2016

Title: M-DNA/Transition Metal Dichalcogenide Hybrid Structure-based Bio-FET sensor with Ultra-high Sensitivity
Authors: Hyung-Youl Park†, Sreekantha Reddy Dugasani†, Dong-Ho Kang, Gwangwe Yoo, Jinok Kim, Bramaramba Gnapareddy, Jaeho Jeon, Minwoo Kim, Young Jae Song, Sungjoo Lee, Jonggon Heo, Young Jin Jeon, Sung Ha Park & Jin-Hong Park
(† Hyung-Youl Park. and Sreekantha Reddy Dugasani contributed equally to this work)

Published Date: 24th October 2016(Online)
Journal Reference: Scientific Reports 6, Article number: 35733 (2016)

Abstract :
Here, we report a high performance biosensor based on (i) a Cu2+-DNA/MoS2 hybrid structure and (ii) a field effect transistor, which we refer to as a bio-FET, presenting a high sensitivity of 1.7 × 103 A/A. This high sensitivity was achieved by using a DNA nanostructure with copper ions (Cu2+) that induced a positive polarity in the DNA (receptor). This strategy improved the detecting ability for doxorubicin-like molecules (target) that have a negative polarity. Very short distance between the biomolecules and the sensor surface was obtained without using a dielectric layer, contributing to the high sensitivity. We first investigated the effect of doxorubicin on DNA/MoS2 and Cu2+-DNA/MoS2 nanostructures using Raman spectroscopy and Kelvin force probe microscopy. Then, we analyzed the sensing mechanism and performance in DNA/MoS2- and Cu2+-DNA/MoS2-based bio-FETs by electrical measurements (ID-VG at various VD) for various concentrations of doxorubicin. Finally, successful operation of the Cu2+-DNA/MoS2 bio-FET was demonstrated for six cycles (each cycle consisted of four steps: 2 preparation steps, a sensing step, and an erasing step) with different doxorubicin concentrations. The bio-FET showed excellent reusability, which has not been achieved previously in 2D biosensors.

Title: Zinc Oxide Nanorods Shielded with an Ultrathin Nickel Layer: Tailoring of Physical Properties
Authors: Devika Mudusu, Koteeswara Reddy Nandanapalli, Sreekantha Reddy Dugasani, Sung Ha Park & Charles W. Tu

Published Date: 23th June 2016(Online)
Journal Reference: Scientific Reports 6, Article number: 28561 (2016)

Abstract :
We report on the development of Ni-shielded ZnO nanorod (NR) structures and the impact of the Ni layer on the ZnO NR properties. We developed nickel-capped zinc oxide nanorod (ZnO/Ni NR) structures by e-beam evaporation of Ni and the subsequent annealing of the ZnO/Ni core/shell nanostructures. The core/shell NRs annealed at 400 °C showed superior crystalline and emission properties. More interestingly, with the increase of annealing temperature, the crystallinity of the Ni shells over the ZnO NRs gradually changed from polycrystalline to single crystalline. The presence of the Ni layer as a polycrystalline shell completely hindered the light emission and transmission of the ZnO NR cores. Further, the band gap of ZnO NRs continuously decreased with the increase of annealing temperature.

Title: Morphological and Optoelectronic Characteristics of Double and Triple Lanthanide Ion-Doped DNA Thin Films
Authors: Mallikarjuna Reddy Kesama†, Sreekantha Reddy Dugasani†, Sanghyun Yoo, Prathamesh Chopade, Bramaramba Gnapareddy, and Sung Ha Park
(†M.R.K. and S.R.D. contributed equally to this work)

Published Date: 11th May 2016
Journal Reference: ACS Appl. Mater. Interfaces, 2016, 8 (22), pp 14109–14117

Abstract :
Double and triple lanthanide ion (Ln3+)-doped synthetic double crossover (DX) DNA lattices and natural salmon DNA (SDNA) thin films are fabricated by the substrate assisted growth and drop-casting methods on given substrates. We employed three combinations of double Ln3+-dopant pairs (Tb3+–Tm3+, Tb3+–Eu3+, and Tm3+–Eu3+) and a triple Ln3+-dopant pair (Tb3+–Tm3+–Eu3+) with different types of Ln3+, (i.e., Tb3+ chosen for green emission, Tm3+ for blue, and Eu3+ for red), as well as various concentrations of Ln3+ for enhancement of specific functionalities. We estimate the optimum concentration of Ln3+ ([Ln3+]O) wherein the phase transition of Ln3+-doped DX DNA lattices occurs from crystalline to amorphous. The phase change of DX DNA lattices at [Ln3+]O and a phase diagram controlled by combinations of [Ln3+] were verified by atomic force microscope measurement. We also developed a theoretical method to obtain a phase diagram by identifying a simple relationship between [Ln3+] and [Ln3+]O that in practice was found to be in agreement with experimental results. Finally, we address significance of physical characteristics—current for evaluating [Ln3+]O, absorption for understanding the modes of Ln3+ binding, and photoluminescence for studying energy transfer mechanisms—of double and triple Ln3+-doped SDNA thin films. Current and photoluminescence in the visible region increased as the varying [Ln3+] increased up to a certain [Ln3+]O, then decreased with further increases in [Ln3+]. In contrast, the absorbance peak intensity at 260 nm showed the opposite trend, as compared with current and photoluminescence behaviors as a function of varying [Ln3+]. A DNA thin film with varying combinations of [Ln3+] might provide immense potential for the development of efficient devices or sensors with increasingly complex functionality.

Title: Growth and Detachment of 5 Helix DNA Ribbons
Authors: Bashar Saima, Hwang Si Un, Lee Junwye, Amin Rashid, Dugasani Sreekantha Reddy, Ha Tai Hwan, Park Sung Ha
Published Date: 1st Apr 2016
Journal Reference: Journal of Nanoscience and Nanotechnology, Volume 16, Number 4, April 2016, pp. 4126-4130(5)

Abstract :
We report on the concentration-dependent surface-assisted growth and time-temperature-dependent detachment of one-dimensional 5 helix DNA ribbons (5HR) on a mica substrate. The growth coverage ratio was determined by varying the concentration of the 5HR strands in a test tube, and the detachment rate of 5HR on mica was determined by varying the incubation time at a fixed temperature on a heat block. The topological changes in the concentration-dependent attachment and the time-temperature-dependent detachment for 5HR on mica were observed via atomic force microscopy. The observations indicate that 5HR started to grow on mica at ∼10 nM and provided full coverage at ∼50 nM. In contrast, 5HR at 65 °C started to detach from mica after 5 min and was completely removed after 10 min. The growth and detachment coverage show a sinusoidal variation in the growth ratio and a linear variation with a rate of detachment of 20%/min, respectively. The physical parameters that control the stability of the DNA structures on a given substrate should be studied to successfully integrate DNA structures for physical and chemical applications.

Title: Metal electrode dependent field effect transistors made of lanthanide ion-doped DNA crystals
Authors: Sreekantha Reddy Dugasani, Taehyun Hwang, Jang Ah Kim, Bramaramba Gnapareddy, Taesung Kim and Sung Ha Park
Published Date: 8th Feb 2016
Journal Reference: Journal of Physics D: Applied Physics, Volume 49, Number 10

Abstract :
We fabricated lanthanide ion (Ln3+, e.g. Dy3+, Er3+, Eu3+, and Gd3+)-doped self-assembled double-crossover (DX) DNA crystals grown on the surface of field effect transistors (FETs) containing either a Cr, Au, or Ni electrode. Here we demonstrate the metal electrode dependent FET characteristics as a function of various Ln3+. The drain–source current (I ds), controlled by the drain–source voltage (V ds) of Ln3+-doped DX DNA crystals with a Cr electrode on an FET, changed significantly under various gate voltages (V g) due to the relative closeness of the wltrathin Nickel Layer: Tailoring of Physical Properties Devika Mudusu, Koteeswara Reddy Nandanapalli, Sreekantha Reddy Dugasani, Sung Ha Park & Charles W. Tu ork function of Cr to the energy band gap of Ln3+-DNA crystals compared to those of Au and Ni. For Ln3+-DNA crystals on an FET with either a Cr or Ni electrode at a fixed V ds, I ds decreased with increasing V g ranging from  −2 to 0 V and from 0 to  +3 V in the positive and negative regions, respectively. By contrast, I ds for Ln3+-DNA crystals on an FET with Au decreased with increasing V g in only the positive region due to the greater electronegativity of Au. Furthermore, Ln3+-DNA crystals on an FET exhibited behaviour sensitive to V g due to the appreciable charge carriers generated from Ln3+. Finally, we address the resistivity and the mobility of Ln3+-DNA crystals on an FET with different metal electrodes obtained from I ds–V ds and I ds–V g curves. The resistivities of Ln3+-DNA crystals on FETs with Cr and Au electrodes were smaller than those of pristine DNA crystals on an FET, and the mobility of Ln3+-DNA crystals on an FET with Cr was relatively higher than that associated with other electrodes.

