Prof. Alexander Kotlyar

DNA-based nanotechnology

The DNA molecule, well known from biology for containing the genetic code of all living species, has caught the attention of chemists and physicists as a possible candidate to wire electronic materials in a programmable way by virtue of its recognition and self-assembling properties. The realization of self-assembled DNA-based conductive architectures will enable to reduce the size of the current devices by ~1000 times and will shift the production process from complicated and defect-rich lithographic processes to processes that are based on self-assembly and self-organization.

Several non-canonical DNA-derivatives have shown the potential for robust charge transport. Chief among these are metallized DNA and guanine quadruplex (G4). The latter molecule composed of four G-strands has higher electrical polarizability [Livshits G. I., et al. (2014) Advanced Materials 26, 5067] and conductance [Livshits G. I., et al. (2014) Nature Nanotechnology, 9, 1040-1046] versus natural double-stranded DNA, due to enhanced p-p stacking between the bases and relatively low ionization potential of guanine, compared to other nucleic bases. These G4-nanowires can be assembled into complex two-dimensional and three-dimensional DNA architectures and integrate functional units along with other molecular electronic components yielding interconnected networks, DNA-based nano-devices and nano-circuits.

The main goal of this research will be the creation, by self-assembly, of a fabric of interconnected DNA-based molecular switches and wires that can, in the future, open a way to the realization of a nano-scale transistors and devices and that can be used to build computer chips and form the basis of a new type of information processing architecture.  

Biomedical Applications of plasmonic nanoparticle structures

Due to their attractive electronic, optical, and thermal properties noble metal nanoparticles have attracted huge interest of chemist, physicists and biologists. The nanometric size, unique optical, electrical and chemical properties led to a broad range of the metal particles application in various research fields, including nanophotonics, nanoelectronics,  optoelectronics,  nanomedicine and others. In particular, the particles have been rather successfully used in therapy and diagnostics of cancer. One of the main challenges, however that limits application of noble metal particles in biomedicine, is their low stability under physiological conditions. At physiological salt concentrations (~150 mM NaCl) most of particles precipitate out of the solution. To overcome this challenge, we have developed protocols for coating gold and silver nanoparticles with single-stranded DNA and G-quadruplexes [Lubitz I., & Kotlyar A. (2011)  Bioconjugate Chem.,  22, 482; Borovok N.,  et al. (2012) Bioconjugate Chem. 23, 916;  Lubitz I., & Kotlyar A. (2011)   Bioconjugate Chem. 22, 2043]. These DNA-coated particles are stable under physiological conditions and can be administered directly into the blood stream.

The main goal of this research will be the creation stable plasmonic nano-constructs for cancer therapy. The particles will be functionalized with: 1 – Fab fragments of antibodies that will direct them towards cancer cells; 2 – Trojan peptides and nuclear localization sequences that will transport of nanoparticles through the cell and nucleus membranes and 3 – DNA (or Protein Nucleic Acid, PNA) sequences that will bind either to promoter regions or to the human telomere sequence at the end of chromosomes in order to inhibit transcription and chromosomes separation during the cell division.

Success in this project may lead production of novel nanoparticle-based therapeutics for cancer treatment. 

A.B. Kotlyar, N. Borovok, T. Molotsky, L. Fadeev, M. Gozin “In vitro synthesis of uniform Poly(dG)-Poly(dC) by Klenow exo– fragment of Polymerase I” (2005) Nucl. Acid Res., 33, 525-535;

A.B. Kotlyar , N. Borovok, T. Molotsky, D. Klinov, B. Dwir, E. Kapon “Synthesis of novel poly(dG)-poly(dG)-poly(dC) triplex structure by Klenow exo- fragment of DNA polymerase I” (2005) Nucl. Acid Res., 33, 6515-6521;

A.B. Kotlyar, N. Borovok, T. Molotsky, H. Cohen, E. Shapir, D. Porath “Long Monomolecular G4-DNA Nanowires” (2005)  Adv. Materials 17, 1901-1905;

O. Lomanets, G. Shemer, G. Markovich, T. Molotsky, I. Lubitz, A.B. Kotlyar “Chirality of silver nanoparticles synthesized on DNA” (2006)  J. Am. Chem. Soc., 128, 11006 – 11007;

