NanoSci E+ Nanopore Project
The Nanopore Site was created as part of a Nanoscience ERA Net project on "novel force spectroscopy suing nanopores". Thje project started in 2009 and will finished in 2013.
The aim of the NanoSci E+ Nanopore project was to interface biological nanopores with solid-state devices to develop a novel method of force spectroscopy on the single molecule level. The consortium working on the project included the following researchers:
Loic Auvray (U Paris Diderot)
Cees Dekker (Delft)
Ulrich Keyser (PI, Cambridge)
Mathias Winterhalter (Bremen)
Junior Members
Jo Gornall and Chandrashekhar Kulkarni (Cambridge)
Mahendran Kozhinjampara (Bremen)
Benjamin Cressiot (Evry)
Stefan Kowalczyk (Delft)
The aim of the NanoSci E+ Nanopore project was to interface biological nanopores with solid-state devices to develop a novel method of force spectroscopy on the single molecule level. The consortium working on the project included the following researchers:
Loic Auvray (U Paris Diderot)
Cees Dekker (Delft)
Ulrich Keyser (PI, Cambridge)
Mathias Winterhalter (Bremen)
Junior Members
Jo Gornall and Chandrashekhar Kulkarni (Cambridge)
Mahendran Kozhinjampara (Bremen)
Benjamin Cressiot (Evry)
Stefan Kowalczyk (Delft)
Nanosci E+ Publications (7/5/2013 sorted by first author name)
N. A. Bell, C. R. Engst, M. Ablay, G. Divitini, C. Ducati, T. Liedl, and U. F. Keyser, DNA origami nanopores.
Nano Lett 12 (1), 512 (2012).10.1021/nl204098n
B. Cressiot, A. Oukhaled, G. Patriarche, M. Pastoriza-Gallego, J. M. Betton, L. Auvray, M. Muthukumar, L. Bacri, and J. Pelta, Protein Transport through a Narrow Solid-State Nanopore at High Voltage: Experiments and Theory.
Acs Nano 6 (7), 6236 (2012).Doi 10.1021/Nn301672g
J. L. Gornall, K. R. Mahendran, O. J. Pambos, L. J. Steinbock, O. Otto, C. Chimerel, M. Winterhalter, and U. F. Keyser, Simple Reconstitution of Protein Pores in Nano Lipid Bilayers.
Nano Letters 11 (8), 3334 (2011).Doi 10.1021/Nl201707d
A. R. Hall, J. M. Keegstra, M. C. Duch, M. C. Hersam, and C. Dekker, Translocation of Single-Wall Carbon Nanotubes Through Solid-State Nanopores (vol 11, pg 2446, 2011).
Nano Letters 12 (2), 1112 (2012).Doi 10.1021/Nl300143f
A. R. Hall, A. Scott, D. Rotem, K. K. Mehta, H. Bayley, and C. Dekker, Hybrid pore formation by directed insertion of alpha-haemolysin into solid-state nanopores.
Nature Nanotechnology 5 (12), 874 (2010).10.1038/nnano.2010.237
S. W. Kowalczyk and C. Dekker, Measurement of the Docking Time of a DNA Molecule onto a Solid-State Nanopore.
Nano Letters 12 (8), 4159 (2012).Doi 10.1021/Nl301719a
S. W. Kowalczyk, A. R. Hall, and C. Dekker, Detection of Local Protein Structures along DNA Using Solid-State Nanopores.
Nano Letters 10 (1), 324 (2010).10.1021/nl903631m
S. W. Kowalczyk, L. Kapinos, T. R. Blosser, T. Magalhaes, P. van Nies, R. Y. H. Lim, and C. Dekker, Single-molecule transport across an individual biomimetic nuclear pore complex.
Nature Nanotechnology 6 (7), 433 (2011).Doi 10.1038/Nnano.2011.88
S. W. Kowalczyk, D. B. Wells, A. Aksimentiev, and C. Dekker, Slowing down DNA Translocation through a Nanopore in Lithium Chloride. Nano Letters 12 (2), 1038 (2012).Doi 10.1021/Nl204273h
K. R. Mahendran, U. Lamichhane, M. Romero-Ruiz, S. Nussberger, and M. Winterhalter, Polypeptide Translocation Through the Mitochondrial TOM Channel: Temperature-Dependent Rates at the Single-Molecule Level.
J Phys Chem Lett 4 (1), 78 (2013).Doi 10.1021/Jz301790h
K. R. Mahendran, M. Romero-Ruiz, A. Schlosinger, M. Winterhalter, and S. Nussberger, Protein Translocation through Tom40: Kinetics of Peptide Release.
Biophysical Journal 102 (1), 39 (2012).DOI 10.1016/j.bpj.2011.11.4003
C. Merstorf, B. Cressiot, M. Pastoriza-Gallego, A. Oukhaled, J. M. Betton, L. Auvray, and J. Pelta, Wild type, mutant protein unfolding and phase transition detected by single-nanopore recording.
