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

lebowitz at helix.nih.gov lebowitz at helix.nih.gov
Thu May 1 09:31:46 PDT 2008


Dear All,

Preferential hydration of DNA in different salt solutions is a an issue
that Vinograd's lab worked on ages ago.

# The Net Hydration of T-4 Bacteriophage Deoxyribonucleic Acid and the
Effect of Hydration on Buoyant Behavior in a Density Gradient at
Equilibrium in the Ultracentrifuge
# John E. Hearst and Jerome Vinograd
# Proceedings of the National Academy of Sciences of the United States of
America, Vol. 47, No. 7 (Jul. 15, 1961), pp. 1005-1014


As the water activity of the Cs salt solution increases the buoyant
density decreases, i.e., the preferential hydration increases.  DNA in Cs
sulfate  is buoyant at density of 1.4 whereas DNA in CsCl is buoyant at a
density of 1.7. Using a series of Cs salts with large differences in water
activity Hearst and Vinograd could extrapolate to the anhydrous density of
duplex DNA of 2.12. The preferential hydration of DNA can be very
substantial depending on the salt solution so direct measurements of the
vbar are called for in agreement with expression that one must be
cautious.

Jack Lebowitz (stepping out of retirement for a little input re my old field)

> 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
>
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