Study of polymer molecules and conformations with a nanopore
Abstract
The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.
- Inventors:
-
- Lexington, MA
- Fayetteville, AR
- Delft, NL
- Cambridge, MA
- Issue Date:
- Research Org.:
- Harvard College
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1011416
- Patent Number(s):
- 7846738
- Application Number:
- 10/918,959
- Assignee:
- CHO
- Patent Classifications (CPCs):
-
C - CHEMISTRY C12 - BIOCHEMISTRY C12Q - MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
G - PHYSICS G01 - MEASURING G01N - INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- DOE Contract Number:
- US patent application 10/918,959
- Resource Type:
- Patent
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Golovchenko, Jene A, Li, Jiali, Stein, Derek, and Gershow, Marc H. Study of polymer molecules and conformations with a nanopore. United States: N. p., 2010.
Web.
Golovchenko, Jene A, Li, Jiali, Stein, Derek, & Gershow, Marc H. Study of polymer molecules and conformations with a nanopore. United States.
Golovchenko, Jene A, Li, Jiali, Stein, Derek, and Gershow, Marc H. Tue .
"Study of polymer molecules and conformations with a nanopore". United States. https://www.osti.gov/servlets/purl/1011416.
@article{osti_1011416,
title = {Study of polymer molecules and conformations with a nanopore},
author = {Golovchenko, Jene A and Li, Jiali and Stein, Derek and Gershow, Marc H},
abstractNote = {The invention features methods for evaluating the conformation of a polymer, for example, for determining the conformational distribution of a plurality of polymers and to detect binding or denaturation events. The methods employ a nanopore which the polymer, e.g., a nucleic acid, traverses. As the polymer traverses the nanopore, measurements of transport properties of the nanopore yield data on the conformation of the polymer.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Dec 07 00:00:00 EST 2010},
month = {Tue Dec 07 00:00:00 EST 2010}
}
Works referenced in this record:
Ion-beam sculpting at nanometre length scales
journal, July 2001
- Li, Jiali; Stein, Derek; McMullan, Ciaran
- Nature, Vol. 412, Issue 6843, p. 166-169
Alignment and sensitive detection of DNA by a moving interface
journal, September 1994
- Bensimon, A.; Simon, A.; Chiffaudel, A.
- Science, Vol. 265, Issue 5181
Detection of mutations in the apolipoprotein CII gene by denaturing gradient gel electrophoresis. Identification of the splice site variant apolipoprotein CII-Hamburg in a patient with severe hypertriglyceridemia
journal, July 1998
- Nauck, Markus S.; Nissen, Henrik; Hoffmann, Michael M.
- Clinical Chemistry, Vol. 44, Issue 7
Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore
journal, October 2000
- Movileanu, Liviu; Howorka, Stefan; Braha, Orit
- Nature Biotechnology, Vol. 18, Issue 10
Transcription by T7 RNA polymerase using benzo[a]pyrene-modified templates
journal, January 1991
- Nath, Surend T.; Romana, Louis J.
- Carcinogenesis, Vol. 12, Issue 6
DNA molecules and configurations in a solid-state nanopore microscope
journal, August 2003
- Li, Jiali; Gershow, Marc; Stein, Derek
- Nature Materials, Vol. 2, Issue 9
Permissive sites and topology of an outer membrane protein with a reporter epitope.
journal, January 1991
- Charbit, A.; Ronco, J.; Michel, V.
- Journal of Bacteriology, Vol. 173, Issue 1
Pore formation by LamB of Escherichia coli in lipid bilayer membranes.
journal, January 1986
- Benz, R.; Schmid, A.; Nakae, T.
- Journal of Bacteriology, Vol. 165, Issue 3
RNA polymerase-dependent mechanism for the stepwise T7 phage DNA transport from the virion into E. coli
journal, January 1982
- Zavriev, S. K.; Shemyakin, M. F.
- Nucleic Acids Research, Vol. 10, Issue 5
Voltage-Driven DNA Translocations through a Nanopore
journal, April 2001
- Meller, Amit; Nivon, Lucas; Branton, Daniel
- Physical Review Letters, Vol. 86, Issue 15
"Reversed" alamethicin conductance in lipid bilayers
journal, April 1991
- Taylor, R. J.; de Levie, R.