Title: Ultra-low Doping on Two-Dimensional Transition Metal Dichalcogenides using DNA Nanostructure Doped by a Combination of Lanthanide and Metal Ions
Authors: Dong-Ho Kang†, Sreekantha Reddy Dugasani†, Hyung-Youl Park, Jaewoo Shim, Bramaramba Gnapareddy, Jaeho Jeon, Sungjoo Lee, Yonghan Roh, Sung Ha Park & Jin-Hong Park
(†D.K. and S.R.D. contributed equally to this work)
Published Date: 3rd Feb 2016
Journal Reference: Scientific Reports 6, Article number: 20333 (2016)

Abstract :
Here, we propose a novel DNA-based doping method on MoS2 and WSe2 films, which enables ultra-low n- and p-doping control and allows for proper adjustments in device performance. This is achieved by selecting and/or combining different types of divalent metal and trivalent lanthanide (Ln) ions on DNA nanostructures, using the newly proposed concept of Co-DNA (DNA functionalized by both divalent metal and trivalent Ln ions). The available n-doping range on the MoS2 by Ln-DNA is between 6 × 109 and 2.6 × 1010 cm−2. The p-doping change on WSe2 by Ln-DNA is adjusted between −1.0 × 1010 and −2.4 × 1010 cm−2. In Eu3+ or Gd3+-Co-DNA doping, a light p-doping is observed on MoS2 and WSe2 (~1010 cm−2). However, in the devices doped by Tb3+ or Er3+-Co-DNA, a light n-doping (~1010 cm−2) occurs. A significant increase in on-current is also observed on the MoS2 and WSe2 devices, which are, respectively, doped by Tb3+- and Gd3+-Co-DNA, due to the reduction of effective barrier heights by the doping. In terms of optoelectronic device performance, the Tb3+ or Er3+-Co-DNA (n-doping) and the Eu3+ or Gd3+-Co-DNA (p-doping) improve the MoS2 and WSe2 photodetectors, respectively. We also show an excellent absorbing property by Tb3+ ions on the TMD photodetectors.

2015

Title: Enhanced nonlinear optical characteristics of copper-ion-doped double crossover DNAs
Authors: Byeongho Park, Byung Jic Lee, Sreekantha Reddy Dugasani, Youngho Cho, Chulki Kim, Minah Seo, Taikjin Lee, Young Min Jhon, Jaebin Choi, Seok Lee, Sung Ha Park, Seong Chan Jun, Dong-Il Yeom, Fabian Rotermund and Jae Hun Kim
Published Date: 15th Oct 2015
Journal Reference: Nanoscale, 2015,7, 18089-18095

Abstract :
The modification of deoxyribonucleic acid (DNA) samples by sequencing the order of bases and doping copper ions opens the possibility for the design of novel nanomaterials exhibiting large optical nonlinearity. We investigated the nonlinear characteristics of copper-ion doped double crossover DNA samples for the first time to the best of our knowledge by using Z-scan and four-wave mixing methods. To accelerate the nonlinear characteristics, we prepared two types of unique DNA nanostructures composed of 148 base pairs doped with copper ions with a facile annealing method. The outstanding third-order nonlinear optical susceptibility of the copper-ion-doped DNA solution, 1.19 × 10−12 esu, was estimated by the conventional Z-scan measurement, whereas the four-wave mixing experiment was also investigated. In the visible spectral range, the copper-ion-doped DNA solution samples provided competent four-wave mixing signals with a remarkable conversion efficiency of −4.15 dB for the converted signal at 627 nm. The interactions between DNA and copper ions contribute to the enhancement of nonlinearity due to structural and functional changes. The present study signifies that the copper-ion-doped double crossover DNA is a potential candidate as a highly efficient novel material for further nonlinear optical applications.

Title: Coverage percentage and coverage rate of different DNA nanostructures grown on a mica substrate
Authors: Saima Bashar, Seungjae Kim, Si Un Hwang, Sreekantha Reddy Dugasani, Tai Hwan Ha, Sung Ha Park
Published Date: Nov 2015
Journal Reference: Current Applied Physics, Volume 15, Issue 11, November 2015, Page 1358-1363

Abstract :
In this study, we simultaneously grew different DNA nanostructures, including 5 helix ribbon (5HR), double-crossover (DX), and double-crossover with single hairpin (DX-SH) lattices, on a mica substrate, and we analyzed the concentration-dependent coverage percentages of 5HR at a fixed concentration of DX ([DX]), DX at a fixed [5HR], and DX-SH with both fixed [5HR] and [DX]. The structural features of the various nanostructures formed through mica-assisted growth annealing were confirmed via atomic force microscopy. To assess the temperature-dependent coverage rates on the given substrates, we introduced two simple models, i.e., the equipartition model (EPM) and the un-equipartition model (UEPM) which provide information on the amount of coverage for each of the given temperature. EPM provides an equal amount of the coverage percentage per temperature change due to its linear nature, but UEPM does not since it has a non-linear nature. The coverage percentages obtained by these models allow us to calculate, as a function of temperature, the coverage rates of 5HR at a fixed [DX] and DX-SH for both fixed [5HR] and [DX]. Although with EPM the coverage rates for the 5HR and DX-SH decreased linearly as the temperature decreased, they decreased non-linearly as the temperature decreased with UEPM.

Title: Coverage percentage and raman measurement of cross-tile and scaffold cross-tile based DNA nanostructures
Authors: Bramaramba Gnapareddy, Sang Jung Ahn, Sreekantha Reddy Dugasani, Jang Ah Kim, Rashid Amin, Sekhar Babu Mitta, Srivithya Vellampatti, Byeonghoon Kim, Atul Kulkarni, Taesung Kim, Kyusik Yun, Thomas H. LaBean, Sung Ha Park
Published Date: 1st Nov 2015
Journal Reference: Colloids and Surfaces B: Biointerfaces, Volume 135, 1 November 2015, Pages 677–681

Abstract :
We present two free-solution annealed DNA nanostructures consisting of either cross-tile CT1 or CT2. The proposed nanostructures exhibit two distinct structural morphologies, with one-dimensional (1D) nanotubes for CT1 and 2D nanolattices for CT2. When we perform mica-assisted growth annealing with CT1, a dramatic dimensional change occurs where the 1D nanotubes transform into 2D nanolattices due to the presence of the substrate. We assessed the coverage percentage of the 2D nanolattices grown on the mica substrate with CT1 and CT2 as a function of the concentration of the DNA monomer. Furthermore, we fabricated a scaffold cross-tile (SCT), which is a new design of a modified cross-tile that consists of four four-arm junctions with a square aspect ratio. For SCT, eight oligonucleotides are designed in such a way that adjacent strands with sticky ends can produce continuous arms in both the horizontal and vertical directions. The SCT was fabricated via free-solution annealing, and self-assembled SCT produces 2D nanolattices with periodic square cavities. All structures were observed via atomic force microscopy. Finally, we fabricated divalent nickel ion (Ni2+)- and trivalent dysprosium ion (Dy3+)-modified 2D nanolattices constructed with CT2 on a quartz substrate, and the ion coordinations were examined via Raman spectroscopy.