ACS Chem Biol 7 (4), 652 (2012).10.1021/cb2004737
N. Modi, M. Winterhalter, and U. Kleinekathofer, Computational modeling of ion transport through nanopores. Nanoscale 4 (20), 6166 (2012).Doi 10.1039/C2nr31024d
O. Otto, F. Czerwinski, J. L. Gornall, G. Stober, L. B. Oddershede, R. Seidel, and U. F. Keyser, Real-time particle tracking at 10,000 fps using optical fiber illumination.
Opt Express 18 (22), 22722 (2010).
O. Otto, J. L. Gornall, G. Stober, F. Czerwinski, R. Seidel, and U. F. Keyser, High-speed video-based tracking of optically trapped colloids. J Optics-Uk 13 (4) (2011).Artn 044011 Doi 10.1088/2040-8978/13/4/044011
O. Otto, L. J. Steinbock, D. W. Wong, J. L. Gornall, and U. F. Keyser, Note: Direct force and ionic-current measurements on DNA in a nanocapillary.
Review of Scientific Instruments 82 (8) (2011).Artn 086102 Doi 10.1063/1.3623502
A. Oukhaled, B. Cressiot, L. Bacri, M. Pastoriza-Gallego, J. M. Betton, E. Bourhis, R. Jede, J. Gierak, L. Auvray, and J. Pelta, Dynamics of Completely Unfolded and Native Proteins through Solid-State Nanopores as a Function of Electric Driving Force.
Acs Nano 5 (5), 3628 (2011).Doi 10.1021/Nn1034795
M. Pastoriza-Gallego, L. Rabah, G. Gibrat, B. Thiebot, F. G. Goot, L. Auvray, J. M. Betton, and J. Pelta, Dynamics of Unfolded Protein Transport through an Aerolysin Pore.
Journal of the American Chemical Society 133 (9), 2923 (2011).Doi 10.1021/Ja1073245
M. Romero-Ruiz, K. R. Mahendran, R. Eckert, M. Winterhalter, and S. Nussberger, Interactions of mitochondrial presequence peptides with the mitochondrial outer membrane preprotein translocase TOM.
Biophys J 99 (3), 774 (2010).10.1016/j.bpj.2010.05.010 S0006-3495(10)00609-0 [pii]
G. F. Schneider, S. W. Kowalczyk, V. E. Calado, G. Pandraud, H. W. Zandbergen, L. M. Vandersypen, and C. Dekker, DNA translocation through graphene nanopores.
Nano Lett 10 (8), 3163 (2010).10.1021/nl102069z
P. R. Singh, I. Barcena-Uribarri, N. Modi, U. Kleinekathofer, R. Benz, M. Winterhalter, and K. R. Mahendran, Pulling peptides across nanochannels: resolving peptide binding and translocation through the hetero-oligomeric channel from Nocardia farcinica.
Acs Nano 6 (12), 10699 (2012).10.1021/nn303900y
W. Suginta, W. Chumjan, K. R. Mahendran, P. Janning, A. Schulte, and M. Winterhalter, Molecular Uptake of Chitooligosaccharides through Chitoporin from the Marine Bacterium Vibrio harveyi.
Plos One 8 (1) (2013).ARTN e55126 DOI 10.1371/journal.pone.0055126
Nano Lett 12 (1), 512 (2012).10.1021/nl204098n
B. Cressiot, A. Oukhaled, G. Patriarche, M. Pastoriza-Gallego, J. M. Betton, L. Auvray, M. Muthukumar, L. Bacri, and J. Pelta, Protein Transport through a Narrow Solid-State Nanopore at High Voltage: Experiments and Theory.
Acs Nano 6 (7), 6236 (2012).Doi 10.1021/Nn301672g
J. L. Gornall, K. R. Mahendran, O. J. Pambos, L. J. Steinbock, O. Otto, C. Chimerel, M. Winterhalter, and U. F. Keyser, Simple Reconstitution of Protein Pores in Nano Lipid Bilayers.
Nano Letters 11 (8), 3334 (2011).Doi 10.1021/Nl201707d
A. R. Hall, J. M. Keegstra, M. C. Duch, M. C. Hersam, and C. Dekker, Translocation of Single-Wall Carbon Nanotubes Through Solid-State Nanopores (vol 11, pg 2446, 2011).
Nano Letters 12 (2), 1112 (2012).Doi 10.1021/Nl300143f
A. R. Hall, A. Scott, D. Rotem, K. K. Mehta, H. Bayley, and C. Dekker, Hybrid pore formation by directed insertion of alpha-haemolysin into solid-state nanopores.
