Publications
Title : Spectroscopic properties of artificial DNA nanostructures
Authors : Rashid Amin, Atul Kulkarni, Junwye Lee, Chang-Won Lee, Sung Ha Park, and Taesung Kim
Published Date : Sep, 2011.
Journal Reference : Current Applied Physics 11 (2011) 1233-1236
Abstract :
Structural DNA nanotechnology is a rational process for the construction of new bionanostructures. One of the important physical properties of bionanostructures is their optical behavior. The optical evaluation of DNA molecules is normally performed in the ultraviolet range for quantification measurements. Here, we have fabricated four geometrically different DNA nanostructures - a ribbon, a tube, and lattices without and with hairpin loops - based on a simple duplex DNA with crossover junctions. Then we evaluated the spectroscopic properties of DNA nanostructures for quantitative classification and differentiation of DNA samples in visible light instead of ultraviolet light. In order to achieve a good spectroscopic measurement, a polymer optical fiber with a micro cuvette-based spectroscopic system was implemented for good sensitivity.
Title : Artificial DNA Lattice Fabrication by Non-Complementarity and Geometrical Incompatibility
Authors : Jihoon Shin , Junghoon Kim , Rashid Amin , Seungjae Kim , Young Hun Kwon , and Sung Ha Park
Published Date : May 28, 2011.
Journal Reference : ACS Nano, 2011, 5 (6), pp 5175-5179
arXiv : arXiv : 1105.6370 [cond-mat.mes-hall]
Abstract :
Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the DNA oligonucleotide must match for lattices to form. Here we present a fabrication scheme of DNA nanostructures with non-complementary and/or geometrically incompatible DNA oligonucleotides, which contradicts conventional DNA structure creation rules. Quantitative analyses of DNA lattice sizes were carried out to verify the unfavorable binding occurrences which correspond to errors in algorithmic self-assembly. Further studies of these types of bindings may shed more light on the exact mechanisms at work in the self-assembly of DNA nanostructures.
Title : Intrinsic DNA curvature of double-crossover tiles
Authors : Seungjae Kim, Junghoon Kim, Pengfei Qian, Jihoon Shin, Rashid Amin, Sang Jung Ahn, Thomas H LaBean, Moon Ki Kim and Sung Ha Park
Published Date : May 4, 2011.
Journal Reference : Nanotechnology 22 245706
arXiv : arXiv:1105.2127 [cond-mat.mes-hall]
Abstract :
A theoretical model which takes into account the structural distortion of double-crossover DNA tiles has been studied to investigate its effect on lattice formation sizes. It has been found that a single vector appropriately describes the curvature of the tiles, of which a higher magnitude hinders lattice growth. In conjunction with these calculations, normal mode analysis reveals that tiles with relative higher frequencies have an analogous effect. All the theoretical results are shown to be in good agreement with experimental data.
Title : NANOBIOTECHNOLOGY: AN INTERFACE BETWEEN NANOTECHNOLOGY AND BIOTECHNOLOGY
Authors : Rashid Amin, Sieun Hwang,and Sung Ha Park
Published Date : Apr, 2011.
Journal Reference : NANO Vol. 6, No. 2 101-111
Abstract :
Nanotechnology is one of the most important emerging fields of science in this century. It deals with designing, construction, investigation, and utilization of systems at the nanoscale. Another interesting research discipline of current day is biotechnology, which gives us a way to understand biological system and to utilize our knowledge for industrial manufacturing. Nanobiotechnology lies at the interface of these two research fields. It exploits nanotechnology and biotechnology to analyze and create nanobiosystems to meet a wide variety of challenges and develops a wide range of applications
Title : Complete separation of triangular gold nanoplates through selective precipitation under CTAB micelles in aqueous solution
Authors : Tai Hwan Ha, Yoon Jeong Kim, and Sung Ha Park
Published Date : Mar 12th 2010.
Journal Reference : Chem. Commun., 2010, 46, 3164-3166
Abstract :
Triangular gold nanoplates in CTAB solution were selectively precipitated on a glass wall in ambient conditions and the nanoplates could be easily recovered by a brief sonication.
Title : ARTIFICIALLY DESIGNED DNA NANOSTRUCTURES
Authors : Rashid Amin, Soyeon Kim, Sung Ha Park, and Thomas H. LaBean
Published Date : Jun, 2009.
Journal Reference : NANO Vol. 4, No. 3 119-139
Abstract :
In the field of structural DNA nanotechnology, researchers create artificial DNA sequences to self-assemble into target molecular superstructures and nanostructures. The well-understood Watson-Crick base-pairing rules are used to encode assembly instructions directly into the DNA molecules. A wide variety of complex nanostructures has been created using this method. DNA directed self-assembly is now being adapted for use in the nanofabrication of functional structures for use in electronics, photonics, and medical applications.