- Biophysical Journal, Vol. 59, Issue 4, p. 873-879
Fluorescence measurement of the kinetics of DNA injection by bacteriophage .lambda. into liposomes
journal, October 1988
- Novick, Steven L.; Baldeschwieler, John D.
- Biochemistry, Vol. 27, Issue 20
Single-channel currents recorded from membrane of denervated frog muscle fibres
journal, April 1976
- Neher, Erwin; Sakmann, Bert
- Nature, Vol. 260, Issue 5554
The voltage-dependent activity of Escherichia coli porins in different planar bilayer reconstitutions
journal, December 1989
- Lakey, Jeremy H.; Pattus, Franc
- European Journal of Biochemistry, Vol. 186, Issue 1-2
Images of a lipid bilayer at molecular resolution by scanning tunneling microscopy.
journal, February 1987
- Smith, D. P.; Bryant, A.; Quate, C. F.
- Proceedings of the National Academy of Sciences, Vol. 84, Issue 4
Nanopores with a spark for single-molecule detection
journal, July 2001
- Wang, Hui; Branton, Daniel
- Nature Biotechnology, Vol. 19, Issue 7
Electrokinetic measurements with submicron particles and pores by the resistive pulse technique
journal, September 1977
- DeBlois, Ralph W.; Bean, Charles P.; Wesley, Roy K. A.
- Journal of Colloid and Interface Science, Vol. 61, Issue 2, p. 323-335
The F pilus of Escherichia coli appears to support stable DNA transfer in the absence of wall-to-wall contact between cells.
journal, January 1990
- Harrington, L. C.; Rogerson, A. C.
- Journal of Bacteriology, Vol. 172, Issue 12
Induction of DNA replication by transcription in the region upstream of the human c-myc gene in a model replication system.
journal, October 1996
- Ohba, R.; Matsumoto, K.; Ishimi, Y.
- Molecular and Cellular Biology, Vol. 16, Issue 10
Characterization of Nucleic Acids by Nanopore Analysis
journal, October 2002
- Deamer, David W.; Branton, Daniel
- Accounts of Chemical Research, Vol. 35, Issue 10
Single-molecule analysis of DNA-protein complexes using nanopores
journal, March 2007
- Hornblower, Breton; Coombs, Amy; Whitaker, Richard D.
- Nature Methods, Vol. 4, Issue 4
Bacillus subtilis spoIIIE protein required for DNA segregation during asymmetric cell division
journal, April 1994
- Wu, L.; Errington, J.
- Science, Vol. 264, Issue 5158
Stochastic sensors inspired by biology
journal, September 2001
- Bayley, Hagan; Cremer, Paul S.
- Nature, Vol. 413, Issue 6852, p. 226-230
Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel
journal, March 2001
- Vercoutere, Wenonah; Winters-Hilt, Stephen; Olsen, Hugh
- Nature Biotechnology, Vol. 19, Issue 3
Adapting to nanoscale events
journal, April 1999
- Branton, Daniel; Golovchenko, Jene
- Nature, Vol. 398, Issue 6729
Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP
journal, February 1985
- Ollis, D. L.; Brick, P.; Hamlin, R.
- Nature, Vol. 313, Issue 6005
Artificial transmembrane ion channels from self-assembling peptide nanotubes
journal, May 1994
- Ghadiri, M. Reza; Granja, Juan R.; Buehler, Lukas K.
- Nature, Vol. 369, Issue 6478
DNA conformation and base number simultaneously determined in a nanopore
journal, September 2007
- Fologea, Daniel; Brandin, Eric; Uplinger, James
- ELECTROPHORESIS, Vol. 28, Issue 18
Genetic analysis of membrane protein topology by a sandwich gene fusion approach.
journal, October 1990
- Ehrmann, M.; Boyd, D.; Beckwith, J.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 19
Electroporation and electrophoretic DNA transfer into cells. The effect of DNA interaction with electropores
journal, November 1992
- Sukharev, S. I.; Klenchin, V. A.; Serov, S. M.
- Biophysical Journal, Vol. 63, Issue 5, p. 1320-1327
Open channel noise. V. Fluctuating barriers to ion entry in gramicidin A channels
journal, March 1990
- Heinemann, S. H.; Sigworth, F. J.
