Methods for separation of polymeric compounds

Slater, Gary W.; McCormick, Laurette C.; Barron, Annelise E.; Meagher, Robert J.

Title: Methods for separation of polymeric compounds

Patent · Tue May 13 00:00:00 EDT 2008

OSTI ID:1531555

Slater, Gary W.; McCormick, Laurette C.; Barron, Annelise E.; Meagher, Robert J.

Recently two techniques using free solution electrophoresis to separate charged-uncharged polymer conjugates have proven successful: End Labeled Free Solution Electrophoresis (ELFSE) for DNA sequencing, and Free Solution Conjugate Electrophoresis (FSCE) for molar mass profiling of uncharged polymers. Previous attempts have been made to analyze experimental data generated by these new techniques for the electrophoresis of molecules with varying charge distributions. However, the importance of the ends of the polymers in determining the polymer's overall mobility was neglected in previous work. Through a careful investigation and a reanalysis of the experimental data, it is determined here that this “end effect” critically impacts the behavior of polymers and charged-uncharged polymer conjugates during electrophoresis. In this way, the invention provides for methods that exploit this “end effect” for the separation of polymeric molecules on the basis of size, including for example DNA separation and sequencing techniques.

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Research Organization:: Univ. of Ottawa, Ottawa, CA (United States); Northwestern Univ., Evanston, IL (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: FG02-99ER62789

Assignee:: University of Ottawa (Ottawa, CA); Northwestern University (Evanston, IL)

Patent Number(s):: 7,371,533

Application Number:: 11/241,990

OSTI ID:: 1531555

Resource Relation:: Patent File Date: 2005-10-04

Country of Publication:: United States

Language:: English

References (36)