Title : Programming DNA Tube Circumferences
Authors : Peng Yin, Rizal F. Hariadi, Sudheer Sahu, Harry M. T. Choi, Sung Ha Park, Thomas H. LaBean, and John H. Reif
Published Date : Aug 8, 2008.
Journal Reference : Science 321, 824 (2008)
Abstract :
Synthesizing molecular tubes with monodisperse, programmable circumferences is an important goal shared by nanotechnology, materials science, and supermolecular chemistry. We program molecular tube circumferences by specifying the complementarity relationships between modular domains in a 42-base single-stranded DNA motif. Single-step annealing results in the self-assembly of long tubes displaying monodisperse circumferences of 4, 5, 6, 7, 8, 10, or 20 DNA helices.
Title : Toward Reliable Algorithmic Self-Assembly of DNA Tiles: A Fixed-Width Cellular Automaton Pattern
Authors : Kenichi Fujibayashi, Rizal Hariadi, Sung Ha Park, Erik Winfree, and Satoshi Murata
Published Date : Dec 28, 2007.
Journal Reference : Nano Lett., Vol. 8, No. 7
Abstract :
Bottom-up fabrication of nanoscale structures relies on chemical processes to direct self-assembly. The complexity, precision, and yield achievable by a one-pot reaction are limited by our ability to encode assembly instructions into the molecules themselves. Nucleic acids provide a platform for investigating these issues, as molecular structure and intramolecular interactions can encode growth rules. Here, we use DNA tiles and DNA origami to grow crystals containing a cellular automaton pattern. In a one-pot annealing reaction, 250 DNA strands first assemble into a set of 10 free tile types and a seed structure, then the free tiles grow algorithmically from the seed according to the automaton rules. In our experiments, crystals grew to 300 nm long, containing 300 tiles with an initial assembly error rate of 1.4% per tile. This work provides evidence that programmable molecular self-assembly may be sufficient to create a wide range of complex objects in one-pot reactions.
Title : Stepwise Self-Assembly of DNA Tile Lattices Using dsDNA Bridges
Authors : Sung Ha Park, Gleb Finkelstein, and Thomas H. LaBean
Published Date : Dec 12, 2007.
Journal Reference : JACS, Vol. 130, 40-41
Abstract :
The simple helical motif of double-strand DNA (dsDNA) has typically been judged to be uninteresting for assembly in DNA-based nanotechnology applications. In this letter, we demonstrate construction of superstructures consisting of heterogeneous DNA motifs using dsDNA in conjunction with more complex, cross-tile building blocks. Incorporation of dsDNA bridges in stepwise assembly processes can be used for controlling length and directionality of superstructures and is analogous to the "reprogramming" of sticky-ends displayed on the DNA tiles. Two distinct self-assembled DNA lattices, fixed-size nanoarrays, and extended 2D crystals of nanotracks with nanobridges, are constructed and visualized by high-resolution, liquid-phase atomic force microscopy.
Title : Optimized fabrication and electrical analysis of silver nanowires templated on DNA molecules
Authors : Sung Ha Park, Matthew Prior, Thomas LaBean, and Gleb Finkelstein
Published Date : Apr, 2006.
Journal Reference : APL, Vol. 89, 033901-1 -033901-3
Abstract :
We report on the electrical conductivity measurement of silver nanowires templated on native lambda-bacteriophage and synthetic double-stranded DNA molecules. After an electroless chemical deposition, the metallized DNA wires have a diameter down to 15nm and are among the thinnest metallic nanowires available to date. Two-terminal I-V measurements demonstrating various conduction behaviors are presented. DNA templated functional nanowires may, in the near future, be targeted to connect at specific locations on larger-scale circuits and represent a potential breakthrough in the self-assembly of nanometer-scale structures for electronics layout.
Title : Finite-size, fully addressable DNA tile lattices formed by hierarchical assembly procedures
Authors : Sung Ha Park, Constantin Pistol, Sang Jung Ahn, John H. Reif, Alvin R. Lebeck, Chris Dwyer, and Thomas H. LaBean
Published Date : Jan, 2006.
Journal Reference : Angew. Chem. Int. Ed., Vol. 45, 735-739
Title : Self-assembled DNA Nanotubes
Authors : Thomas H. LaBean and Sung Ha Park
Published Date : Jan, 2006.
Journal Reference : Nanotechnologies for the Life Sciences (Book Series): Vol. 2. Biological and Pharmaceutical Nanomaterials, Edited by C. Kumar, 1-20
Title : Three-helix bundle DNA tiles self-assemble into 2D lattice or 1D templates for silver nanowires
Authors : Sung Ha Park, Robert Barish, Hanying Li, John H. Reif, Hao Yan, and Thomas H. LaBean
Published Date : Mar, 2005.
