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Hi John-<br>
I wouldn't count on my memory for anything, so any insights/recollections are welcome. I have no idea where I got that number...
<br>
Vern Schumaker and Bruno Zimm did a fair amount of work with large DNA molecules, but it is better represented as a flexible polymer than as a rod. Also, it is important to note that at very large sizes, asymmetric particles will show a speed-dependent sedimentation.
Below is the abstract from their paper. <br>
I am assuming that the rods are stiff and have a uniform diameter (not a mixture of lateral association). Best wishes,<br>
Tom<br>
<br>
<br>
<div class="cit"><span role="menubar"><a role="menuitem" href="http://www.ncbi.nlm.nih.gov/pubmed/963220?dopt=Abstract#" title="Biophysical chemistry.">Biophys Chem.</a></span> 1976 Jul;5(1-2):265-70.</div>
<h1>Anomalies in sedimentation. V. Chains at high fields, practical consequences.</h1>
<div class="auths"><a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Zimm%20BH%5BAuthor%5D&cauthor=true&cauthor_uid=963220">Zimm BH</a>,
<a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Schumaker%20VN%5BAuthor%5D&cauthor=true&cauthor_uid=963220">
Schumaker VN</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed?term=Zimm%20CB%5BAuthor%5D&cauthor=true&cauthor_uid=963220">
Zimm CB</a>.</div>
<div class="abstr">
<h3>Abstract</h3>
<div class="">
<p>The theory of a preceding paper [B.H. Zimm, Biophys, Chem. 1 (1974) 279] is used to calculate a numerical table for the change of sedimentation coefficient with centrifugal field for chain molecules. A simple formula is found to fit the results within 1.3%
up to the centrifugal field at which S/So = 0.377; this formula is S/So=(1+0.1155y2)-1/4, where y is proportional to M2/So times the centripetal acceleration, M being the molecular weight and So the sedimentation coefficient at zero acceleration. Applying
this formula to DNA, we conclude that at a given centrifuge speed the sedimentation coefficient must reach a maximum at a particular molecular weight and be smaller at higher molecular weights. The value of the maximum depends on the conditions, but can come
at less than 150 S for DNA under typical conditions. When a maximum is present, the profile of a sedimenting non-homogeneous band is also severely distorted.</p>
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<div style="direction: ltr;" id="divRpF502793"><font color="#000000" face="Tahoma" size="2"><b>From:</b> John Philo [jphilo@mailway.com]<br>
<b>Sent:</b> Thursday, May 08, 2014 12:03 PM<br>
<b>To:</b> rasmb@list.rasmb.org<br>
<b>Cc:</b> Laue, Thomas<br>
<b>Subject:</b> RE: [RASMB] Sedimentation of rods<br>
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<div dir="ltr" align="left"><font color="#0000ff" face="Arial" size="2"><span class="889325315-08052014">Tom, I don't think your recollection of a constant value of ~2.7 S is correct in general for protein rods. For very long rods (high length to diameter ratios)
the sedimentation coefficient does become independent of length, but the sedimentation coefficient value will be determined by the buoyant mass per unit length, which of course depends strongly on the rod diameter.
</span></font></div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial" size="2"><span class="889325315-08052014"></span></font> </div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial" size="2"><span class="889325315-08052014">I did once run velocity on some carbon nanotubes, but due to this very weak length dependence it provides very poor separation by length.
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<div dir="ltr" align="left"><font color="#0000ff" face="Arial" size="2"><span class="889325315-08052014"></span></font> </div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial" size="2"><span class="889325315-08052014">SEDNTERP will of course calculate length/diameter ratios for shorter rods (cylinders) out to ratios of about 10.
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<div dir="ltr" align="left"><font color="#0000ff" face="Arial" size="2"><span class="889325315-08052014"></span></font> </div>
<div dir="ltr" align="left"><font color="#0000ff" face="Arial" size="2"><span class="889325315-08052014">John</span></font></div>
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<font face="Tahoma" size="2"><b>From:</b> rasmb-bounces@list.rasmb.org [mailto:rasmb-bounces@list.rasmb.org]
<b>On Behalf Of </b>Laue, Thomas<br>
<b>Sent:</b> Thursday, May 08, 2014 8:42 AM<br>
<b>To:</b> RASMB List ?[rasmb@list.rasmb.org]?<br>
<b>Subject:</b> [RASMB] Sedimentation of rods<br>
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Hi all-<br>
We are looking at a protein that forms rods. I have little background on systems like this, and am looking for some guidance. In particular, my recollection is that for long rods, as the rod length increases, the s collapses back to a constant ~2.7 s.
<br>
Any wisdom will be welcome.<br>
Best wishes,<br>
Tom<br>
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