- Biophysical Journal, Vol. 57, Issue 3, p. 499-514
Channel architecture in maltoporin: dominance studies with lamB mutations influencing maltodextrin binding provide evidence for independent selectivity filters in each subunit.
journal, January 1989
- Ferenci, T.; Lee, K. S.
- Journal of Bacteriology, Vol. 171, Issue 2
Mechanism of sugar transport through the sugar-specific LamB channel ofEscherichia coli outer membrane
journal, December 1987
- Benz, Roland; Schmid, Angela; Vos-Scheperkeuter, Greetje H.
- The Journal of Membrane Biology, Vol. 100, Issue 1
Optimizing planar lipid bilayer single-channel recordings for high resolution with rapid voltage steps
journal, August 1990
- Wonderlin, W. F.; Finkel, A.; French, R. J.
- Biophysical Journal, Vol. 58, Issue 2, p. 289-297
Probing the topology of a bacterial membrane protein by genetic insertion of a foreign epitope; expression at the cell surface.
journal, November 1986
- Charbit, A.; Boulain, J. C.; Ryter, A.
- The EMBO Journal, Vol. 5, Issue 11
Mutagenesis by random linker insertion into the lamB gene of Escherichia coli K12
journal, November 1986
- Boulain, Jean Claude; Charbit, Alain; Hofnung, Maurice
- MGG Molecular & General Genetics, Vol. 205, Issue 2
Rapid nanopore discrimination between single polynucleotide molecules
journal, February 2000
- Meller, A.; Nivon, L.; Brandin, E.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 3
Domain of E. coli DNA polymerase I showing sequence homology to T7 DNA polymerase
journal, February 1985
- Ollis, D. L.; Kline, C.; Steitz, T. A.
- Nature, Vol. 313, Issue 6005
A protein-conducting channel in the endoplasmic reticulum
journal, May 1991
- Simon, Sanford M.; Blobel, Günter
- Cell, Vol. 65, Issue 3, p. 371-380
Sequencing and the Single Channel
journal, December 1999
- Andersen, Olaf Sparre
- Biophysical Journal, Vol. 77, Issue 6, p. 2899-2901
Amino acid residues required for fast Na(+)-channel inactivation: charge neutralizations and deletions in the III-IV linker.
journal, November 1992
- Patton, D. E.; West, J. W.; Catterall, W. A.
- Proceedings of the National Academy of Sciences, Vol. 89, Issue 22
A neutral amino acid change in segment IIS4 dramatically alters the gating properties of the voltage-dependent sodium channel.
journal, January 1990
- Auld, V. J.; Goldin, A. L.; Krafte, D. S.
- Proceedings of the National Academy of Sciences, Vol. 87, Issue 1
Characterization of individual polynucleotide molecules using a membrane channel
journal, November 1996
- Kasianowicz, J. J.; Brandin, E.; Branton, D.
- Proceedings of the National Academy of Sciences, Vol. 93, Issue 24
Determinants of membrane protein topology.
journal, December 1987
- Boyd, D.; Manoil, C.; Beckwith, J.
- Proceedings of the National Academy of Sciences, Vol. 84, Issue 23
Sequence-specific detection of individual DNA strands using engineered nanopores
journal, July 2001
- Howorka, Stefan; Cheley, Stephen; Bayley, Hagan
- Nature Biotechnology, Vol. 19, Issue 7
Hydrophobic substitution mutations in the S4 sequence alter voltage-dependent gating in shaker K+ channels
journal, August 1991
- Lopez, George A.; Ian, Yuh Nung; Ian, Lily Yeh
- Neuron, Vol. 7, Issue 2, p. 327-336
Open channel noise. IV. Estimation of rapid kinetics of formamide block in gramicidin A channels
journal, October 1988
- Heinemann, S. H.; Sigworth, F. J.
- Biophysical Journal, Vol. 54, Issue 4, p. 757-764
The potential and challenges of nanopore sequencing
book, August 2009
- Rodgers, Peter; Branton, Daniel; Deamer, David W
- Nanoscience and Technology: A Collection of Reviews from Nature Journals, p. 261-268
Nanopores and nucleic acids: prospects for ultrarapid sequencing
journal, April 2000
- Deamer, David W.; Akeson, Mark
- Trends in Biotechnology, Vol. 18, Issue 4, p. 147-151
Open channel noise. III. High-resolution recordings show rapid current fluctuations in gramicidin A and four chemical analogues
journal, December 1987
- Sigworth, F. J.; Urry, D. W.; Prasad, K. U.