H. Cohen, T. Sapir  N., Borovok, T. Molotsky, R. Felice, A.B. Kotlyar, D. Porath “Polarizability of G4-DNA Observed by Electrostatic Force Microscopy Measurements” (2007)   Nano Letters, 7, 981-986;

D. Klinov, K. Atlasov, A. Kotlyar, B. Dwir, E. Kapon “DNA Nanopositioning and Alignment by Electron-Beam-Induced Surface Chemical Patterning” (2007) Nano Letters, 7, 3583-3587;

D. Klinov, B. Dwir, E. Kapon, N. Borovok, T. Molotsky, A.B. Kotlyar “High-resolution atomic-force imaging of duplex and triplex DNA molecules” (2007) Nanotechnology 18, 225102 (8pp);

I. Lubitz, N. Borovok, A.B. Kotlyar ‘Interaction of monomolecular G4-DNA nanowires with TMPyP: evidence for intercalation’ (2007) Biochemistry, 46, 12925-12929;

E. Shapir, H. Cohen, A. Calzolari, C. Cavazzoni, D.A. Ryndyk, G. Cuniberti, A. Kotlyar, R. Di Felice, D. Porath “Electronic structure of single DNA molecules resolved by transverse scanning tunneling spectroscopy” (2008) Nature Materials, 7, 68-74;

N. Borovok, T. Molotsky, J. Ghabboun, D. Porath, A. Kotlyar “Efficient procedure of preparation and properties of long uniform G4-DNA nanowires” (2008) Anal. Biochem., 374, 71-78;

N. Borovok, N, Iram, D. Zikich, J. Ghabboun, G. Livshits D. Porath, A. Kotlyar “Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition” (2008)  Nucl. Acid Res., 36, 5050-5060;

D. Zikich, N. Borovok, T. Molotsky, A. Kotlyar (2010) “Synthesis and AFM characterization of poly(dG)-poly(dC)-gold nanoparticle conjugates” Bioconjug. Chem., 21, 544-547;

I. Lubitz, D. Zikich, A. Kotlyar  ”Specific high-affinity binding of Thiazole Orange to Triplex and G-quadruplex DNA’ (2010) Biochemistry, 49, 3567-3574;

I. Lubitz, A. Kotlyar “Self-assembled G4-DNA-silver nanoparticle structures” (2011)  Bioconjug. Chem., 22, 482-487;

E. Shapir, G. Brancolini, T. Molotsky, A. Kotlyar, R. Di Felice, D. Porath “Energy gap reduction in DNA by complexation with metal ions” Adv. Materials, 23, 4290-4294;

A. Kotlyar “Synthesis of long DNA-based nanowires” (2011)  Methods Mol. Biol., 749, 115-140; 

I. Lubitz,  A. Kotlyar “G4-DNA-Coated Gold Nanoparticles: Synthesis and Assembly” Bioconjug. Chem., 22, 2043-2047;

N. Borovok, E. Gillon, A. Kotlyar (2012) “Synthesis and Assembly of Conjugates Bearing Specific Numbers of DNA Strands per Gold Nanoparticle” Bioconjug. Chem., 23, 916–922;

Sh. Halamish, G. Eidelshtein, A. Kotlyar “Plasmon-coupled Nanostructures Comprising Finite Number of Gold Particles” (2013) Plasmonics, 8, 745–748;        

G.I. Livshits, J. Ghabboun, N. Borovok, A.B. Kotlyar, D. Porath “Comparative Electrostatic Force Microscopy of Tetra‐and Intra‐molecular G4‐DNA”  (2014) Adv. Materials, 26, pp.4981-4985, 2014

G.I. Livshits, A. Stern, D. Rotem, N. Borovok, G. Eidelshtein, A. Migliore, E. Penzo, S. J. Wind, R. Di Felice, S. S. Skourtis, J. C. Cuevas, L. Gurevich, A. B. Kotlyar,  D. Porath “Long-range charge transport in single G4-DNA molecules”  Nature Nanotechnology 9, 1040-1046.