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Journal of Self-Assembly and Molecular Electronics (SAME)

Editors-in-Chief: Peter Fojan and Leonid Gurevich

ISSN: 2245-4551 (Print Version),

ISSN: 2245-8824 (Online Version)
Vol: 1   Issue: 1

Published In:   January 2013

Publication Frequency: Continuous Article Publication

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Molecular Combing of DNA: Methods and Applications

doi: 10.13052/same2245-4551.116
Zeinab Esmail Nazari and Leonid Gurevich

Institute of Physics and Nanotechnology, Aalborg University, 9220 Aalborg, Denmark

Abstract: [+]    |    Download File [ 12933KB ]   |    Read Article Online

Abstract: First proposed in 1994, molecular combing of DNA is a technique that allows adsorption and alignment of DNA on the surface with no need for prior modification of the molecule. Since then, many variations of the original method have been devised and used in a wide range of applications from genomic studies to nanoelectronics. While molecular combing has been applied in a variety of DNA-related studies, no comprehensive review has been published on different combing methods proposed so far. In this review, the underlying mechanisms of molecular combing of DNA are described followed by discussion of the main methods in molecular combing as well as its major applications in nanotechnology.

Keywords: Molecular combing of DNA, DNA stretching, AFM

Self-Assembled DNA-Based Structures for Nanoelectronics

doi: 10.13052/same2245-4551.115
Veikko Linko1 and J. Jussi Toppari2

1Physics Department, Walter Schottky Institute, TechnischeUniversitätMünchen, 85748 Garching near Munich, Germany
2Department of Physics, Nanoscience Center, University of Jyväskylä, P.O. Box 35, 40014Jyväskylä, Finland

Abstract: [+]    |    Download File [ 6367KB ]   |    Read Article Online

Abstract: Recent developments in structural DNA nanotechnology have made complexand spatially exactly controlled self-assembled DNA nanoarchitectureswidely accessible. The available methods enable large variety ofdifferent possible shapes combined with the possibility of using DNAstructures as templates for high-resolution patterning of nano-objects,thus opening up various opportunities for diverse nanotechnologicalapplications. These DNA motifs possess enormous possibilities to beexploited in realization of molecular scale sensors and electronicdevices, and thus, could enable further miniaturization of electronics.However, there are arguably two main issues on making use of DNA-based electronics: (1) incorporation of individual DNA designs into largerextrinsic systems is rather challenging, and (2) electrical properties ofDNA molecules and the utilizable DNA templates themselves, are not yetfully understood. This review focuses on the above mentioned issues andalso briefly summarizes the potential applications of DNA-basedelectronic devices.

Keywords: Self-assembly, DNA nanostructures, electrical conductivity of DNA, carbon nanotubes, nanoparticles

Formation of Dimers Composed of a Single Short dsDNA Connecting Two Gold Nanoparticles

doi: 10.13052/same2245-4551.114
Haya Dachlika, Avigail Stern, Dvir Rotem and Danny Porath

Institute of Chemistry and The Harvey M. Krueger Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel

Abstract: [+]    |    Download File [ 7349KB ]   |    Read Article Online

Abstract: We report synthesis of dimers composed of a single short double-stranded (ds)DNA molecule connecting two gold nanoparticles (GNPs). Such structures may be useful for electrical transport measurements through dsDNA molecules and for other research purposes. When the DNA molecules are short with respect to the size of the GNP, gel electrophoresis cannot separate GNPs with different numbers of DNA molecules attached to them. We present two methods to separate GNPs connected to single short thiolated single-stranded (ss)DNA. The separation is performed by hybridizing the DNA/GNP conjugates with long, partially complementary, ssDNA or with complementary ssDNA connected to GNPs of smaller size. The separated GNPs with a single short ssDNAwere used to form dimers consisting of GNPs connected by a {it single} short dsDNAmolecule.