Title: Chemical and Physical Characteristics of Doxorubicin Hydrochloride Drug-Doped Salmon DNA Thin Films
Authors: Bramaramba Gnapareddy, Sreekantha Reddy Dugasani, Taewoo Ha, Bjorn Paulson, Taehyun Hwang, Taesung Kim, Jae Hoon Kim, Kyunghwan Oh and Sung Ha Park
Published Date: 31st July 2015
Journal Reference: Scientific Reports 5, Article number: 12722

Abstract :
Double-stranded salmon DNA (SDNA) was doped with doxorubicin hydrochloride drug molecules (DOX) to determine the binding between DOX and SDNA, and DOX optimum doping concentration in SDNA. SDNA thin films were prepared with various concentrations of DOX by drop-casting on oxygen plasma treated glass and quartz substrates. Fourier transform infrared (FTIR) spectroscopy was employed to investigate the binding sites for DOX in SDNA, and electrical and photoluminescence (PL) analyses were used to determine the optimum doping concentration of DOX. The FTIR spectra showed that up to a concentration of 30μM of DOX, there was a tendency for binding with a periodic orientation via intercalation between nucleosides. The current and PL intensity increased as the DOX concentration increased up to 30μM, and then as the concentration of DOX further increased, we observed a decrease in current as well as PL quenching. Finally, the optical band gap and second band onset of the transmittance spectra were analyzed to further verify the DOX binding and optimum doping concentration into SDNA thin films as a function of the DOX concentration.

Title: A methanol VOC sensor using divalent metal ion-modified 2D DNA lattices
Authors: Hyeong-U Kim, Sreekantha Reddy Dugasani, Atul Kulkarni, Bramaramba Gnapareddy, Jang Ah Kim, Sung Ha Park and Taesung Kim
Published Date: 29th July 2015
Journal Reference: RSC Adv., 2015,5, 67712-67717

Abstract :
In the present study, an optical fiber sensor using pristine DNA and metal ion-modified DNA (M-DNA) double-crossover (DX) lattices was fabricated for detecting volatile organic compounds (VOCs) in the range of their threshold limit values (TLVs). The selective incorporation of metal ions, such as cobalt ions (Co2+), with appropriate concentrations into the DNA DX lattice has to be considered since excess metal ions can be bound nonspecifically and degrade the functions of the M-DNA DX lattices. The peak intensity of light reflected from a Co2+-modified DNA (Co-DNA) DX lattice was observed to be about 32% greater than that from the pristine DNA DX lattice in the presence of a relatively high 11 897 ppm concentration of the VOC methanol, and was also observed to be greater in the presence of 95 to 475 ppm methanol. The change in the intensity of the reflected light due to the VOC interaction with the pristine DNA and the Co-DNA lattices corresponded to the differences in surface morphology visualized by atomic force microscopy and the differences in intensities from Raman spectroscopy.

Title: Surface enhanced Raman scattering based molecule detection using self-assembled DNA nanostructures
Authors: Myoungsoon Kim, Junwye Lee, Sreekantha Reddy Dugasani, Nam Huh, Sung Ha Park, Sang Chul Park
Published Date: 17th Jun 2015(Online), Sep 2015(Offline, to be expected)
Journal Reference: Current Applied Physics Volume 15, Issue 9, September 2015, Pages 1032–1035

Abstract :
A novel method of Surface Enhanced Raman Scattering (SERS) based molecular detection was developed using self-assembled DNA nanostructures. Molecule detection using rigid, shape-controllable DNA nanostructures provides significant advantages such as accurate control of the particle distance and geometrical programmability of the DNA nanostructure. We successfully detected the Cy3 dye, a Raman-active molecule, at 1461, 1590, and 1619 cm−1 using a Ag-enhanced Au-DNA nanostructure. Consequently, DNA-guided SERS detection is expected to contribute significantly to molecular detecting systems in the near future.

Title: Streptavidin bound DNA open tube and Zn2+-doped DNA open lattice
Authors: Srivithya Vellampatti, Sekhar Babu Mitta, Jang Ah Kim, Taehyun Hwang, Sreekantha Reddy Dugasani, Taesung Kim and Sung Ha Park
Published Date: 25th Feb 2015(Online), Aug 2015(Offline, be expected)
Journal Reference: Current Applied physics Volume 15, Issue 8, 851-856

Abstract :
DNA is one of the most promising molecules for use in nanotechnology because it has a nanoscale size and also has the ability for self-assembly. In this paper, we discuss the use of free-solution growth for a 1D DNA open tube (OT) and substrate-assisted growth for a 2D open lattice (OL), which can both achieve similar design schemes. We introduced biotinylated OT and OL, which can be bound with streptavidin for visualization, to verify via atomic force microscopy that dimensional structures have in fact been formed. Additionally the coverage ratio controlled by the concentration of the DNA monomer was analyzed to understand the lattice growth on the substrate. The DNA lattices were observed to start growing on the substrate at a concentration of around 1 nM (threshold) and to achieve full coverage at 10 nM (saturation concentration). Finally, the Raman spectra and the current–voltage characteristics of Zn2+-doped OLs were obtained in order to demonstrate the feasibility of using such methods to produce useful materials for nanodevices and biosensors. As [Zn2+] increases above the critical value of 0.5 mM, the Raman peaks gradually decrease. The resistance decreases up to the critical value of [Zn2+], and then decreases [Zn2+] continues to increase.

Title: Hall transport of divalent metal ion modified DNA lattices
Authors: Sreekantha Reddy Dugasani, Keun Woo Lee, Si Joon Kim, Sanghyun Yoo, Bramaramba Gnapareddy, Joohye Jung, Tae Soo Jung, Saima Bashar, Hyun Jae Kim, and Sung Ha Park
Published Date: 29th June 2015(Offline)
Journal Reference: Appl. Phys. Lett. 106, 263702 (2015)

Abstract :
We investigate the Hall transport characteristics of double-crossover divalent metal ion (Cu 2+, Ni 2+, Zn 2+, and Co2+)-modified DNA (M-DNA) lattices grown on silica via substrate-assisted growth. The electronic characteristics of the M-DNA lattices are investigated by varying the concentration of the metal ions and then conducting Hall measurements, including resistivity, Hall mobility, carrier concentration, and magneto resistance. The tendency of the resistivity and Hall mobility was to initially decrease as the ion concentration increased, until reaching the saturation concentration (Cs ) of each metal ion, and then to increase as the ion concentration increased further. On the other hand, the carrier concentration revealed the opposite tendency as the resistivity and Hall mobility. The specific binding (≤Cs ) and the nonspecific aggregates (>Cs ) of the ions into the DNA lattices were significantly affected by the Hall characteristics. The numerical ranges of the Hall parameters revealed that the M-DNA lattices with metal ions had semiconductor-like characteristics. Consequently, the distinct characteristics of the electrical transport through M-DNA lattices will provide useful information on the practical use of such structures in physical devices and chemical sensors.

Title: Substrate-assisted 2D DNA lattices and algorithmic lattices from single-stranded tiles
Authors: Junghoon Kim, Tai Hwan Ha and Sung Ha Park
Published Date: 18th Jun 2015(Online)
Journal Reference: Nanoscale, 2015, Accepted Manuscript

Abstract :
We present a simple route to circumvent kinetic traps which affect many types of DNA nanostructures in their self-assembly process. Using this method, a new 2D DNA lattice made up of short, single-stranded tile (SST) motifs was created. Previously, the growth of SST DNA assemblies was restricted to 1D (tubes and ribbons) or finite-sized 2D (molecular canvases). By utilizing the substrate-assisted growth method, sets of SSTs were designed as unit cells to self-assemble into periodic and aperiodic 2D lattices which continuously grow both along and orthogonal to the helical axis. Notably, large-scale (~1 μm^2) fully periodic 2D lattices were fabricated using a minimum of just 2 strand species. Furthermore, the ability to create 2D lattices from a few motifs enables certain rules to be encoded into these SSTs to carry out algorithmic self-assembly. A set of these motifs were designed to execute simple 1-input 1-output COPY and NOT algorithms, the space-time manifestations which were aperiodic 2D algorithmic SST lattices. The methodology presented here can be straightforwardly applied to other motifs which fall into this type of kinetic trap to create novel DNA crystals.

