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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Lake,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Thank you for taking the time to respond to my question.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>John Sumida<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Molecular Analysis Facility<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>University of Washington<o:p></o:p></span></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Lake Paul [mailto:lake.n.paul@gmail.com] <br><b>Sent:</b> Thursday, June 06, 2019 3:56 PM<br><b>To:</b> John Sumida <jpsumida@uw.edu><br><b>Cc:</b> RASMB <rasmb@list.rasmb.org><br><b>Subject:</b> Re: [RASMB] AUC measurements in CsCl?<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>John,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>To answer your first question, CsCl is not needed to determine the MW of your DNA. Just make sure have the appropriate ionic strength in solution. You will be spinning this slowly, e.g. 10000 rpm or lower. One sample at a time and scan as fast as possible.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Equilibrium on such a large particle is going to take literally forever. I would not do an equilibrium experiment on a 10 MDa particle.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The SV experiment should suffice to get a pretty good molecular weight.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Lake<o:p></o:p></p></div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div><div><p class=MsoNormal>On Thu, Jun 6, 2019, 5:51 PM John Sumida <<a href="mailto:jpsumida@uw.edu">jpsumida@uw.edu</a>> wrote:<o:p></o:p></p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear RASMB,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>First I have to thank all those who curate this list server as over the last 10 years as a manager of the lab I run, it has and continues to prove a hugely valuable resource for me and the people I serve.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>My question today has to do with the analysis of DNA and it stems from a user interest in performing an AUC equilibrium experiment in the presence of CsCl. My experience to date has been with nanomaterials and proteins so DNA is a new material for me, however I am under the impression that running AUC samples in presence of CsCl is problematical because of the gradient CsCl itself will generate. <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>The estimated mass of the species of interest is in the range of 10 mega Daltons; this is also a size regime that is new to me.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>The objective of the experiment is to characterize nucleic acids extracted from cells which will have a label increasing the mass of the nucleic acid depending on the number of times it has been replicated.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Two questions:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Is CsCl necessary to determine the size distribution of molecular species >10MDa?<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Can a CsCl experiment be performed using equilibrium measurements?<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thank you for considering my question.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Best regards,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>John Sumida<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Molecular Analysis Facility<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>University of Washington<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#333333;background:white'>In many spheres of human endeavor, from science to business to education to economic policy, good decisions depend on good measurement.</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#333333;background:white'>Ben Bernanke</span><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p></div></div><p class=MsoNormal>_______________________________________________<br>RASMB mailing list<br><a href="mailto:RASMB@list.rasmb.org" target="_blank">RASMB@list.rasmb.org</a><br><a href="http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org" target="_blank">http://list.rasmb.org/listinfo.cgi/rasmb-rasmb.org</a><o:p></o:p></p></blockquote></div></div></div></div></body></html>