[RASMB] v-bar estimates/measurements for G-Quadruplexes

[Jo Butler]

Dear Cody,

You are correct to be cautious, since the partial specific volume is 
also dependent on co-solvation, which includes the counter-ions bound by 
the macromolecule.  In the case of nucleic acids, with their high charge 
density and binding of >0.8 monovalent ions/base (and higher for 
divalent), this can produce large effects.  One only has to look at the 
difference in density for NaDNA and CsDNA to take the point.

Jo

Cody Craig wrote:
> Hi All,
>
> Is there a good reference for estimating the partial specific volume 
> of deoxyguanosine/deoxyguanosine monophosphate in a quadruplex?  The 
> literature indicates that the observed partial specific volume of 
> nucleotides is context specific (single stranded is different than 
> double stranded), which makes me hesitant to use either of these 
> values for my calculations.
>
> Thanks in advance,
>
> Cody Craig
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-- 
Dr P.J.G. Butler,
MRC Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 0QH, UK.
Tel. +44 (0)1223 402296