Title: Tunable near white light photoluminescence of lanthanide ion (Dy3+, Eu3+ and Tb3+) doped DNA lattices
Authors: Sreekantha Reddy Dugasani, Byeongho Park, Bramaramba Gnapareddy, Sreedhara Reddy Pamanji, Sanghyun Yoo, Keun Woo Lee, Seok Lee, Seong Chan Jun, Jae Hun Kim, Chulki Kim and Sung Ha Park
Published Date: 17th Jun 2015(Online)
Journal Reference: RSC Adv., 2015,5, 55839-55846

Abstract :
For more than two decades, structural DNA nanotechnology has been investigated, yet researchers still have not clearly determined the functional changes and the applicability of DNA structures resulting from the introduction of a variety of ions. Lanthanide ions, such as Dy3+, Eu3+ and Tb3+, are interesting rare earth ions that have unique characteristics applicable to photonics. Here, we have constructed lanthanide ion doped double-crossover DNA lattices, a new class of functional DNA lattices, grown on a silica substrate. Deformation-free lattices were fabricated on a given substrate, and dopant ions were introduced to study their photoluminescence characteristics. The photoluminescence of the lanthanide ion-doped DNA lattices exhibited broad emission spectra in the visible region and a tendency of near white light emission composed of various colours. The intensity of the distinct spectral lines produced by the photoluminescence increased as the doping concentration of the ions reached the critical point, and the intensity then decreased with a further increase in the ions. Photoluminescence quenching was also observed when the excitation wavelength increased. These phenomena are the result of energy transfer between the DNA and the dopant ions. Finally, we make use of chromaticity diagrams to identify the colour coordinates of the luminescence produced by the lanthanide ion-doped DNA lattices, and this information may be useful to construct efficient bio-photonic devices or sensors in the future.

Title: Construction and characterization of Cu2+, Ni2+, Zn2+, and Co2+ modified-DNA crystals
Authors: Sreekantha Reddy Dugasani, Myoungsoon Kim, In-yeal Lee, Jang Ah Kim, Bramaramba Gnapareddy, Keun Woo Lee, Taesung Kim, Nam Huh, Gil-Ho Kim, Sang Chul Park and Sung Ha Park
Published Date: 18th Jun 2015(Online), 26th Jun 2015(Offline)
Journal Reference: 2015 Nanotechnology 26 275604

Abstract :
We studied the physical characteristics of modified-DNA (M-DNA) double crossover crystals fabricated via substrate-assisted growth with various concentrations of four different divalent metallic ions, Cu2+, Ni2+, Zn2+, and Co2+. Atomic force microscopy (AFM) was used to test the stability of the M-DNA crystals with different metal ion concentrations. The AFM images show that M-DNA crystals formed without deformation at up to the critical concentrations of 6 mM of [Cu2+], 1.5 mM of [Ni2+], 1 mM of [Zn2+], and 1 mM of [Co2+]. Above these critical concentrations, the M-DNA crystals exhibited deformed, amorphous structures. Raman spectroscopy was then used to identify the preference of the metal ion coordinate sites. The intensities of the Raman bands gradually decreased as the concentration of the metal ions increased, and when the metal ion concentrations increased beyond the critical values, the Raman band of the amorphous M-DNA was significantly suppressed. The metal ions had a preferential binding order in the DNA molecules with G?C and A?T base pairs followed by the phosphate backbone. A two-probe station was used to measure the electrical current?voltage properties of the crystals which indicated that the m aximum currents of the M-DNA complexes could be achieved at around the critical concentration of each ion. We expect that the functionalized ion-doped M-DNA crystals will allow for efficient devices and sensors to be fabricated in the near future.

Title: Optical Band Gap and Hall Transport Characteristics of Lanthanide-Ion-Modified DNA Crystals
Authors: Sreekantha Reddy Dugasani, Taewoo Ha, Si Joon Kim, Bramaramba Gnapareddy, Sanghyun Yoo, Keun Woo Lee, Tae Soo Jung, Hyun Jae Kim, Sung Ha Park, and Jae Hoon Kim
Published Date: 29 May 2015(Online), 25th June 2015(Offline)
Journal Reference: J. Phys. Chem. C, 2015, 119 (25), pp 14443–14449

Abstract :
Lanthanide-ion-modified DNA crystals are fabricated on quartz and silica substrates via surface-assisted growth, and the optical band gap and electrical Hall transport are measured at room temperature for these crystals. The optical band gap of these crystals shows an increasing behavior, and the second band onset showed the inverted V shape upon increasing the lanthanide ion concentration. At a particular concentration, each lanthanide ion into the DNA crystals exhibited low resistivity, low Hall mobility, high free carrier concentration, and a minimum magneto resistance. The experimental results show feasibility in controlling important physical parameters, such as the band gap energy and Hall parameters, by adjusting the concentration of the lanthanide ion. When combined with the existing structural versatility of DNA nanostructures, these functional tunabilities will be crucial for the future development of DNA-based nanoelectronic and biophotonic devices.

Title: Self-replication of DNA rings

Authors: Junghoon Kim, Junwye Lee, Shogo Hamada, Satoshi Murata and Sung Ha Park
Published Date: 11 May 2015(Online) June 2015(Offline)
Journal Reference: Nature Nanotechnology 10, 528-533 (2015)
Press : 한겨레Science On, May 20th,(2015)
            Phys.org, May 28th,(2015)
            現代化学 Chemistry Today(Japanese), No.534, Sep 1st,(2015)

Abstract :
Biology provides numerous examples of self-replicating machines, but artificially engineering such complex systems remains a formidable challenge. In particular, although simple artificial self-replicating systems including wooden blocks magnetic systems modular robots and synthetic molecular systems have been devised, such kinematic self-replicators are rare compared with examples of theoretical cellular self-replication. One of the principal reasons for this is the amount of complexity that arises when you try to incorporate self-replication into a physical medium. In this regard, DNA is a prime candidate material for constructing self-replicating systems due to its ability to self-assemble through molecular recognition. Here, we show that DNA T-motifs, which self-assemble into ring structures can be designed to self-replicate through toehold-mediated strand displacement reactions. The inherent design of these rings allows the population dynamics of the systems to be controlled. We also analyse the replication scheme within a universal framework of self-replication25 and derive a quantitative metric of the self-replicability of the rings.

Title: Broadband supercontinuum generation using a hollow optical fiber filled with copper-ion-modified DNA
Authors: Youngho Cho, Byeongho Park, Juyeong Oh, Minah Seo, Kwanil Lee, Chulki Kim, Taikjin Lee, Deok Ha Woo, Seok Lee, Hyung Min Kim, HyukJae Lee, Kyunghwan Oh, Dong-Il Yeom, Sreekantha Reddy Dugasani, Sung Ha Park, and Jae Hun Kim
Published Date: 18th May 2015(Offline)
Journal Reference: Optic Express Vol.23, Issue 10, pp. 13537-13544 (2015)

Abstract :
We experimentally demonstrated supercontinuum generation through a hollow core photonic bandgap fiber (HC-PBGF) filled with DNA nanocrystals modified by copper ions in a solution. Both double-crossover nano DNA structure and copper-ion-modified structure provided a sufficiently high optical nonlinearity within a short length of hollow optical fiber. Adding a higher concentration of copper ion into the DNA nanocrystals, the bandwidth of supercontinuum output was monotonically increased. Finally, we achieved the bandwidth expansion of about 1000 nm to be sufficient for broadband multi-spectrum applications.

Title: Fabrication of Multi-layered DNA Nanostructures Using Single-strand and Double-crossover Tile Connectors
Authors: Anshula Tandon, Sekhar Babu M, Srivithya Vellampatti, Byeonghoon Kim, Junwye Lee, Soyeon Kim, Junyoung Son and Sung Ha Park
Published Date: 04 May 2015(Online)
Journal Reference: RSC Adv., 2015,5, 43234-43241

Abstract :
DNA is an excellent and extraordinarily versatile building block that can be used to construct nanoscale objects and arrays of increasing complexity, and as a result, a considerable amount of progress has been made in DNA-directed molecular self-assembly. Here, we demonstrate the sequential fabrication of three-dimensional multi-layered DNA nanostructures by utilizing single strand and double-crossover tile (DX) designs via substrate-assisted growth and multi-step annealing. We used both layering and connector tiles to synthesize the base layer for both the single strand-based and DX tile-based designs. Layering without and with connector tiles was used to produce double-layer and multi-layer designs for single strand-based designs, but only layering tiles were used for the DX tile-based design. Connector tiles provided appropriate sticky-end sets to form the designed lattice structures. Atomic force microscopy revealed that the spacing between the tiles was in good agreement with the design scheme, but the heights of the multi-layered nanostructures were found to be slightly lower than expected due to suppression by the substrate. This kind of step-wise multi-layer assembly may produce a variety of spacings to incorporate different guest molecules or aid the attachment of various types of biomolecules and nanomaterials in parallel arrays along the layers.

