[RASMB] nucleic acid vbar

[Jacob Lebowitz]

Hi All,

Adding some additional considerations re nucleic acids. The values 
cited for the vbar of DNA are most likely the value at a 50% G-C 
content. There is a very significant variation of the vbar with base 
composition. When buoyant density experiments were popular, in the 
days of saber tooth tiger hunting, investigators measured the G-C 
content of DNA in high concentrations of Cs salts. The buoyant 
density for unmodified double stranded DNA was a linear function of 
the G-C content, for CsCl p=1.660+0.098X where X is the fraction 
of  G-C in the DNA. With large DNA molecules it was possible to 
separate DNAs based on their G-C content in a CsCl density gradient 
experiments. The buoyant density of DNA and RNA are different with 
the latter much higher implying that RNA has a much higher solvated 
density and hence lower vbar. Hydration is also an important 
consideration, the buoyant density of DNA in CsCl is in the 1.7 range 
whereas it is in the 1.4 range in Cs2SO4. These days most 
investigators would have a well characterized nucleic acid of known 
molecular weight for interaction studies. Very often this is 
synthetic DNA or RNA where vbar will vary with base composition, 
hydration and counter ions. Under these circumstances, the best 
approach is to measure the vbar of the nucleic acid by sedimentation 
equilibrium since you know the MW of the nucleic acid from the 
sequence which is usually confirmed by MS analysis.

Jack



At 07:22 AM 8/29/2007, Tom Laue wrote:
>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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