BioNano-Switch EC Project

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Project Reports
(order of date submitted)

Reporting Stage 1:

  1. Interim Management Report No 1 (Deliverable D4) - Summary of Progress.
  2. Periodic Activity Report No. 1 (Deliverable D1) - Executive Summary.
  3. Periodic Management Report No. 1 (Deliverable D5) - Summary.

Reporting Stage 2:

  1. Periodic Activity Report No 2 (Deliverable D2) - Executive Summary.
  2. Interim Management Report No 2 (Deliverable D6) - Summary of Progress.
  3. Periodic Activity Report No 3 (Deliverable D3) - Executive Summary.

Reporting Stage 3:

  1. Periodic Activity Report No. 4 (Deliverable D30) - Executive Summary.
  2. Final Management Report - Summary.

Research and Scientific Papers Published:

UOP:

Youell, J. & K. Firman, Biological molecular motors for nanodevices. Nanotechnology Perceptions 3: 75-96 (2007).

Youell, J. and K. Firman, EcoR124I: from plasmid-encoded restriction modification system to nanodevice.  Microbiology and Molecular Biology Reviews. 72(2): 365–377. (2008).

NPLML:

Kazakova, O., Perkins, G., Gallop, J. and Cohen, L. Scanned micro-Hall microscope for detection of biofunctionalized magnetic beads.  Appl. Phys. Lett. 90, 162502. (2007).

O. Kazakova, J. C. Gallop, D. C. Cox, E. Brown, A. Cuenat, and K. Suzuki. ‘Optimization of 2DEG InAs/GaSb Hall Sensors for Single Particle Detection’.  IEEE Trans. on Magn. 44, 4480 (2008).

O. Kazakova, J. C. Gallop, P. See, D. Cox, G. K. Perkins, J. D. Moore, and L. F. Cohen. ‘Detection of a micron-sized magnetic particle using InSb Hall sensor’. IEEE Trans. on Magn. 45, 4499 (2009).

R. D. Boyd, L. Winkless, A. Cuenat, O. Kazakova, (2009). New metrology for the development of bio-inspired devices based on scanning probe microscopy force measurements. Submitted to Langmuir.

ENS:

Lionnet, T., Dawid, A., Bigot, S., Barre, F.-X., Saleh, O.A., Heslot, F., Allemand, J.-F., Bensimon, D. and Croquette, V. "DNA mechanics as a tool to probe Helicase and Translocase activity", invited review. Nucl. Acid. Res. 34 , 4232-4244. (2006).

Lionnet, T., M. M. Spiering, S. C. Benkovic, D. Bensimon & V. Croquette.  "Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism".  Proc Natl Acad Sci USA 104: 19790-19795. (2007).

Allemand, J. F., G. Charvin, V. Croquette, G. Lia & D. Bensimon.  "The manipulation of single biomolecules". Interdisciplinary Science Reviews 32: 149-162. (2007). 

Lionnet, T., Allemand, J.-F., Revyakin, A., Strick, T.R., Saleh, O.A., Bensimon, D. and Croquette, V.  "Single molecule studies using magnetic traps". In: "Single Molecule Techniques". Cold Spring Harbor Laboratory Press. (2007).

P. Neveu, I. Aujard, C. Benbrahim, T. Le Saux, J.-F. Allemand, S. Vriz, D. Bensimon and L. Jullien.  "A Caged Retinoic Acid for Use with One- and Two-Photon Excitation in Zebrafish Embryos".  Angew.Chem. 47, 3744-3746 (2008).

G. Lia, S. Semsey, D.E.A. Lewis, S.Adhya, D. Bensimon, D. Dunlap and L. Finzi.  "The antiparallel loops in gal DNA". Nucl. Acid. Res. 36, 4204-4210 (2008).

F.Mosconi, T.Julou, N.Desprat,D.Sinha, J.F.Allemand, V.Croquette and D. Bensimon.  "Some nonlinear challenges in biology", invited paper Nonlinearity 21, T131-T147 (2008).

F.Mosconi, J.F.Allemand, D. Bensimon and V.Croquette.  "Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers".  Phys.Rev.Lett. 102, 078301 (2009).

P.Neveu, D.Sinha, P.Kettunen, S.Vriz, L.Jullien and D.Bensimon.  "Single Cell Physiology", in Proceedings of the Nobel Symposium on Single Molecule Spectroscopy in Chemistry, Physics and Biology, ed. R.Rigler and J.Widengren (2009).