Title: DNA reusability and optoelectronic characteristics of streptavidin-conjugated DNA crystals on a quartz substrate
Authors: Bramaramba Gnapareddy, Taewoo Ha, Sreekantha Reddy Dugasani, Jang Ah Kim, Byeonghoon Kim, Taesung Kim, Jae Hoon Kim and Sung Ha Park
Published Date: 21 Apr 2015(Online)
Journal Reference: RSC Adv., 2015,5, 39409-39415

Abstract :
We demonstrate self-assembled double-crossover (DX) DNA crystal growth and coverage on quartz by the substrate assisted growth method. Here we introduced the novel concept of a reusability process to fabricate the DX crystals on a given substrate with a 10 nM DNA concentration, which is equal to the saturation concentration and this concentration is enough to fully cover the substrate with DX crystals. Also the DX crystals with biotinylated oligonucleotides (DXB) were constructed based on the structure of immobile crossover branched junctions. Upon streptavidin conjugation with DNA, the Raman band intensities were increased as compared to pristine DX crystals which indicate the strong bonding between the biotinylated DXB crystals and streptavidin. The DX crystals showed a relatively higher current than streptavidin conjugated DXB crystals because of the electrically insulating characteristic of streptavidin. Furthermore, the optical band gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) as well as the second band onset were determined and discussed. The HOMO–LUMO band gaps of DNA crystals, DNA crystals with biotins, and DNA crystals with biotins and streptavidin showed an inverted V-shape and the second band onsets – consistent with the electrical characteristics – revealed the increasing behavior with protein conjugation.

Title: Assembly of a tile-based multilayered DNA nanostructure
Authors: Junyoung Son, Junywe Lee, Anshula Tandon, Byeonghoon Kim, Sanghyun Yoo, Chang-Won Lee and Sung Ha Park
Published Date: 12th Mar 2015(Online), 21th Apr 2015(Offline)
Journal Reference: Nanoscale, 2015, 7, 6492-6497

Abstract :
The Watson–Crick complementarity of DNA is exploited to construct periodically patterned nanostructures, and we herein demonstrate tile-based three dimensional (3D) multilayered DNA nanostructures that incorporate two design strategies: vertical growth and horizontal layer stacking with substrate-assisted growth. To this end, we have designed a periodically holed double–double crossover (DDX) template that can be used to examine the growth of the multilayer structures in both the vertical and horizontal directions. For vertical growth, the traditional 2D double crossover (DX) DNA lattice is seeded and grown vertically from periodic holes in the DDX template. For horizontal stacking, the DDX layers are stacked by binding the connector tiles between each layer. Although both types of multilayers exhibited successful formation, the observations with an atomic force microscope indicated that the DDX layer growth achieved with the horizontal stacking approach could be considered to be slightly better relative to the vertical growth of the DX layers in terms of uniformity, layer size, and discreteness. In particular, the newly designed DDX template layer provided a parallel arrangement between each domain with substrate-assisted growth. This kind of layer arrangement suggests a possibility of using our design scheme in the construction of other periodic structures.

2014

Title: Functional graphene composite films for surface plasmon resonance sensor technology
Authors: Jang Ah Kim, Taehyun Hwang, Dugasani, S.R., Atul, K., Sung Ha Park and Taesung Kim
Published Date: 5 Nov 2014
Journal Reference: SENSORS, 2014 IEEE

Abstract :
In this study, a surface plasmon resonance (SPR) based fiber optic sensors coated with pristine graphene and functionalized graphene composite film were evaluated. Graphene synthesized by chemical vapor deposition (CVD) is transferred on the sensing area of the optical fiber. The sensor operates based on the principle that SPR changes according to the refractive indices of analytes. This sensor was evaluated with structural DNA lattice functionalized with biotin (DXB) and streptavidin (SA). To the best of our knowledge, this is the first ever attempt to use graphene as a replacement for conventional metal films. The exact SPR phenomena and the red-shift of 7.276 nm signals for the DXB and SA combination were observed. We believe that the use of graphene as the metallic film in the SPR sensor will lead to a new area of study in biochemical sensing technology.

Title: Ternary and senary representations using DNA double-crossover tiles
Authors: Kim B, Jo S, Son J, Kim J, Kim MH, Hwang SU, Dugasani SR, Kim BD, Liu WK, Kim MK, Park SH
Published Date: 24th October 2014
Journal Reference: Nanotechnology [2014, 25(10):105601]

Abstract :
The information capacity of DNA double-crossover (DX) tiles was successfully increased beyond a binary representation to higher base representations. By controlling the length and the position of DNA hairpins on the DX tile, ternary and senary (base-3 and base-6) digit representations were realized and verified by atomic force microscopy. Also, normal mode analysis was carried out to study the mechanical characteristics of each structure.

Title: Assembling CdSe/ZnS core–shell quantum dots on localized DNA nanostructures
Authors: Junwye Lee, Jongtaek Lee, Sung Mo Yeon, Sunmin Min, Jinwoo Kim, Hyeokwoo Choi, Sunho Kim, Jonghyun Koo, Kyungseob Kim, Sung Ha Park and Yonghan Roh
Published Date: 8th October 2014
Journal Reference: RSC Adv., 2014, 4, 53201-53205

Abstract :
We have demonstrated the assembly of CdSe/ZnS core–shell quantum dots (Qdots) on DNA templates that could potentially be used in practical devices and sensors. Qdots were aligned on one and two dimensional DNA nanostructures through electrostatic interaction between Qdots and DNA nanostructures. About 2 to 3 times larger adsorption ratios of Qdots on DNA templates were observed on both positively and negatively charged substrates. Moreover, assembled Qdots on DNA templates exhibit significant improvement in electric characteristics with a distinct semiconductor-like plateau. The results obtained in this research show the specific complementary relationship between Qdots and DNA nanostructures: the DNA nanostructures guide precise control of Qdot assembly on desired places and assembled Qdots help to increase the functionality of complexes. These approaches open up opportunities to control accurate positioning of specific nano and biomaterials with full functionality and efficiency in a given system.

Title: Combining Protein-Shelled Platinum Nanoparticles with Graphene to Build a Bionanohybrid Capacitor
Authors: Boi Hoa San, Jang Ah Kim, Atul Kulkarni, Sang Hyun Moh, Sreekantha Reddy Dugasani, Vinod Kumar Subramani, Nanasaheb D. Thorat, Hyun Ho Lee, Sung Ha Park, Taesung Kim and Kyeong Kyu Kim
Published Date: 12th August 2014
Journal Reference: ACS Nano, 2014, 8 (12), pp 12120–12129

Abstract :
The electronic properties of biomolecules and their hybrids with inorganic materials can be utilized for the fabrication of nanoelectronic devices. Here, we report the charge transport behavior of protein-shelled inorganic nanoparticles combined with graphene and demonstrate their possible application as a bionanohybrid capacitor. The conductivity of PepA, a bacterial aminopeptidase used as a protein shell (PS), and the platinum nanoparticles (PtNPs) encapsulated by PepA was measured using a field effect transistor (FET) and a graphene-based FET (GFET). Furthermore, we confirmed that the electronic properties of PepA-PtNPs were controlled by varying the size of the PtNPs. The use of two poly(methyl methacrylate) (PMMA)-coated graphene layers separated by PepA-PtNPs enabled us to build a bionanohybrid capacitor with tunable properties. The combination of bioinorganic nanohybrids with graphene is regarded as the cornerstone for developing flexible and biocompatible bionanoelectronic devices that can be integrated into bioelectric circuits for biomedical purposes.

