Home Page Researchers Danny Porath

Danny Porath

Institute of Chemistry
Faculty of Science
The Hebrew University, Jerusalem 91904, Israel
Tel: +972-2-6586948; Fax: +972-2-6586987;
E-mail: danny.porath@mail.huji.ac.il;
Website: http://chem.ch.huji.ac.il/~porath/


From bio-inspired systems for nanoelectronics to physico-inspired tools to study bio-systems

Our research is bi-directional: In the first direction we use bio-templated systems to realize one-dimensional conducting nanowires and nanodevices to investigate electrical charge transport in these systems for nanoelectronics and nanotechnology applications. Examples of the bio-templated systems are DNA and its synthetic derivatives and the ring shaped SP1 protein hybridized with various nanoparticles to form memory units, logic machines, large memory arrays and protein-particles conducting chains. Within this frame we measured electrical charge transport in dsDNA, revealed the energy level spectrum of dsDNA, showed polarizability of DNA derivatives and more. We also demonstrated charging, memory and logic operations in the hybrid SP1-nanoparticle systems. The other research direction focuses on an attempt to use our physical approach and tools to address biological issues. We investigate DNA translocation through narrow, SP1-solid state hybrid nanopores. The objective is to develop methods for rapid DNA sequencing or investigating the interaction of the translocated DNA with proteins. In another project we investigate in-vitro a critical stage in the life cycle of the HIV virus, the integration of the "viral DNA" into "cellular DNA", on the single molecule level using atomic force microscopy imaging. The research is conducted by my group in close collaboration with several groups from complementary fields.

DNA-Based Nanoelectronics:
Conductivity through one-dimensional nanowires is a central theme in nanoelectronics. There are two main families of nanowires that are considered: carbon nanotubes and the like, that manifest excellent conductivity and mechanical properties but lack specific recognition and their present synthesis methods do not enable to control their structure and length. The other is polymers, e.g., DNA and protein-nanoparticles hybrids that enable good control on their structure and length and provide recognition and self-assembly but their conductivity is limited by structural factors. We investigate the morphology and electrical properties of candidates from the latter family and attempt, in collaboration with other groups (see below), to develop nanowires that will have the self-assembly properties together with considerably improved conductivity. DNA and its derivatives are leading candidates for application as molecular nanowires due to the double-strand recognition that allows self-assembly, the accurate synthesis of the molecule, the enormous density of information packing in DNA and the well established enzymatic machinery.

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The conductivity of DNA in itself was investigated by several methods using atomic force microscopy  (AFM). We find that 26 base-pairs long DNA can conduct relatively high currents (220 nA @ 2V), indicating a coherent transport mechanism, in dissonance with previous results obtained from experiments in solution.

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(a) The conductivity of long DNA single molecules measure with a stencil-defined electrode and a cAFM tip as the moving electrode. (b) Topography image shows a partly protruding G4 DNA molecule from the evaporated electrode. The X?s mark the locations where I-V measurements were taken. (c) I-V, corresponding to the X?s in (b).

The DNA energy level spectra are investigated also by scanning tunneling microscopy (STM) and spectroscopy (STS). <

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STM imaging and STS spectroscopy of single DNA molecules. Upper inset shows gold atoms.

In parallel we attempt the following candidates as wires with improved electrical properties: (a) various types of G4-DNA, a very stable DNA molecule made of consecutive planar arrangements of 4 guanine (G) bases (tetrades) connected with four poly-G strands and stabilized by metal ions. (b) M-DNA, a double stranded DNA in which a divalent metal ion is incorporated into each base-pair of the duplex. An almost linear arrangement of divalent metal ions separated by inter-base distances (~3.4 A) in both structures may impose unusual conduction properties on the DNA molecule. (c) PC-DNA - (Polymer Coated DNA) DNA molecules. The conductivity along single molecules is monitored by direct electrical transport measurements between metal nanoelectrodes. These molecules, which are produced by the groups of A. Kotlyar and S. Yitzchaik, are investigated and tested by my group to serve as molecular nanowires. The development of such molecular wires and devices that will be based on them may lay a foundation for DNA-based nanoelectronics.

Protein-nanoparticle hybrids nanoelectronics structures:

SP1 protein, hybridized with a nanoparticle, produced by the group of O. Shoseyov, is a building block for alternative structures to realize nanoelectronics applications. These structures can form ultra dense arrays for memory applications and for "lego-like" constructions of nanowires and networks, as seen in the figure below.

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SP1 images and structures: (a) TEM image (averaged) and (b) AFM image of SP1 proteins array. (c) SP1 array with schematic of nanoparticles that will serve for the memory. (d) A suggested nanowire and nanostructure.

