~5%.
Best wishes,
Tom
Arthur Rowe wrote:
>
>     Yes, the vbar of nucleic acids depends heavily on the cation(s)
>     present, and can vary at least over the range 0.52 - 0.55 ml/g:
>     Pearce, Rowe & Turnock, (1975) J. Mol. Biol.  *97*  193-205. If
>     the exact value matters to you, I doubt that there is any way of
>     avoiding doing an actual measurement, using a modern DDM.
>
>     Regards to all
>
>     Arthur
>
>
>     Bloomfield, Crothers & Tinoco show the salt dependence of vbar for
>     Cs and NaDNA (taken from Eisenberg (1976), so .55 is a traditional
>     starting point, not a fact.
>
>     >>> On 8/26/2007 at 2:56 PM, in message
>     <200708261956.l7QJuWtc008982 at biochem.uthscsa.edu>, Borries Demeler
>     <demeler at biochem.uthscsa.edu> wrote:
>     There seems to be a consensus to use a vbar of .55 ccm/g for DNA
>     and RNA. Does
>     anyone know if there is a function that predicts variations in
>     vbar with temperature
>     like there is for peptides? Or is .55 the best value to use - are
>     there any
>     references on this?
>
>     Thanks, -borries
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