DNA-based Nanowires and Nanodevices

( The research is funded by the European Information Society of Technologies)

Current microelectronics is rigorously based on silicon. This will remain so for at least a decade. However, after that, major problems are foreseen with the further miniaturization of the Si devices. Aternative approaches should therefore be explored. DNA-based electronics is a prime example of an entirely alternative approach. It will take advantage of the unprecedented recognition and assembling properties of DNA. DNA-based nanoelectronic devices will enable one to reduce the size of the current devices by ~1000 times.

A specific innovative focus of this project is to investigate novel DNA-based derivatives and modifications that hold potential for improved properties with respect to native DNA. The derivatives that we suggest, G4-DNA (G-quadruplexes) and M-DNA (DNA-metal complexes) Our novel approach is to chemically alter the native structure in such a way that the DNA derivatives will provide electrical properties that are suitable for molecular electronics, but at the same time will maintain the addressability and structured arrangement that are so attractive in the native DNA. The use of such structured wires may give alternating electrical properties of partial elements along the wires, such that they will act as devices that are extremely small, exceptionally close to each other, and have a very controlled structure.

We also propose to develop new conductive molecular nanowires based on stable complexes of the long (up to micron) double stranded polyG-polyC, triplex-DNA (or DNA triple helice) and momomolecular G4-DNA (quadruple helix made of guanines) with metal nanoparticles. and to use them as building blocks in DNA-based nanodevices .

The research includes a combination of state of the art capabilities for the enzymatic production and manipulation of DNA-based molecules, surface chemistry, scanning probe microscopy, anofabrication, all combined to provide new solutions and information about the core problems at the forefront of the research on conduction through DNA derivatives. Success in this project may provide a key step towards the development of DNA-based nanoelectronic devices.

Novel strong inhibitor of mitochondrial Complex I

Complex I (NADH-ubiquinone oxidoreductase) functions as the main entry point for reducing equivalents into the respiratory chain of mitochondria. This complex is the largest and least well understood component of the respiratory chain. Its primary function is to oxidize NADH in the mitochondrial matrix, thereby reducing ubiquinone to ubiquinol and pumping protons across the inner membrane to drive ATP synthesis. The enzyme is composed of more than 40 different subunits and contains multiple distinct redox components (FMN, a number of iron-sulfur clusters and tightly bound ubiquinones). Complex I is also considered as a major source of superoxide, making it a candidate for increased mitochondrial ROS production and redox signaling. The enzyme is also involved in nitric oxide physiology, induction of the permeability transition, and the regulation of apoptosis.

This project is aimed at studying kinetics and regulation of mitochondrial Complex I. In our laboratory we recently discovered a very potent nucleotide-site directed inhibitor of Complex I which appears to be a derivative of NADH. Preliminary data have shown that the inhibitor almost completely suppress NADH oxidation at sub-micromolar concentration. Preliminary data for the structure of this compound, which we have termed NADH-I, shows that it is a derivative of NADH and might be produced in the cell modulating activity of Complex I in vivo in normal conditions and under periods of oxidative stress. The present application is, thus, to study the properties of NADH-OH, to determine the molecular structure of NADH by NMR and Mass spectrometry, to describe its mode of action, and to determine possible pathways leading to its formation and degradation in mitochondria.

1.          Zikich D, Liu K, Sagiv L, Porath D, Kotlyar A. I-motif nanospheres: unusual self-assembly of long cytosine strands. Small. March 2011, ahead of print.

2.         Lubitz and Kotlyar A. Self-assembled G4-DNA-silver nanoparticle structures. Bioconjugate Chem. Feb 2011, Epub ahead of print.

3.         Zikich D, Lubitz I, Kotlyar A. Ag⁺ -Induced Arrangement of Poly(dC) into Compact Ring-shaped Structures. I.RE.BI.C. 2010, 1, 1-6.

4.         Lubitz, I., Zikich, D., Kotlyar, A.B. Specific High-Affinity Binding of Thiazole Orange to Triplex and G-Quadruplex DNA. Biochemistry. 2010, 49 (17), 3567–3574.

5.         Zikich D, Borovok N, Molotsky T, Kotlyar A. Synthesis and AFM Characterization of Poly(dG)-poly(dC)-gold Nanoparticle Conjugates. Bioconjugate Chem. 2010, 21, 544-547.

6.         Borovok, N, Iram, N, Zikich, D, Ghabboun, J, Livshits, GI, Porath, D, Kotlyar A. Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition. Nucleic Acids Res. 2008, 36 (15): 5050-60.

7.         Lomanets O., Shemer G., Markovich G., Molotsky T., Lubovich I., Kotlyar A.B . Chirality of silver nanoparticles synthesized on DNA. J. Am. Chem. Soc. 2006, 128, 11006 – 11007.

8.         Bardavid, Y., Kotlyar A. B., Yitzchaik S. Conducting polymer coated DNA. Macromolecular  Symposia. 2006, 240, 102-106.

9.         Shapir E, Cohen H, Borovok N, Kotlyar A B, Porath D. High-resolution STM imaging of novel poly(G)-poly(C) DNA molecules. J. Phys. Chem. B. 2006,  110, 4430-4433.

10.       Shapir E., Yi J., Cohen H., Kotlyar A.B., Cuniberti G ., Porath D. The Puzzle of Contrast Inversion In DNA STM Imaging. J. Phys. Chem. B. 2005, 109, 14270 -14274 (letters section-with journal cover).

11.        Kotlyar A.B., Borovok N., Molotsky T., Cohen H., Shapir E., Porath D. Long Monomolecular G4-DNA Nanowires. Adv. Materials. 2005, 17,1901- 1905, (with journal cover – cover of the year).

12.        Tenger K, Khoroshyy P, Leitgeb B, Rakhely G, Borovok N, Kotlyar A. B., Dolgikh DA, Zimanyi L. Complex kinetics of the electron transfer between the photoactive redox label TUPS and the heme of cytochrome C. J Chem. Inf. Model. 2005, 45, 1520-1526.

13.        Belgorodsky B, Fadeev L, Ittah V, Benyamini H, Zelner S, Huppert D, Kotlyar AB , Gozin M. Formation and characterization of stable human serum albumin-tris-malonic acid [C60] fullerene complex. Bioconjug. Chem. 2005, 16 , 1058-1062.

14.       Kotlyar A.B, Karliner J.S, Cecchini G. A novel strong competitive inhibitor of complex I. FEBS Lett . 2005, 579, 4861-4866.

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

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

Patent applications

1. "Organic nanoelectronic conductors", US Patent application 10/362,443, Alexander Kotlyar, Miron Hazani and Danny Porath.
2. "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.

1. Natalya Borovok, senior researcher,  natalbor@post.tau.ac.il
2. Dragoslav Zikich, PhD student, dzikich@gmail.com 
3. Irit Lubitz, PhD student, iritlubitz@gmail.com
4. Tali Tamarin, M.Sc student,  tali.tamarin82@gmail.com
5. Genady Edelshtein, M.Sc student, g.edelshtein@gmail.com
6. Elad Gillon, M.Sc student, egillon@gmail.com