End-label, free-solution capillary electrophoresis of highly charged oligosaccharides Sudor, Jan.; Novotny, Milos V. Analytical Chemistry, Vol. 67, Issue 22 https://doi.org/10.1021/ac00118a026	journal	November 1995
A very thin coating for capillary zone electrophoresis of proteins based on a tri(ethylene glycol)-terminated alkyltrichlorosilane Meagher, Robert J.; Seong, Jiehyun; Laibinis, Paul E. ELECTROPHORESIS, Vol. 25, Issue 3 https://doi.org/10.1002/elps.200305714	journal	February 2004
The molecular end effect and its critical impact on the behavior of charged-uncharged polymer conjugates during free-solution electrophoresis McCormick, Laurette C.; Slater, Gary W. ELECTROPHORESIS, Vol. 26, Issue 9 https://doi.org/10.1002/elps.200410276	journal	May 2005
A new concept for sequencing DNA by capillary electrophoresis Noolandi, Jaan Electrophoresis, Vol. 13, Issue 1 https://doi.org/10.1002/elps.1150130180	journal	January 1992
Free-solution electrophoresis of DNA modified with drag-tags at both ends Meagher, Robert J.; McCormick, Laurette C.; Haynes, Russell D. ELECTROPHORESIS, Vol. 27, Issue 9 https://doi.org/10.1002/elps.200500554	journal	May 2006
A Zimm model for polyelectrolytes in an electric field Long, Didier; Viovy, Jean-Louis; Ajdari, Armand Journal of Physics: Condensed Matter, Vol. 8, Issue 47 https://doi.org/10.1088/0953-8984/8/47/047	journal	November 1996
A New Cloning Method for the Preparation of Long Repetitive Polypeptides without a Sequence Requirement Won, Jong-In; Barron, Annelise E. Macromolecules, Vol. 35, Issue 22 https://doi.org/10.1021/ma020892i	journal	October 2002
Branched polymeric labels used as drag-tags in free-solution electrophoresis of ssDNA Nedelcu, Sorin; Slater, Gary W. ELECTROPHORESIS, Vol. 26, Issue 21 https://doi.org/10.1002/elps.200500471	journal	November 2005
The free solution mobility of DNA Stellwagen, Nancy C.; Gelfi, Cecilia; Righetti, Pier Giorgio Biopolymers, Vol. 42, Issue 6, p. 687-703 https://doi.org/10.1002/(SICI)1097-0282(199711)42:6<687::AID-BIP7>3.0.CO;2-Q	journal	November 1997
Electrophoresis of polyampholytes Long, Didier; Dobrynin, Andrey V.; Rubinstein, Michael The Journal of Chemical Physics, Vol. 108, Issue 3 https://doi.org/10.1063/1.475485	journal	January 1998
Characterization of Glutamine Deamidation in a Long, Repetitive Protein Polymer via Bioconjugate Capillary Electrophoresis Won, Jong-In; Meagher, Robert J.; Barron, Annelise E. Biomacromolecules, Vol. 5, Issue 2 https://doi.org/10.1021/bm034442p	journal	March 2004
End-Label Free-Solution Electrophoresis of the Low Molecular Weight Heparins Sudor, Jan; Novotny, Milos V. Analytical Chemistry, Vol. 69, Issue 16 https://doi.org/10.1021/ac961297f	journal	August 1997
Electrophoresis of the nucleic acids Olivera, Baldomero M.; Baine, Peter; Davidson, Norman Biopolymers, Vol. 2, Issue 3 https://doi.org/10.1002/bip.1964.360020306	journal	June 1964
Molar Mass Profiling of Synthetic Polymers by Free-Solution Capillary Electrophoresis of DNA−Polymer Conjugates Vreeland, Wyatt N.; Desruisseaux, Claude; Karger, Achim E. Analytical Chemistry, Vol. 73, Issue 8, p. 1795-1803 https://doi.org/10.1021/ac001380+	journal	March 2001
Application of capillary electrophoresis to the analysis of the oligomeric distribution of polydisperse polymers Bullock, John Journal of Chromatography A, Vol. 645, Issue 1 https://doi.org/10.1016/0021-9673(93)80631-H	journal	August 1993
Multiplexed, High-Throughput Genotyping by Single-Base Extension and End-Labeled Free-Solution Electrophoresis Vreeland, Wyatt N.; Meagher, Robert J.; Barron, Annelise E. Analytical Chemistry, Vol. 74, Issue 17 https://doi.org/10.1021/ac0258094	journal	September 2002
DNA mobility modifier Barron, Annelise E. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20030088056 US Patent Application 10/197613; 20030088056	patent-application	May 2003
Protein polymer drag-tags for DNA separations by end-labeled free-solution electrophoresis Won, Jong-In; Meagher, Robert J.; Barron, Annelise E. ELECTROPHORESIS, Vol. 26, Issue 11 https://doi.org/10.1002/elps.200410042	journal	June 2005
Simultaneous Action of Electric Fields and Nonelectric Forces on a Polyelectrolyte: Motion and Deformation Long, Didier; Viovy, Jean-Louis; Ajdari, Armand Physical Review Letters, Vol. 76, Issue 20 https://doi.org/10.1103/PhysRevLett.76.3858	journal	May 1996