Keywords: DNA, gold nanoparticles, gel electrophoresis

Synthesis and Properties of Conjugates between Silver Nanoparticles and DNA-PNA Hybrids

doi: 10.13052/same2245-4551.113
Gennady Eidelshtein1, Shay Halamish1, Irit Lubitz1, Marcello Anzola2, Clelia Giannini2and Alexander Kotlyar1

1Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
2Dipartimento di Chimica, UniversitàdegliStudi di Milano, via Venezian 21, 20133 Milano, Italy

Abstract: [+]    |    Download File [ 6969KB ]   |    Read Article Online

Abstract: We describe the preparation and properties of a stable conjugate betweentwo 15 nm silver nanoparticles (AgNPs) and a DNA-PNA hybrid composed of10 guanine-cytosine base pairs. We show that the conjugate isspontaneously formed during incubation of a DNA-PNA hybrid, containingphosphorothioate residues at both ends of the DNA strand with AgNPs. Theconjugate molecules were separated from individual AgNPs andmultiparticle structures by gel electrophoresis. We demonstrate that theabsorption spectrum of the conjugate is broader than that of AgNPs, dueto the interparticleplasmon coupling.

Keywords: Silver nanoparticles, PNA-DNA hybrid, nanomaterials, TEM

Interaction of DNA Bases with Gold Substrates

doi: 10.13052/same2245-4551.112
Marta Rosa, Wenming Sun and Rosa Di Felice

Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy

Abstract: [+]    |    Download File [ 7107KB ]   |    Read Article Online

Abstract: The interaction of molecules with inorganic substrates is a crucial issue for applications in molecular electronics. It influences important factors such as the immobilization efficiency and the charge injection through the interface. Moreover, mechanical aspects connected to the unfolding of biological molecules are important.

We hereby present recent efforts in our group to tackle these problems, based on density functional theory calculations. In particular, we discuss our results on the adsorption of cytosine on Au(111) and on the interaction of guanine, in its natural and size-expanded forms, with small Au clusters. We find that cytosine binds to the Au(111) surface with a mechanism that involves charge sharing, intermediate between chemisorption and physisorption. The investigation of small complexes between guanine and gold clusters reveals the formation of hydrogen bonds: these configurations with unusual bonds are relevant at the corners of nanoparticles, while they can probably be neglected when DNA binds on flat extended metal surfaces.

Keywords: DNA/Au interfaces, Density Functional Theory, Van der Waals, DNA modifications, electronic hybridization

Modeling Charge Transport and Dynamics in Biomolecular Systems

doi: 10.13052/same2245-4551.111
R. Gutierrez1 and G. Cuniberti1,2

1Institute for Materials Science and Max Bergmann Center of Biomaterials,Dresden University of Technology, 01062 Dresden, Germany
2Division of IT Convergence Engineering and National Center forNanomaterials Technology, POSTECH, Pohang 790-784, Republic of Korea;

Abstract: [+]    |    Download File [ 3459KB ]   |    Read Article Online

Abstract: Charge transport at the molecular scale builds the cornerstone ofmolecular electronics (ME), a novel paradigm aiming at the realizationof nanoscale electronics via tailored molecular functionalities.Biomolecular electronics, lying at the borderline between physics,chemistry and biology, can be considered as a sub-field of ME. Inparticular, the potential applications of DNA oligomers either astemplate or as active device element in ME have strongly drawn theattention of both experimentalist and theoreticians in the past years.While exploiting the self-assembling and self-recognition properties ofDNA based molecular systems is meanwhile a well-established field, thepotential of such biomolecules as active devices is much less clearmainly due to the poorly understood charge conduction mechanisms. Onekey component in any theoretical description of charge migration inbiomolecular systems, and hence in DNA oligomers, is the inclusion ofconformational fluctuations and their coupling to the transport process.The treatment of such a problem affords to consider dynamical effects ina non-perturbative way in contrast to, e.g., conventional bulk materials.Here we present an overview of recent work aiming at combining moleculardynamic simulations and electronic structure calculations with chargetransport in coarse-grained effective model Hamiltonians. This hybridmethodology provides a common theoretical starting point to treat chargetransfer/transport in strongly structurally fluctuating molecular-scalephysical systems.

Keywords: Electronic structure, biomolecules, molecular dynamics, quantum transport

River Publishers: Journal of Self-Assembly and Molecular Electronics (SAME)