Journal Reference : Nano Lett., Vol. 5, 693-696
Abstract :
We present a DNA nanostructure, the three-helix bundle (3HB), which consists of three double helical DNA domains connected by six immobile crossover junctions such that the helix axes are not coplanar. The 3HB motif presents a triangular cross-section with one helix lying in the groove formed by the other two. By differential programming of sticky-ends, 3HB tiles can be arrayed in two distinct lattice conformations: one-dimensional filaments and two-dimensional lattices. Filaments and lattices have been visualized by high-resolution, tapping mode atomic force microscopy (AFM) under buffer. Their dimensions are shown to be in excellent agreement with designed structures. We also demonstrate an electroless chemical deposition for fabricating metallic nanowires templated on self-assembled filaments. The metallized nanowires have diameters down to 20 nm and display Ohmic current−voltage characteristic.
Title : Programmable DNA Self-assemblies for Nanoscale Organization of Ligands and Proteins
Authors : Sung Ha Park, Peng Yin, John Reif, Thomas H. LaBean, and Hao Yan
Published Date : Mar, 2005.
Journal Reference : Nano Lett., Vol. 5, 729-733
Abstract :
We demonstrate the precise control of periodic spacing between individual protein molecules by programming the self-assembly of DNA tile templates. In particular, we report the application of two self-assembled periodic DNA structures, two-dimendional nanogrids, and one-dimensional nanotrack, as template for programmable self-assembly of streptavidin protein arrays with controlled density.
Title : Electronic Nanostructures Templated on Self-assembled DNA Scaffolds
Authors : Sung Ha Park, Hao Yan, John Reif, Thomas LaBean, and Gleb Finkelstein
Published Date : Jul, 2004.
Journal Reference : Nanotechnology, Vol. 15, S525-S527
Abstract :
We report on the self-assembly of one- and two-dimensional DNA scaffolds, which serve as templates for the targeted deposition of ordered nanoparticles and molecular arrays. The DNA nanostructures are easy to reprogram, and we demonstrate two distinct conformations: sheets and tubes. The DNA tubes and individual DNA molecules are metallized in solution to produce ultra-thin metal wires.
Title : DNA nanotubes self-assembled from TX tiles as templates for conducting nanowires
Authors : Dage Liu, Sung Ha Park, John Reif, and Thomas LaBean
Published Date : Jan, 2004.
Journal Reference : PNAS, Vol. 101, No. 3, 717-722
Abstract :
DNA-based nanotechnology is currently being developed as a general assembly method for nanopatterned materials that may find use in electronics, sensors, medicine, and many other fields. Here we present results on the construction and characterization of DNA nanotubes, a self-assembling superstructure composed of DNA tiles. Triple-crossover tiles modified with thiol-containing double-stranded DNA stems projected out of the tile plane were used as the basic building blocks. Triple-crossover nanotubes display a constant diameter of ≈25 nm and have been observed with lengths up to 20 μm. We present high-resolution images of the constructs, experimental evidence of their tube-like nature as well as data on metallization of the nanotubes to form nanowires, and electrical conductivity measurements through the nanowires. DNA nanotubes represent a potential breakthrough in the self-assembly of nanometer-scale circuits for electronics layout because they can be targeted to connect at specific locations on larger-scale structures and can subsequently be metallized to form nanometer-scale wires. The dimensions of these nanotubes are also perfectly suited for applications involving interconnection of molecular-scale devices with macroscale components fabricated by conventional photolithographic methods.
Title : DNA templated self-assembly of protein and nanoparticle linear arrays
Authors : Hanying Li, Sung Ha Park, John Reif, Thomas LaBean, and Hao Yan
Published Date : Dec, 2003.
Journal Reference : J.Am.Chem.Soc., Vol. 126, 418-419, January
Abstract :
Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Here we report an experiment using a linear array of DNA triple crossover tiles to controllably template the self-assembly of single-layer or double-layer linear arrays of streptavidin molecules and streptavidin-conjugated nanogold particles through biotin-streptavidin interaction. The organization of streptavidin and its conjugated gold nanoparticles into periodic arrays was visualized by atomic force microscopy and scanning electron microscopy.
Title : DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires
Authors : Hao Yan, Sung Ha Park, Gleb Finkelstein, John H. Reif, and Thomas H. LaBean
Published Date : Sep, 2003.