- Biophysical Journal, Vol. 52, Issue 6, p. 1055-1064
Unzipping Kinetics of Double-Stranded DNA in a Nanopore
journal, June 2003
- Sauer-Budge, Alexis F.; Nyamwanda, Jacqueline A.; Lubensky, David K.
- Physical Review Letters, Vol. 90, Issue 23
Electronic Counting and Sizing of Bacteria
journal, July 1958
- Kubitschek, Herbert E.
- Nature, Vol. 182, Issue 4630
Improved patch-clamp techniques for high-resolution current recording from cells and cell-free membrane patches
journal, August 1981
- Hamill, O. P.; Marty, A.; Neher, E.
- Pflügers Archiv - European Journal of Physiology, Vol. 391, Issue 2
Effect of point mutations on the in-vitro pore properties of maltoporin, a protein of Escherichia coli outer membrane
journal, June 1988
- Dargent, Bénédicte; Charbit, Alain; Hofnung, Maurice
- Journal of Molecular Biology, Vol. 201, Issue 3, p. 497-506
Selectivity for maltose and maltodextrins of maltoporin, a pore-forming protein of E. coli outer membrane
journal, August 1987
- Dargent, Bénédicte; Rosenbusch, Jürg; Pattus, Franc
- FEBS Letters, Vol. 220, Issue 1, p. 136-142
Microsecond Time-Scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments Within Single RNA Molecules
journal, December 1999
- Akeson, Mark; Branton, Daniel; Kasianowicz, John J.
- Biophysical Journal, Vol. 77, Issue 6, p. 3227-3233
Molecular architecture and electrostatic properties of a bacterial porin
journal, December 1991
- Weiss, M.; Abele, U.; Weckesser, J.
- Science, Vol. 254, Issue 5038
Two types of inactivation in Shaker K+ channels: Effects of alterations in the carboxy-terminal region
journal, October 1991
- Hoshi, Toshinori; Zagotta, William N.; Aldrich, Richard W.
- Neuron, Vol. 7, Issue 4, p. 547-556
SpoIIIE strips proteins off the DNA during chromosome translocation
journal, July 2008
- Marquis, K. A.; Burton, B. M.; Nollmann, M.
- Genes & Development, Vol. 22, Issue 13
Single Ion-Channel Recordings Using Glass Nanopore Membranes
journal, September 2007
- White, Ryan J.; Ervin, Eric N.; Yang, Tinglu
- Journal of the American Chemical Society, Vol. 129, Issue 38
Biophysical and molecular mechanisms of Shaker potassium channel inactivation
journal, October 1990
- Hoshi, T.; Zagotta, W.; Aldrich, R.
- Science, Vol. 250, Issue 4980
Sandwiched Graphene−Membrane Superstructures
journal, December 2009
- Titov, Alexey V.; Král, Petr; Pearson, Ryan
- ACS Nano, Vol. 4, Issue 1
A cluster of hydrophobic amino acid residues required for fast Na(+)-channel inactivation.
journal, November 1992
- West, J. W.; Patton, D. E.; Scheuer, T.
- Proceedings of the National Academy of Sciences, Vol. 89, Issue 22
Improved stability of black lipid membranes by coating with polysaccharide derivatives bearing hydrophobic anchor groups
journal, May 1986
- Moellerfeld, J.; Prass, W.; Ringsdorf, H.
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 857, Issue 2, p. 265-270
Alamethicin. A rich model for channel behavior
journal, January 1984
- Hall, J. E.; Vodyanoy, I.; Balasubramanian, T. M.
- Biophysical Journal, Vol. 45, Issue 1, p. 233-247
Blockade of a mitochondrial cationic channel by an addressing peptide: An electrophysiological study
journal, December 1989
- Henry, Jean-Pierre; Chich, Jean-François; Goldschmidt, Denise
- The Journal of Membrane Biology, Vol. 112, Issue 2
Counting polymers moving through a single ion channel
journal, July 1994
- Bezrukov, Sergey M.; Vodyanoy, Igor; Parsegian, V. Adrian
- Nature, Vol. 370, Issue 6487