With these building blocks we already demonstrated charging, set/reset and ternary logic operation.

DNA translocation in nanopores towards DNA sequencing and investigating other bio-related phenomena:

We investigate translocation of DNA through nanopores. The objective is to develop methods for rapid DNA sequencing or investigating the interaction of the translocated DNA with proteins. We are using solid state nanopores that are prepared by TEM drilling in SiN membrane and in some cases this process is followed by atomic layer deposition (ALD). In one study we made SP1 protein - solid-state hybrid nanopores, that are managed to reduce the DNA translocation speed. In addition, we investigate solid state nanopores that are flanked by carbon nanotubes or graphene as electrodes The research is conducted by my group in collaboration with the groups of O. Shoseyov, R. Yerushalmi and other European groups within the frame of an EU project.

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Monitoring the HIV-1 integrase enzymatic activity using AFM:

We investigate in-vitro a critical stage in the life cycle of the HIV virus, the integration of the "viral DNA" into "cellular DNA", on the single molecule level using AFM imaging. The research is conducted by my group in collaboration with the groups of A. Friedler and A. Loyter.

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AFM images of intermediate stages of in-vitro integration reaction: (a) DNA molecules before reaction (~500 nm). (b) a DNA molecule with integrase dimer on each end. (c) DNA molecule looped with ab integrase tetramer. (d) A long DNA molecule after 4 integrations.

Specific research topics related to Nanoscience and Nanotechnology:

  • Investigation of the morphology, electrical properties and energy spectra of DNA, G4-DNA, and M-DNA by atomic force microscopy and related methods, by scanning tunneling microscopy and spectroscopy (STM/STS) and by direct electrical transport measurements.
  • Development and investigation of new DNA-based nanowires and nanodevices using the above methods and above candidates in collaboration with other groups.
  • Investigation of DNA translocation in solid-state nanopores towards DNA sequencing and other, also bio-oriented, applications.
  • Development of ultra dense memory arrays and nanoelectronic wires and networks made of SP1-nanoparticles hybrids in collaboration with other groups.
  • Investigation of a critical stage in the HIV life cycle: the integration of viral DNA into the host DNA, by AFM on the single molecule level.

List of publications in Nanoscience and Nanotechnology (2010-2012)

  • "Novel materials for molecular electronics - synthesis and characterization of long G4-DNA", Dvir Rotem, Gennady Eidelshtein, Alexander Kotlyar and Danny Porath, in "Guanine Quartets: Structures and Applications", Eds.: Lea Spindler and Wolfgang Fritzsche, Royal Society of Chemistry (2012).
  • ?Quasi 3D imaging of DNA-gold nanoparticle tetrahedral structures.? Stern, A., D. Rotem, I. Popov, and D. Porath, Journal of Physics-Condensed Matter, 24 (2012).
  • ?Wiring of Redox Enzymes on Three Dimensional Self-Assembled Molecular Scaffold?, Marco Frasconi, Arnon Heyman, Izhar Medalsy, Danny Porath, Franco Mazzei, and Oded Shoseyov, Langmuir In press27, 12606, (2011).
  • ?Energy gap reduction in DNA by complexation with metal ions?, Errez Shapir, Giorgia Brancolini, Tatiana Molotsky, Alexander B. Kotlyar, Rosa Di Felice, and Danny Porath, Advanced Materials, 23, 4290, (2011).
  • ?Self-Assembly: I-Motif Nanospheres: Unusual Self-Assembly of Long Cytosine Strands?, Dragoslav Zikic, Ke Liu, Lior Sagiv, Danny Porath and Alexander Kotlyar, Small, 7, 1028 (2011).
  • ?The Electronic Structure of G4-DNA by Scanning Tunneling Spectroscopy?, Errez Shapir, Lior Sagiv, Tatiana Molotsky, Alexander Kotlyar, Rosa Di Felice and Danny Porath, Journal of Physical Chemistry C, 114, 22079 (2010).
  • ?SP1 Protein-Gold Nanoparticle Hybrids as Building Blocks for Nanofabrication of One-Dimensional Systems?, Izhar Medalsy, Or Dgany, Arnon Heyman, Oded Shoseyov, Mukhles Sowwan and Danny Porath, in Bionanotechnology: Global Prospects II, Ed. David E. Reisner ? CRC Press (2010).
  • ?Logic implementations using a single nanoparticle?protein hybrid?, Izhar Medalsy, Arnon Heyman, Michael Klein, Oded Shoseyov, F. Remacle, R.D. Levine and Danny Porath, Nature Nanotechnology (Article) 5, 451 (2010).