Title: n- and p-Type Doping Phenomenon by Artificial DNA and M-DNA on Two-Dimensional Transition Metal Dichalcogenides
Authors: Hyung-Youl Park, Sreekantha Reddy Dugasani, Dong-Ho Kang, Jeaho Jeon, Sung Kyu Jang, Sungjoo Lee, Yonghan Roh, Sung Ha Park and Jin-Hong Park
Published Date: 11th August 2014
Journal Reference: ACS Nano, 2014, 8 (11), pp 11603–11613

Abstract :
Deoxyribonucleic acid (DNA) and two-dimensional (2D) transition metal dichalcogenide (TMD) nanotechnology holds great potential for the development of extremely small devices with increasingly complex functionality. However, most current research related to DNA is limited to crystal growth and synthesis. In addition, since controllable doping methods like ion implantation can cause fatal crystal damage to 2D TMD materials, it is very hard to achieve a low-level doping concentration (nondegenerate regime) on TMD in the present state of technology. Here, we report a nondegenerate doping phenomenon for TMD materials (MoS2 and WSe2, which represent n- and p-channel materials, respectively) using DNA and slightly modified DNA by metal ions (Zn2+, Ni2+, Co2+, and Cu2+), named as M-DNA. This study is an example of interdisciplinary convergence research between DNA nanotechnology and TMD-based 2D device technology. The phosphate backbone (PO4–) in DNA attracts and holds hole carriers in the TMD region, n-doping the TMD films. Conversely, M-DNA nanostructures, which are functionalized by intercalating metal ions, have positive dipole moments and consequently reduce the electron carrier density of TMD materials, resulting in p-doping phenomenon. N-doping by DNA occurs at ∼6.4 × 1010 cm–2 on MoS2 and ∼7.3 × 109 cm–2 on WSe2, which is uniform across the TMD area. p-Doping which is uniformly achieved by M-DNA occurs between 2.3 × 1010 and 5.5 × 1010 cm–2 on MoS2 and between 2.4 × 1010 and 5.0 × 1010 cm–2 on WSe2. These doping levels are in the nondegenerate regime, allowing for the proper design of performance parameters of TMD-based electronic and optoelectronic devices (VTH, on-/off-currents, field-effect mobility, photoresponsivity, and detectivity). In addition, by controlling the metal ions used, the p-doping level of TMD materials, which also influences their performance parameters, can be controlled. This interdisciplinary convergence research will allow for the successful integration of future layered semiconductor devices requiring extremely small and very complicated structures.

Title: Fabrication and characterization of PNA–DNA hybrid nanostructures
Authors: Bramaramba Gnapareddy, Jang Ah Kim, Sreekantha Reddy Dugasani, Anshula Tandon, Byeonghoon Kim, Saima Bashar, Ji Ah Choi, Goon Ho Joe, Taesung Kim, Tai Hwan Ha and Sung Ha Park
Published Date: 31st July 2014
Journal Reference: RSC Adv., 2014, 4, 35554-35558

Abstract :
Although the distinct properties and synthesis methodology of peptide nucleic acid (PNA) molecules have been established by extensive studies, the construction of an artificial nanostructure made from PNA has been examined in only a few reports. Here we study the feasibility of constructing PNA–DNA hybrid nanostructures by conventional free solution annealing and substrate assisted growth methods. For conventional free solution annealing, we introduced a 2-step annealing procedure to mitigate the self-aggregation of PNA in the formation of stable PNA–DNA hybrid structures. Atomic force microscopy images revealed the formation of PNA–DNA hybrid nanostructures smaller than normal DNA and the Raman band intensities of the hybrid gradually decreased as a few DNA strands were replaced by PNA possibly due to the fast binding properties of PNA and the structural stress between PNA and DNA.

Title: Energy Band Gap and Optical Transition of Metal Ion Modified Double Crossover DNA Lattices
Authors: Sreekantha Reddy Dugasani, Taewoo Ha, Bramaramba Gnapareddy, Kyujin Choi, Junwye Lee, Byeonghoon Kim, Jae Hoon Kim and Sung Ha Park
Published Date: 20th June 2014
Journal Reference: ACS Appl. Mater. Interfaces, 2014, 6 (20), pp 17599–17605

Abstract :
We report on the energy band gap and optical transition of a series of divalent metal ion (Cu2+, Ni2+, Zn2+, and Co2+) modified DNA (M–DNA) double crossover (DX) lattices fabricated on fused silica by the substrate-assisted growth (SAG) method. We demonstrate how the degree of coverage of the DX lattices is influenced by the DX monomer concentration and also analyze the band gaps of the M–DNA lattices. The energy band gap of the M–DNA, between the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO), ranges from 4.67 to 4.98 eV as judged by optical transitions. Relative to the band gap of a pristine DNA molecule (4.69 eV), the band gap of the M–DNA lattices increases with metal ion doping up to a critical concentration and then decreases with further doping. Interestingly, except for the case of Ni2+, the onset of the second absorption band shifts to a lower energy until a critical concentration and then shifts to a higher energy with further increasing the metal ion concentration, which is consistent with the evolution of electrical transport characteristics. Our results show that controllable metal ion doping is an effective method to tune the band gap energy of DNA-based nanostructures.

Title: Nanoscale topographical replication of graphene architecture by artificial DNA nanostructures
Authors: Y. Moon, J. Shin, S. Seo, S. R. Dugasani, S. H. Woo, T. Park, S. H. Park, and J. R. Ahn
Published Date: 9th June 2014
Journal Reference: Appl. Phys. Lett. 104, 231904 (2014)

Abstract :
Despite many studies on how geometry can be used to control the electronic properties of graphene, certain limitations to fabrication of designed graphene nanostructures exist. Here, we demonstrate controlled topographical replication of graphene by artificial deoxyribonucleic acid (DNA) nanostructures. Owing to the high degree of geometrical freedom of DNA nanostructures, we controlled the nanoscale topography of graphene. The topography of graphene replicated from DNA nanostructures showed enhanced thermal stability and revealed an interesting negative temperature coefficient of sheet resistivity when underlying DNA nanostructures were denatured at high temperatures.

Title: Approaches to label-free flexible DNA biosensors using low-temperature solution-processed InZnO thin-film transistors
Authors: Joohye Jung, Si Joon Kim, Keun Woo Lee, b, Doo Hyun Yoon, Yeong-gyu Kim, Hee Young Kwak, Sreekantha Reddy Dugasani, Sung Ha Park, Hyun Jae Kim
Published Date: 15 May 2014
Journal Reference: Biosensors and Bioelectronics 55 (2014) 99-105

Abstract :
Low-temperature solution-processed In–Zn–O (IZO) thin-film transistors (TFTs) exhibiting a favorable microenvironment for electron transfer by adsorbed artificial deoxyribonucleic acid (DNA) have extraordinary potential for emerging flexible biosensor applications. Superb sensing ability to differentiate even 0.5 μL of 50 nM DNA target solution was achieved through using IZO TFTs fabricated at 280 °C. Our IZO TFT had a turn-on voltage (Von) of −0.8 V, on/off ratio of 6.94×105, and on-current (Ion) value of 2.32×10−6 A in pristine condition. A dry-wet method was applied to immobilize two dimensional double crossover tile based DNA nanostructures on the IZO surface, after which we observed a negative shift of the transfer curve accompanied by a significant increase in the Ion and degradation of the Von and on/off ratio. As the concentration of DNA target solution increased, variances in these parameters became increasingly apparent. The sensing mechanism based on the current evolution was attributed to the oxidation of DNA, in which the guanine nucleobase plays a key role. The sensing behavior obtained from flexible biosensors on a polymeric substrate fabricated under the identical conditions was exactly analogous. These results compare favorably with the conventional field-effect transistor based DNA sensors by demonstrating remarkable sensitivity and feasibility of flexible devices that arose from a different sensing mechanism and a low-temperature process, respectively.

Title: Long dsRNA-Mediated RNA Interference and Immunostimulation: A Targeted Delivery Approach Using Polyethyleneimine Based Nano-Carriers
Authors: S. Sajeesh, Tae Yeon Lee, Sun Woo Hong, Pooja Dua, Jeong Yong Choe, Aeyeon Kang, Wan Soo Yun, Changsik Song, Sung Ha Park, Soyoun Kim, Chiang Li, and Dong-ki Lee
Published Date: 12th February 2014
Journal Reference: Mol. Pharmaceutics, 2014, 11 (3), pp 872–884

Abstract :
RNA oligonucleotides capable of inducing controlled immunostimulation combined with specific oncogene silencing via an RNA interference (RNAi) mechanism provide synergistic inhibition of cancer cell growth. With this concept, we previously designed a potent immunostimulatory long double stranded RNA, referred to as liRNA, capable of executing RNAi mediated specific target gene silencing. In this study, we developed a highly effective liRNA based targeted delivery system to apply in the treatment of glioblastoma multiforme. A stable nanocomplex was fabricated by complexing multimerized liRNA structures with cross-linked branched poly(ethylene imine) (bPEI) via electrostatic interactions. We show clear evidence that the cross-linked bPEI was quite effective in enhancing the cellular uptake of liRNA on U87MG cells. Moreover, the liRNA-PEI nanocomplex provided strong RNAi mediated target gene silencing compared to that of the conventional siRNA-PEI complex. Further, the bPEI modification strategy with specific ligand attachment assisted the uptake of the liRNA-PEI complex on the mouse brain endothelial cell line (b.End3). Such delivery systems combining the beneficial elements of targeted delivery, controlled immunostimulation, and RNAi mediated target silencing have immense potential in anticancer therapy.