A new concept for separating nucleic acids by electrophoresis in solution using hybrid synthetic end labelled-nucleic acid molecules Noolandi, Jaan Electrophoresis, Vol. 14, Issue 1 https://doi.org/10.1002/elps.11501401108	journal	January 1993
Comblike, Monodisperse Polypeptoid Drag-Tags for DNA Separations by End-Labeled Free-Solution Electrophoresis (ELFSE) Haynes, Russell D.; Meagher, Robert J.; Won, Jong-In Bioconjugate Chemistry, Vol. 16, Issue 4 https://doi.org/10.1021/bc0496915	journal	July 2005
End-labeled free-solution electrophoresis of DNA Meagher, Robert J.; Won, Jong-In; McCormick, Laurette C. ELECTROPHORESIS, Vol. 26, Issue 2 https://doi.org/10.1002/elps.200410219	journal	January 2005
Free-solution electrophoresis of DNA Heller, Christoph; Slater, Gary W.; Mayer, Pascal Journal of Chromatography A, Vol. 806, Issue 1 https://doi.org/10.1016/S0021-9673(97)00656-0	journal	May 1998
Screening for genetic mutations Carlsson, Christina; Jonsson, Mats; Nordén, Bengt Nature, Vol. 380, Issue 6571 https://doi.org/10.1038/380207a0	journal	March 1996
Electrophoresis of Composite Molecular Objects. 2. Competition between Sieving and Frictional Effects in Polymer Solutions Desruisseaux, Claude; Drouin, Guy; Slater, Gary W. Macromolecules, Vol. 34, Issue 15 https://doi.org/10.1021/ma000448k	journal	July 2001
Critical factors for high-performance physically adsorbed (dynamic) polymeric wall coatings for capillary electrophoresis of DNA Doherty, Erin A. S.; Berglund, K. Derek; Buchholz, Brett A. ELECTROPHORESIS, Vol. 23, Issue 16, p. 2766-2776 https://doi.org/10.1002/1522-2683(200208)23:16<2766::AID-ELPS2766>3.0.CO;2-S	journal	August 2002
A theoretical study of the possible use of electroosmotic flow to extend the read length of DNA sequencing by end-labeled free solution electrophoresis McCormick, Laurette C.; Slater, Gary W. ELECTROPHORESIS, Vol. 27, Issue 9 https://doi.org/10.1002/elps.200500573	journal	May 2006
Electrophoretic mobility of composite objects in free solution: Application to DNA separation Long, Didier; Ajdari, Armand Electrophoresis, Vol. 17, Issue 6 https://doi.org/10.1002/elps.1150170628	journal	January 1996
Profiling Solid-Phase Synthesis Products by Free-Solution Conjugate Capillary Electrophoresis Vreeland, Wyatt N.; Slater, Gary W.; Barron, Annelise E. Bioconjugate Chemistry, Vol. 13, Issue 3 https://doi.org/10.1021/bc0155871	journal	May 2002
Theory of DNA Sequencing Using Free-Solution Electrophoresis of Protein-DNA Complexes Mayer, Pascal.; Slater, Gary W.; Drouin, Guy. Analytical Chemistry, Vol. 66, Issue 10 https://doi.org/10.1021/ac00082a029	journal	May 1994
Tandem Isotachophoresis-Zone Electrophoresis via Base-Mediated Destacking for Increased Detection Sensitivity in Microfluidic Systems Vreeland, Wyatt N.; Williams, Stephen J.; Barron, Annelise E. Analytical Chemistry, Vol. 75, Issue 13 https://doi.org/10.1021/ac0259921	journal	July 2003
Electrophoresis of Composite Molecular Objects. 1. Relation between Friction, Charge, and Ionic Strength in Free Solution Desruisseaux, Claude; Long, Didier; Drouin, Guy Macromolecules, Vol. 34, Issue 1 https://doi.org/10.1021/ma0002702	journal	January 2001
Separating DNA sequencing fragments without a sieving matrix Ren, Hongji; Karger, Achim E.; Oaks, Frank Electrophoresis, Vol. 20, Issue 12, p. 2501-2509 https://doi.org/10.1002/(SICI)1522-2683(19990801)20:12<2501::AID-ELPS2501>3.0.CO;2-H	journal	August 1999
Efficient method for the preparation of peptoids [oligo(N-substituted glycines)] by submonomer solid-phase synthesis Zuckermann, Ronald N.; Kerr, Janice M.; Kent, Stephen B. H. Journal of the American Chemical Society, Vol. 114, Issue 26 https://doi.org/10.1021/ja00052a076	journal	December 1992
Capillary electrophoretic separation of uncharged polymers using polyelectrolyte engines McCormick, L. C.; Slater, G. W.; Karger, A. E. Journal of Chromatography A, Vol. 924, Issue 1-2 https://doi.org/10.1016/S0021-9673(01)00990-6	journal	July 2001
Mobilities of Labeled and Unlabeled Single-Stranded DNA in Free Solution Electrophoresis Voelkel, A. R.; Noolandi, J. Macromolecules, Vol. 28, Issue 24 https://doi.org/10.1021/ma00128a031	journal	November 1995

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