Significant publications:

  • ?Logic implementations using a single nanoparticle?protein hybrid?, Izhar Medalsy, Arnon Heyman, Michael Klein, Oded Shoseyov, F. Remacle, R.D. Levine and Danny Porath, Nature Nanotechnology (Article) 5, 451 (2010).
  • ?Protein Scaffold Engineering Towards Tunable Surface Attachment?, Arnon Heyman, Izhar Medalsy, Oron Bet Or, Or Dgany, Maya Gotlieb, Danny Porath, and Oded Shoseyov, Angewandte Chemie Int. Ed., 48, 9290 (2009).
  • ?A DNA sequence scanned?, Danny Porath, Nature Nanotechnology 4, 476 (2009).
  • ?Electronic structure of single DNA molecules resolved by transverse scanning tunneling spectroscopy?, Errez Shapir, Hezy Cohen, Arrigo Calzolari, Carlo Cavazzoni, Dmitry A. Ryndyk, Gianaurelio Cuniberti, Alexander Kotlyar, Rosa Di Felice, and Danny Porath, Nature Materials 7, 68 (2008).
  • ?SP1 Protein Based Nanostructures and Arrays?, Izhar Medalsy, Or Dgany, Mukhles Sowwan, Hezy Cohen, Alevtyna Yukashevska, Sharon G. Wolf, Amnon Wolf, Abraham Koster, Orna Almog, Ira Marton, Yehonathan Pouny, Arie Altman, Oded Shoseyov and Danny Porath, Nano Letters 8, 473 (2008).
  • ?Polarizability of G4-DNA Observed by EFM Measurements?, Hezy Cohen, Tomer Sapir, Natalia Borovok, Tatiana Molotsky, Rosa Di Felice, Alexander B. Kotlyar, and Danny Porath, Nano Letters 7, 981 (2007).

New patents and patents utilization:

  • "Multi-site modified sp1 polypeptides and uses thereof", Arnon Heyman, Izhar Medalsy, Danny Porath and Oded Shoseyov
  • "Organic nanoelectronic conductors", US Patent application 10/362,443, Alexander Kotlyar, Miron Hazani and Danny Porath
  • "Enzymatic synthesis of uniform PolyG-PolyC and G4 wires and their derivatives". (Ramot's file No. 2004032-00-00), Alexander Kotlyar, Natalia Borovok and Danny Porath

Cooperation with other universities in Israel:

Within Hebrew University:
Oded Shoseyov, Assaf Friedler, Yossi Paltiel, Avraham Loyter, Shlomo Yitzchaik, Roie Yerushalmi, Yossi Shlomai, Shlomo Magdasi

With other universities:
Alexander Kotlyar, Abraham Nitzan, Gil Markovich, Yael Hanein

Research grants

  • EU-FET - Rapid DNA sequencing
  • ISF - Investigating the electrical transport mechanisms in DNA
  • BSF - Charge transport through single DNA molecules
  • DFG - Single Molecule based ultra high density memory
  • Academia Sinica, Taiwan - Bio-inspired organic/inorganic hybrid electronic devices
  • Academia Sinica, Taiwan - Using naotechnology for developing kinase
  • FTA- Hybrid Nanomaterials
  • The Minerva Center for Bio-Hybrid Complex Systems, The Hebrew University of Jerusalem

Honors and awards:

  • 2000 Excellent postdoctoral award of the Americal Vacuum Society Meeting, Boston
  • 2007 The Israel Chemical Society Prize for the Outstanding Young Scientist for 2007
  • 2009 Postdoc work ("Direct measurement of electrical transport through DNA molecules", Nature 403, 635 (2000)) selected as "Classics of Science" by Thomson Reuters following ~900 citations: Science Watch, Podcast interview
  • 2009 Erasmus Mundus research scholar for Nanoscience and Nanotechnology

Students, postdocs and researchers:

Staff scientist: Dr. Dvir Rotem, Dr. Yariv Pinto, Dr. Igor Brodski
Postdocs: Dr. Claude Nogues, Dr. Jamal Gabbhon, Dr. Ke Liu, Dr. Haichao Huang
Ph.D. students: Hezy Cohen, Gideon Livshits, Wenting Zhao (2 month visit in my group), Nurit Yaffe (in collaboration with J. Shlomai), Avigail Stern-Slutzkin, Roman Zhuravel, Guy Koplovitz, Abeer Karmi
M.Sc students: Daniela Ullien, Guy Hamou, Limor Harel, Lev Tal-Or, Avital Tal, Maya Gotlieb, Lior Sagiv, Tomer Sapir, Haya Dachlika, Michelle Sykes

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