Title: A 2D DNA Lattice as an Ultrasensitive Detector for Beta Radiations
Authors: Sreekantha Reddy Dugasani, Jang Ah Kim, Byeonghoon Kim, Pranav Joshirao, Bramaramba Gnapareddy, Chirag Vyas, Taesung Kim, Sung Ha Park and Vijay Manchanda
Published Date: 29th January 2014
Journal Reference: ACS Appl. Mater. Interfaces, 2014, 6 (4), pp 2974-2979

Abstract :
There is growing demand for the development of efficient ultrasensitive radiation detectors to monitor the doses administered to individuals during therapeutic nuclear medicine which is often based on radiopharmaceuticals, especially those involving beta emitters. Recently biological materials are used in sensors in the nanobio disciplines due to their abilities to detect specific target materials or sites. Artificially designed two-dimensional (2D) DNA lattices grown on a substrate were analyzed after exposure to pure beta emitters, 90Sr-90Y. We studied the Raman spectra and reflected intensities of DNA lattices at various distances from the source with different exposure times. Although beta particles have very low linear energy transfer values, the significant physical and chemical changes observed throughout the extremely thin, ∼0.6 nm, DNA lattices suggested the feasibility of using them to develop ultrasensitive detectors of beta radiations.

2013

Title: Graphene based fiber optic surface plasmon resonance for bio-chemical sensor applications
Authors: Jang Ah Kim, Taehyun Hwang, Sreekantha Reddy Dugasani, Rashid Amin, Atul Kulkarni, Sung Ha Park, & Taesung Kim 
Published Date : Oct, 2013
Journal Reference : Sensors and Actuators B 187 (2013) 426-433

Abstract :
In this study, a surface plasmon resonance (SPR) based fiber optic sensor coated with graphene is introduced. A graphene film synthesized by thermal chemical vapor deposition (TCVD) is transferred onto the sensing area of the optical fiber. The detection mechanism of this sensor is based on the principle that the SPR signal changes according to the refractive indices of analytes. Biotinylated Double Crossover DNA (DXB) lattice and protein Streptavidin (SA) were used for the evaluation. To the best of our knowledge, this is the first attempt to use graphene as a replacement for conventional metal films. The exact SPR phenomena and the red-shift of 7.276 nm for the DXB and SA combination were observed. 

Title: Low-Cost Label-Free Electrical Detection of Artificial DNA Nanostructures Using Solution-Processed Oxide Thin-Film Transistors
Authors: Si Joon Kim, Joohye Jung, Keun Woo Lee, Doo Hyun Yoon, Tae Soo Jung, Sreekantha Reddy Dugasani, Sung Ha Park and Hyun Jae Kim
published date: 27th September 2013
Journal Reference: ACS Appl. Mater. Interfaces, 2013, 5 (21), pp 10715–10720

Abstract :
A high-sensitivity, label-free method for detecting deoxyribonucleic acid (DNA) using solution-processed oxide thin-film transistors (TFTs) was developed. Double-crossover (DX) DNA nanostructures with different concentrations of divalent Cu ion (Cu2+) were immobilized on an In–Ga–Zn–O (IGZO) back-channel surface, which changed the electrical performance of the IGZO TFTs. The detection mechanism of the IGZO TFT-based DNA biosensor is attributed to electron trapping and electrostatic interactions caused by negatively charged phosphate groups on the DNA backbone. Furthermore, Cu2+ in DX DNA nanostructures generates a current path when a gate bias is applied. The direct effect on the electrical response implies that solution-processed IGZO TFTs could be used to realize low-cost and high-sensitivity DNA biosensors.

Title: Hairpin embedded DNA lattices grown on a mica substrate
Authors: Saima Bashar, Chang-Won Lee, Junwye Lee, Byeonghoon Kim, Bramaramba Gnapareddy, Jihoon Shin, Sreekantha Reddy Dugasani and Sung Ha Park
published date: 27th August 2013
Journal Reference: RSC Adv., 2013, 3, 19876-19879

Abstract :
We constructed hairpin-embedded double crossover (DX) tile-based DNA lattices using a substrate-assisted growth method. The in situ growth of protruding hairpin tiles on a substrate during annealing demonstrates the feasibility of substrate-assisted self-assembly even with geometrical hindrances.

Title : Green synthesis of silver nanoparticles and their application for the development of optical fiber based hydrogen peroxide sensor
Authors : Chandrakant K. Tagad, Sreekantha Reddy Dugasani, Rohini Aiyer, Sungha Park, Atul Kulkarni, & Sushma Sabharwala,
Published Date : July 05, 2013
Journal Reference : Sensors and Actuators B 183 (2013) 144–149

Abstract :
Green synthesis of nanoparticles and their applications in sensing area is of great interest to the research community. Herein we report a green approach for the synthesis of silver nanoparticles (Ag NPs) by using locust bean gum (LBG) polysaccharide and its application to detect hydrogen peroxide (H2O2). Ag NPs were synthesized by mixing optimized weight percent of LBG with a known quantity of silver nitrate (AgNO3) at 55–60 °C. Synthesized Ag NPs were characterized by UV–vis spectroscopy and atomic force microscopy (AFM). The size of synthesized Ag NPs was in the range of 18–51 nm depending upon the concentration of LBG and AgNO3. Further, a low cost and portable optical fiber based sensor using LBG stabilized Ag NPs was developed for monitoring the H2O2 concentration as low as 0.01 mM.

Title: Quantitative analysis of molecular-level DNA crystal growth on a 2D surface
Authors: Junwye Lee, Shogo Hamada, Si Un Hwang, Rashid Amin, Junyoung Son, Sreekantha Reddy Dugasani, Satoshi Murata & Sung Ha Park
published date: 2nd July 2013
Journal Reference: Scientific Reports 3, Article number: 2115

Abstract :
Crystallization is an essential process for understanding a molecule's aggregation behavior. It provides basic information on crystals, including their nucleation and growth processes. Deoxyribonucleic acid (DNA) has become an interesting building material because of its remarkable properties for constructing various shapes of submicron-scale DNA crystals by self-assembly. The recently developed substrate-assisted growth (SAG) method produces fully covered DNA crystals on various substrates using electrostatic interactions and provides an opportunity to observe the overall crystallization process. In this study, we investigated quantitative analysis of molecular-level DNA crystallization using the SAG method. Coverage and crystal size distribution were studied by controlling the external parameters such as monomer concentration, annealing temperature, and annealing time. Rearrangement during crystallization was also discussed. We expect that our study will provide overall picture of the fabrication process of DNA crystals on the charged substrate and promote practical applications of DNA crystals in science and technology.

Title: A novel nanometric DNA thin film as a sensor for alpha radiation
Authors: Atul Kulkarni, Byeonghoon Kim, Sreekantha Reddy Dugasani, Pranav Joshirao, Jang Ah Kim, Chirag Vyas, Vijay Manchanda, Taesung Kim & Sung Ha Park
published date: 24th June 2013
Journal Reference: Scientific Reports 3, Article number: 2062

Abstract :
The unexpected nuclear accidents have provided a challenge for scientists and engineers to develop sensitive detectors, especially for alpha radiation. Due to the high linear energy transfer value, sensors designed to detect such radiation require placement in close proximity to the radiation source. Here we report the morphological changes and optical responses of artificially designed DNA thin films in response to exposure to alpha radiation as observed by an atomic force microscope, a Raman and a reflectance spectroscopes. In addition, we discuss the feasibility of a DNA thin film as a radiation sensing material. The effect of alpha radiation exposure on the DNA thin film was evaluated as a function of distance from an 241Am source and exposure time. Significant reflected intensity changes of the exposed DNA thin film suggest that a thin film made of biomolecules can be one of promising candidates for the development of online radiation sensors.

Title : Magnetic Characteristics of Copper Ion-Modified DNA Thin Films
Authors : Sreekantha Reddy Dugasani, Namhoon Lee, Junwye Lee, Byeonghoon Kim, Si Un Hwang, Keun Woo Lee, Won Nam Kang & Sung Ha Park
Published Date : May, 2013
Journal Reference : Scientific Reports 3, Article number: 1819

Abstract :
We developed a new method of fabricating a divalent copper ion (Cu2+) modified DNA thin film on a glass substrate and studied its magnetic properties. We evaluated the coercive field (Hc), remanent magnetization (Mr), susceptibility (χ), and thermal variation of magnetization with varying Cu2+ concentrations [Cu2+] resulting in DNA thin films. Although thickness of the two dimensional DNA thin film with Cu2+ in dry state was extremely thin (0.6 nm), significant ferromagnetic signals were observed at room temperature. The DNA thin films with a [Cu2+] near 5 mM showed the distinct S-shape hysteresis with appreciable high Hc, Mr and χ at low field (≤600 Oe). These were primarily caused by the presence of small magnetic dipoles of Cu2+ coordination on the DNA molecule, through unpaired d electrons interacting with their nearest neighbors and the inter-exchange energy in the magnetic dipoles making other neighboring dipoles oriented in the same direction.

