Design of self-organizing microtubule networks for molecular communication

In this paper, we investigated approaches to form a self-organizing microtubule network. Microtubules are protein filaments naturally occurring in the aqueous environment of cells. A microtubule network connects multiple nano- or micro-scale objects (i.e., nanomachines). In the paper, we propose two approaches to form an in vitro microtubule network in a self-organizing manner. The first approach utilizes polymerization and depolymerization of microtubules. The second approach utilizes molecular motors to reorganize a microtubule network. In addition, we conducted preliminary in vitro experiments to investigate the feasibility of the proposed approaches. In the preliminary experiments, we observed that a few sender and receiver nanomachines were interconnected with the first approach, and that distinct topologies of microtubules were reorganized with the second approach.

[1]  Dawen Cai,et al.  Tracking single Kinesin molecules in the cytoplasm of mammalian cells. , 2007, Biophysical journal.

[2]  S. Leibler,et al.  Physical Properties Determining Self-Organization of Motors and Microtubules , 2001, Science.

[3]  Niels Galjart,et al.  CLASP1 and CLASP2 bind to EB1 and regulate microtubule plus-end dynamics at the cell cortex , 2005, The Journal of cell biology.

[4]  Viola Vogel,et al.  Engineered networks of oriented microtubule filaments for directed cargo transport. , 2007, Soft matter.

[5]  Jules Moreau,et al.  Molecular Computation by DNA Hairpin Formation , 2000 .

[6]  N. Seeman From genes to machines: DNA nanomechanical devices. , 2005, Trends in biochemical sciences.

[7]  T. Yanagida,et al.  Mechanics of single kinesin molecules measured by optical trapping nanometry. , 1997, Biophysical journal.

[8]  T. Mitchison Localization of an exchangeable GTP binding site at the plus end of microtubules. , 1993, Science.

[9]  Kazuhiro Oiwa,et al.  Molecular Communication: Modeling Noise Effects on Information Rate , 2009, IEEE Transactions on NanoBioscience.

[10]  Liedewij Laan,et al.  Reconstitution of a microtubule plus-end tracking system in vitro , 2007, Nature.

[11]  B. Oakley,et al.  Microtubule nucleation. , 2003, Current opinion in cell biology.

[12]  B. Iglewski,et al.  Bacterial Quorum Sensing in Pathogenic Relationships , 2000, Infection and Immunity.

[13]  Thorsten Lang,et al.  Membrane fusion. , 2003, Cell.

[14]  H. Fujita,et al.  Hybrid nanotransport system by biomolecular linear motors , 2004, Journal of Microelectromechanical Systems.

[15]  Yale E Goldman,et al.  Kinesin and dynein-dynactin at intersecting microtubules: motor density affects dynein function. , 2008, Biophysical journal.

[16]  K. Pavelić,et al.  Medicine on a small scale , 2003, EMBO reports.

[17]  Marileen Dogterom,et al.  Dynamic instability of microtubules is regulated by force , 2003, The Journal of cell biology.

[18]  Kerry Bloom,et al.  It’s a kar9ochore to capture microtubules , 2000, Nature Cell Biology.

[19]  Manfred Schliwa,et al.  Molecular motors , 2003, Nature.

[20]  Joachim O Rädler,et al.  Temporal analysis of active and passive transport in living cells. , 2008, Physical review letters.

[21]  Cees Dekker,et al.  Motor Proteins at Work for Nanotechnology , 2007, Science.

[22]  M. Kirschner,et al.  Beyond self-assembly: From microtubules to morphogenesis , 1986, Cell.

[23]  B. Alberts,et al.  Nucleation of microtubule assembly by a gamma-tubulin-containing ring complex. , 1995, Nature.

[24]  Yixian Zheng,et al.  Nucleation of microtubule assembly by a γ-tubulin-containing ring complex , 1995, Nature.

[25]  M. Kirschner,et al.  Dynamic instability of microtubule growth , 1984, Nature.

[26]  Chris Dwyer,et al.  DNA self-assembled parallel computer architectures , 2004 .

[27]  J. Rothman,et al.  The machinery and principles of vesicle transport in the cell , 2002, Nature Medicine.

[28]  E D Salmon,et al.  Brain microtubule-associated proteins modulate microtubule dynamic instability in vitro. Real-time observations using video microscopy. , 1992, Journal of cell science.

[29]  William Thies,et al.  Abstraction layers for scalable microfluidic biocomputing , 2008, Natural Computing.

[30]  Shoichiro Tsukita,et al.  "Search-and-capture" of microtubules through plus-end-binding proteins (+TIPs). , 2003, Journal of biochemistry.

[31]  T. Mitchison,et al.  Microtubule polymerization dynamics. , 1997, Annual review of cell and developmental biology.

[32]  T. Suda,et al.  A nanosensory device fabricated on a liposome for detection of chemical signals , 2010, Biotechnology and bioengineering.

[33]  M. Schliwa,et al.  Molecular motors , 2003, Nature.

[34]  X. D. Hoa,et al.  Towards integrated and sensitive surface plasmon resonance biosensors: a review of recent progress. , 2007, Biosensors & bioelectronics.

[35]  S. Leibler,et al.  Self-organization of microtubules and motors , 1997, Nature.