Nature Nanotechnology 5 (12), 874 (2010).10.1038/nnano.2010.237
S. W. Kowalczyk and C. Dekker, Measurement of the Docking Time of a DNA Molecule onto a Solid-State Nanopore.
Nano Letters 12 (8), 4159 (2012).Doi 10.1021/Nl301719a
S. W. Kowalczyk, A. R. Hall, and C. Dekker, Detection of Local Protein Structures along DNA Using Solid-State Nanopores.
Nano Letters 10 (1), 324 (2010).10.1021/nl903631m
S. W. Kowalczyk, L. Kapinos, T. R. Blosser, T. Magalhaes, P. van Nies, R. Y. H. Lim, and C. Dekker, Single-molecule transport across an individual biomimetic nuclear pore complex.
Nature Nanotechnology 6 (7), 433 (2011).Doi 10.1038/Nnano.2011.88
S. W. Kowalczyk, D. B. Wells, A. Aksimentiev, and C. Dekker, Slowing down DNA Translocation through a Nanopore in Lithium Chloride. Nano Letters 12 (2), 1038 (2012).Doi 10.1021/Nl204273h
K. R. Mahendran, U. Lamichhane, M. Romero-Ruiz, S. Nussberger, and M. Winterhalter, Polypeptide Translocation Through the Mitochondrial TOM Channel: Temperature-Dependent Rates at the Single-Molecule Level.
J Phys Chem Lett 4 (1), 78 (2013).Doi 10.1021/Jz301790h
K. R. Mahendran, M. Romero-Ruiz, A. Schlosinger, M. Winterhalter, and S. Nussberger, Protein Translocation through Tom40: Kinetics of Peptide Release.
Biophysical Journal 102 (1), 39 (2012).DOI 10.1016/j.bpj.2011.11.4003
C. Merstorf, B. Cressiot, M. Pastoriza-Gallego, A. Oukhaled, J. M. Betton, L. Auvray, and J. Pelta, Wild type, mutant protein unfolding and phase transition detected by single-nanopore recording.
ACS Chem Biol 7 (4), 652 (2012).10.1021/cb2004737
N. Modi, M. Winterhalter, and U. Kleinekathofer, Computational modeling of ion transport through nanopores. Nanoscale 4 (20), 6166 (2012).Doi 10.1039/C2nr31024d
O. Otto, F. Czerwinski, J. L. Gornall, G. Stober, L. B. Oddershede, R. Seidel, and U. F. Keyser, Real-time particle tracking at 10,000 fps using optical fiber illumination.
Opt Express 18 (22), 22722 (2010).
O. Otto, J. L. Gornall, G. Stober, F. Czerwinski, R. Seidel, and U. F. Keyser, High-speed video-based tracking of optically trapped colloids. J Optics-Uk 13 (4) (2011).Artn 044011 Doi 10.1088/2040-8978/13/4/044011
O. Otto, L. J. Steinbock, D. W. Wong, J. L. Gornall, and U. F. Keyser, Note: Direct force and ionic-current measurements on DNA in a nanocapillary.
Review of Scientific Instruments 82 (8) (2011).Artn 086102 Doi 10.1063/1.3623502
A. Oukhaled, B. Cressiot, L. Bacri, M. Pastoriza-Gallego, J. M. Betton, E. Bourhis, R. Jede, J. Gierak, L. Auvray, and J. Pelta, Dynamics of Completely Unfolded and Native Proteins through Solid-State Nanopores as a Function of Electric Driving Force.
Acs Nano 5 (5), 3628 (2011).Doi 10.1021/Nn1034795
M. Pastoriza-Gallego, L. Rabah, G. Gibrat, B. Thiebot, F. G. Goot, L. Auvray, J. M. Betton, and J. Pelta, Dynamics of Unfolded Protein Transport through an Aerolysin Pore.
Journal of the American Chemical Society 133 (9), 2923 (2011).Doi 10.1021/Ja1073245
M. Romero-Ruiz, K. R. Mahendran, R. Eckert, M. Winterhalter, and S. Nussberger, Interactions of mitochondrial presequence peptides with the mitochondrial outer membrane preprotein translocase TOM.
Biophys J 99 (3), 774 (2010).10.1016/j.bpj.2010.05.010 S0006-3495(10)00609-0 [pii]
G. F. Schneider, S. W. Kowalczyk, V. E. Calado, G. Pandraud, H. W. Zandbergen, L. M. Vandersypen, and C. Dekker, DNA translocation through graphene nanopores.
Nano Lett 10 (8), 3163 (2010).10.1021/nl102069z
P. R. Singh, I. Barcena-Uribarri, N. Modi, U. Kleinekathofer, R. Benz, M. Winterhalter, and K. R. Mahendran, Pulling peptides across nanochannels: resolving peptide binding and translocation through the hetero-oligomeric channel from Nocardia farcinica.
Acs Nano 6 (12), 10699 (2012).10.1021/nn303900y
W. Suginta, W. Chumjan, K. R. Mahendran, P. Janning, A. Schulte, and M. Winterhalter, Molecular Uptake of Chitooligosaccharides through Chitoporin from the Marine Bacterium Vibrio harveyi.
Plos One 8 (1) (2013).ARTN e55126 DOI 10.1371/journal.pone.0055126