D.K.Sinha, P.Neveu, N.Gagey, I.Aujard, C.Benbrahim-Bouzidi, T.LeSaux, C.Rampon, C.Gauron, B.Goetz, S.Dubruille, C.Leucht, L.Bally-Cuif, M.Volovitch, D.Bensimon, L.Jullien and S.Vriz. (2009).  "Photocontrol of protein activity in a single cell of a live organism", Nat.Chem.Biol., submitted.

K. C. Neuman, G. Charvin, D. Bensimon and V. Croquette.  "Mechanisms of Chiral Discrimination by Topoisomerase IV". Proc.Nat.Acad.Sci. USA, 106, 6986 (2009).

H.Yokota, Y-W. Han, J.-F. Allemand, X.G. Xi, D.Bensimon, V.Croquette. "Single-molecule visualization of binding modes of helicase to DNA on PEGylated surfaces", Y.Itoa and Y.Harada, Chem.Lett., 38, 308 (2009).

A.Meglio, E.Praly, F.Ding, J.F. Allemand, D.Bensimon and V.Croquette. "Single protein/DNA studies with magnetic traps", Curr. Opin. Struc. Biol. (2009).

M.Manosas, M.M.Spiering, Z. Zhuang, S.J. Benkovic, and V.Croquette, “Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome” Nat.Chem.Bio, 5, 904-912 (2009).

"Magnetic tweezers for the study of DNA tracking motors", M. Manosas,A.Meglio, M.Spiering, F. Ding, S.Benkovic, FX Barre, O.A. Saleh, J.F.Allemand, D.Bensimon and V.CRoquette, Methods in Enzymology, (2010).

Estelle Crozat, Adrien Meglio, Jean-Francois Allemand, Claire E Chivers, Mark Howarth, Catherine Venien-Bryan, Ian Grainge and David J Sherratt.  "Separating speed and ability to displace roadblocks during DNA translocation by FtsK". The EMBO Journal (2010).

TUDelft:

M.T.J. van Loenhout, T. van der Heijden, R. Kanaar, C. Wyman, C. Dekker.  Dynamics of RecA filaments on single stranded DNA. Nucleic Acids Research 37, 4089-4099 (2009).

van Loenhout, M.T.J., van der Heijden, T., Kanaar, R., Wyman, C. and Dekker, C. (2008).  Dynamics of RecA filaments on single strand DNA. Nature Struc. Molec. Biol., submitted.

van der Heijden, T. and C. Dekker. Monte Carlo Simulations of Protein Assembly, Disassembly, and Linear Motion on DNA.  Biophysical Journal 95: 4560-4569. (2008).

van der Heijden, A.H., Modesto, M., Kanaar, R., Wyman, C. and Dekker, C.  Homologous recombination in real time: DNA strand exchange by RecA. Molec. Cell, 30: 530-538. (2008).

Seidel, R., et al., Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I. EMBO J, (2008). 27: 1388-98.

Seidel, R. & C. Dekker. Single-molecule studies of nucleic acid motors. Curr Opin Struct Biol 17: 80-86. (2007).

De Vlaminck, I., Vidic, I., van Loenhout, M.T.J., Kanaar, R., Lebbink, J.H.G. and Dekker, C. Torsional regulation of hRPA-induced unwinding of double-stranded DNA. Nucl. Acids Res., gkq067.

IMIC:

Sisakova, E., L. K. Stanley, M. Weiserova & M. D. Szczelkun. A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I.  Nucleic Acids Res 36: 3939-3949. (2008).

Sisáková, E., Weiserová, M., Dekker, C., Seidel, R. and Szczelkun, M.D. (2008). The Interrelationship of Helicase and Nuclease Domains during DNA Translocation by the Molecular Motor EcoR124I. Journal of Molecular Biology 384: 1273-1286. (2008).

EMPA:

Mihai Gabureac et al., Granular Co–C nano-Hall sensors by focused-beam-induced deposition, Nanotechnology 21 115503, doi: 10.1088/0957-4484/21/11/115503.

L. Bernau et al., The concept of selective depletion in focused electron beam (FEB) induced deposition: Tailoring the metal-to-carbon ratio in high-vacuum microscope chambers, ready for submission, also on http://arxiv.org/abs/1002.2156

INESC-MN:

Monitoring single DNA stretching using magnetoresistive sensors, Lab on a Chip.