Journal Reference : Science, Vol. 301, 1882-1884
Abstract :
A DNA nanostructure consisting of four four-arm junctions oriented with a square aspect ratio was designed and constructed. Programmable self-assembly of 4 × 4 tiles resulted in two distinct lattice morphologies: uniform-width nanoribbons and two-dimensional nanogrids, which both display periodic square cavities. Periodic protein arrays were achieved by templated self-assembly of streptavidin onto the DNA nanogrids containing biotinylated oligonucleotides. On the basis of a two-step metallization procedure, the 4 × 4 nanoribbons acted as an excellent scaffold for the production of highly conductive, uniform-width, silver nanowires.
Title : A Two State DNA Lattice Actuated by DNA Motors
Authors : Liping Feng, Sung Ha Park, John H. Reif, and Hao Yan
Published Date : Jun, 2003.
Journal Reference : Angewandte Chemie Int. Ed., 42, 4342-4346
Title : Magnetic Crossover in the one-dimensional Hubbard Model in the presence of magnetic field
Authors : Armen Kocharian, Nicholas Kioussis, and Sung Ha Park
Published Date : Jun, 2001.
Journal Reference : Journal of Physics: Condensed Matter, Vol. 13, 6759-6772
Abstract :
The ground-state (GS) properties of the one-dimensional (1D) Hubbard model at half-filling are examined in the presence of a magnetic field using the generalized mean-field (GMF) approach, which includes the spin-density and the electron-hole correlations on an equal footing. The GMF formalism provides insight into both the metal-insulator transition and the transition from itinerant to localized magnetism with applied field. The GMF theory can differentiate the energy gap from the antiferromagnetic order parameter in the presence of a magnetic field. The numerical results for the GS energy, the magnetization, the spin susceptibility, and the number of doubly occupied sites are in good agreement with the exact results over a wide range of U/t and h/t. The calculated h-U phase diagram exhibits a magnetic crossover from itinerant electron-hole pairs to a Bose-Einstein condensate state of local pairs. The overall picture of the magnetic crossover in 1D is found to be similar for the simple case of constant density of states, putting the GMF approach on a firmer basis in two and three dimensions.
Title : The One-Dimensional periodic Anderson model: A Mean Field study
Authors : Costas Papatriantafillou, Nicholas Kioussis, Sung Ha Park, and Armen Kocharian
Published Date : Nov, 1999.
Journal Reference : Physica B, Vol. 259-261, 208-209
Abstract :
The ground-state properties of the symmetric Anderson lattice model in one dimension have been studied using a local mean-field decoupling approach and a renormalized perturbation expansion for the self-energy. The total energy, the local moment, the effective hybridization, the density of states, and the momentum distribution function have been calculated as a function of the Coulomb interaction U, the hybridization V, and the band filling. At half-filling, the mean-field results for the antiferromagntic state are in good agreement with those of quantum Monte Carlo simulations. At quarter filling and at relatively large U/2t values, the antiferromagnetic state is favored compared to the ferromagnetic state.
Title : Antiferromagnetism of the half-filled Anderson lattice in one-dimension
Authors : Costas Papatriantafillou, Nicholas Kioussis, and Sung Ha Park
Published Date : Jun, 1999.
Journal Reference : Physical Review B, Vol. 60, 13 355
Abstract :
The ground-state properties of the symmetric periodic Anderson model in one dimension and at half filling have been studied using the local mean-field (LMF) method. We have calculated the ground-state energy, the local f and conduction moment, the effective hybridization, the double occupancy, and the projected f and conduction density of states. The LMF results are in good agreement with Monte Carlo results and with second-order perturbation theory in the fluctuations results, under the extreme conditions of the one dimensionality. The f- and c-projected density of states show that there is a smooth change in the partial density of states with increasing U, from those of an uncorrelated, hybridized system to those expected for a strongly correlated system, in which the conduction band and the f states are decoupled.
Title : One-Dimensional Hubbard model in the presence of magnetic field
Authors : Nicholas Kioussis, Armen Kocharian, and Sung Ha Park
Published Date : May, 1998.
Journal Reference : Journal of Magnetism and Magnetic Materials, Vol. 177-181, 575-576
Abstract :
The ground-state properties of the one-dimensional Hubbard model at half-filling in the presence of magnetic field are examined using the generalized mean-field approximation (GMF), which includes both the spin-density and the electron-hole correlations on an equal footing. The GMF results for the ground-state energy, the electron-hole excitation gap, the magnetization and the susceptibility are compared in one dimension with the exact ones. The GMF approach provides insight into both the magnetism and the Mott—Hubbard localization in the presence of applied field. The numerical results for the ground-state energy, the local moment, the kinetic energy and the number of double occupied sites are overall in good agreement with the exact results. The generalized mean-field formalism allows to separate the single-particle excitations from antiferromagnetic order parameter at relatively large magnetic field.