From: Jo Butler <pjgb@mrc-lmb.cam.ac.uk>
  To  : hbeernin@zoo.uvm.edu
  Date: Thu, 17 Sep 98 18:38:14 +0000

Re: vbar for RNA-Protein complex?

>Date: Thu, 17 Sep 1998 07:46:16 -0400 (EDT)
>From: Hans Beernink <hbeernin@zoo.uvm.edu>
>To: RASMB@bbri.harvard.edu
>Subject: Re: vbar for RNA-Protein complex?
>
>On Thu, 17 Sep 1998, Jo Butler wrote:
>>
>> A reasonable approximation (as good as any calculated value for v-bar)
is
>given
>> by applying the usual equation (summing v-bar * M and dividing by the
sum of
>M),
>> as you would do with an amino acid composition for a protein.
>>
>
>
>Jo, are you aware of any tabulated values for the partial specific volumes
>of deoxy and ribo-nucleic acids?
>
>htb


Hans, this is not a well reported subject.

It is very easy to get banding densities in either caesium chloride or
caesium
sulphate - but these would, at best, correspond to CsDNA and in any case
are
markedly different, so one wonders what they actually are!  (See e.g.
Molecular
Biology and Biochemistry Rubber Book, 2cd edition.)

The best data for DNA I know, despite their age, are those of Cohen and
Eisenberg (1968) Biopolymers 6, 1077-1100.  Here they have measured
density
increments for both NaDNA and CsDNA, together with partial specific
volumes.  It
is worth noting that the APPARENT partial specific volumes, calculated
from the
density increments and solvent densities according to Casassaand
Eisenberg
(1964)  Adv. Prot. Chem. 19, 287-395, are NOT the same as the true
partial
specific volumes reported in this paper, at least for the NaDNA which I
consider
to be generally the more interesting for analytical centrifuge users.

In practice one can derive the following table from Cohen and Eisenberg's
data
(all at 25°C), for the apparent partial specific volumes of NaDNA (f')
at
various NaCl concentrations (I also include the solvent density, rho°):
NaCl (M)      f' (ml/g)      rho° (g/ml)
  0.2          0.540           1.005
  1.0          0.565           1.037
  1.5          0.572           1.056
  2.0          0.579           1.075
  3.0          0.589           1.112
  4.0          0.596           1.148
  4.99         0.595           1.183
 
The density measurements were made using a capillary pycnometer, so it was
a
considerable achievement to work at such high salt concentrations without
problems - the technique is described in some detail - but nowadays it
would be
much easier using an Anton Paar densitimeter.  Perhaps one should get
round to
making a fresh set of measurements, but where would it be accepted for
publication!

I do not know of any similar data for RNA and, myself, usually end up
using an
assumed value of f' = 0.55 ml/g when I want to calculate a molecular
mass for an
RNA:protein complex (just as one typically takes f' = 0.72 ml/g for the
protein).  Looking at the values for NaDNA which I have just listed
above,
perhaps something nearer to 0.525 would be better than 0.55.  Again,
measurement
would be useful.

One defined complex which we did measure some years ago, with a Paar
Densimeter,
was chromatin for which Linda Sperling and I got a value of f' =
0.69ml/g,
quoted in Sperling and Tardieu (1976) FEBS Lett. 64, 89-91.

I hope that these remarks may be helpful,
Yours,

Jo


-----------------------------
Jo Butler, 
MRC LMB,
Cambridge, UK.
Tel:+44 1223 248011
FAX:+44 1223 213556
Email: pjgb@mrc-lmb.cam.ac.uk
-----------------------------