Title: Charge-trap effects of 2D DNA nanostructures implanted in solution-processed InGaZnO thin-film transistor
Authors: Keun Woo Lee, Kyung Min Kim, Si Joon Kim, Sreekantha Reddy Dugasani, Junwye Lee, Sung Ha Park and Hyun Jae Kim
published date: 29th May 2013
Journal Reference: J. Phys. D: Appl. Phys. 46 215102

Abstract :
A double crossover (DX) tile-based 2D DNA nanostructure was fabricated and implanted successfully in solution-processed InGaZnO thin film transistor. Observations indicated that the DNA nanostructure plays an important role as a trap charge centre under high electric field in the memory device. At positive gate voltage the memory device with the DNA shows appreciable trapped charge and at negative gate voltage reveals detrapped negative charge characteristics. Consequently, various dimensional DNA nanostructures may play a central role in nanoscale devices and applications in the near future.

Title : DNA nanotechnology: a future perspective
Authors: Muniza Zahid, Byeonghoon Kim, Rafaqat Hussain, Rashid Amin and Sung H Park
Published Date : Mar, 2013.
Journal Reference Nanoscale Research Letters 2013, 8:119

Abstract :
In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology.

2012

Title : Electrical Responses of Artificial DNA Nanostructures on Solution-Processed In-Ga-Zn-O Thin-Film Transistors with Multistacked Active Layers
Authors : Joohye Jung, Si Joon Kim, Doo Hyun Yoon, Byeonghoon Kim, Sung Ha Park *, and Hyun Jae Kim *
Published Date : Dec, 2012. (online)
Journal Reference : ACS Appl. Mater. Interfaces, 2013, 5 (1), pp 98–102

Abstract :
We propose solution-processed In-Ga-Zn-O (IGZO) thin-film transistors (TFTs) with multistacked active layers for detecting artificial deoxyribonucleic acid (DNA). Enhanced sensing ability and stable electrical performance of TFTs were achieved through use of multistacked active layers. Our IGZO TFT had a turn-on voltage (Von) of −0.8 V and a subthreshold swing (SS) value of 0.48 V/decade. A dry-wet method was adopted to immobilize double-crossover DNA on the IGZO surface, after which an anomalous hump effect accompanying a significant decrease in Von (−13.6 V) and degradation of SS (1.29 V/decade) was observed. This sensing behavior was attributed to the middle interfaces of the multistacked active layers and the negatively charged phosphate groups on the DNA backbone, which generated a parasitic path in the TFT device. These results compared favorably with those reported for conventional field-effect transistor-based DNA sensors with remarkable sensitivity and stability.

Title : The label free DNA sensor using a silicon nanowire array
Authors : Atul Kulkarni, Yang Xu, Chisung Ahn, Rashid Amin, Sung Ha Park, Taesung Kim and Minho Lee
Published Date : May, 2012. (online) Aug, 2012. (offline)
Journal Reference : Journal of Biotechnology. 160, 91-96 (2012)

Abstract :
Biosensors based on silicon nanowire (Si-NW) promise highly sensitive dynamic label free electrical detection of various biological molecules. Here we report Si-NW array electronic devices that function as sensitive and selective detectors of as synthesized 2D DNA lattices with biotins. The Si-NW array was fabricated using top–down approach consists of 250 nanowires of 20 μm in length, equally spaced with an interval of 3.2 μm. Measurements of photoresistivity of the Si-NW array device with streptavidin (SA) attached on biotinylated DNA lattices at different concentration were observed and analyzed.. The conductivity in the DNA lattices with protein SA shows significant change in the photoresistivity of Si-NW array device. This Si-NW based DNA sensor would be one of very efficient devices for direct, label free DNA detection and could provide a pathway to immunological assays, DNA forensics and toxin detection in modern biotechnology.

Title : NMR Studies of Artificial Double-Crossover DNA Tiles
Authors : Murugan Veerapandian, Byeonghoon Kim, Rashid Amin, Junwye Lee, Kyusik Yun, and Sung Ha Park
Published Date : Mar, 2012. (offline)
Journal Reference : J. Nanosci. Nanotechnol. 12, 2300-2310 (2012)

Abstract :
This report documents the design and characterization of DNA molecular nanoarchitectures consisting of artificial double crossover DNA tiles with different geometry and chemistry. The Structural characterization of the unit tiles, including normal, biotinylated and hairpin loop structures, are morphologically studied by atomic force microscopy. The specific proton resonance of the individual tiles and their intra/inter nucleotide relationships are verified by proton nuclear magnetic resonance spectroscopy and 2-dimensional correlation spectral studies, respectively. Significant up-field and down-field shifts in the resonance signals of the individual residues at various temperatures are discussed. The results suggest that with artificially designed DNA tiles it is feasible to obtain structural information of the relative base sequences. These tiles were later fabricated into 2D DNA lattice structures for specific applications such as protein arrangement by biotinylated bulged loops or pattern generation using a hairpin structure.

Title : Artificial DNA nanostructure detection using solution-processed In-Ga-Zn-O thin-film transistors
Authors : Si Joon Kim, Byeonghoon Kim, Joohye Jung, Doo Hyun Yoon, Junwye Lee, Sung Ha Park, and Hyun Jae Kim
Published Date : Mar, 2012.(online)
Journal Reference : APL, Vol. 100, 103702

Abstract :
A method for detecting artificial DNA using solution-processed In-Ga-Zn-O (IGZO) thin-film transistors (TFTs) was developed. The IGZO TFT had a field-effect mobility (μFET) of 0.07 cm2/Vs and an on-current (Ion) value of about 2.68 μA. A dry-wet method was employed to immobilize double-crossover (DX) DNA onto the IGZO surface. After DX DNA immobilization, significant decreases in μFET (0.02 cm2/Vs) and Ion (0.247 μA) and a positive shift of threshold voltage were observed. These results were attributed to the negatively charged phosphate groups on the DNA backbone, which generated electrostatic interactions in the TFT device.

Title : DNA nanotube formation based on normal mode analysis
Authors : PengFei Qian, Sangjae Seo, Junghoon Kim, Seungjae Kim, Byeong Soo Lim, Wing Kam Liu, Bum Joon Kim, Thomas H LaBean, Sung Ha Park and Moon Ki Kim
Published Date : Feb, 2012. (online) Mar, 2012. (offline)
Journal Reference : Nanotechnology 23 105704

Abstract :
Ever since its inception, a popular DNA motif called the cross tile has been recognized to self-assemble into addressable 2D templates consisting of periodic square cavities. Although this may be conceptually correct, in reality, certain types of cross tiles can only form planar lattices if adjacent tiles are designed to bind in a corrugated manner, in the absence of which they roll up to form 3D nanotube structures. Here we present a theoretical study on why uncorrugated cross tiles self-assemble into counterintuitive 3D nanotube structures and not planar 2D lattices. Coarse-grained normal mode analysis (CGNMA) of single and multiple cross tiles within the elastic network model (ENM) was carried out to expound the vibration modes of the systems. While both single and multiple cross tile simulations produce results conducive to tube formations, the dominant modes of a unit of 4 cross tiles (one square cavity), termed as a quadruplet, fully reflect the symmetries of the actual nanotubes found in experiments and firmly endorse circularization of an array of cross tiles.

Title : Size-Controllable DNA Rings with Copper-Ion Modification
Authors : Junwye Lee, Shogo Hamada, Rashid Amin, Sunho Kim, Atul Kilkarni, Taesung Kim, Yonghan Roh, Satoshi Murata, Sung Ha Park
Published Date : Dec, 2011. (online), Feb, 6th, 2012. (offline)
Journal Reference : Small, 2012, 8, No.3, 374-377

Abstract :
Cu2+-modified DNA nanostructures are investigated using differently sized DNA rings that are composed of core and extension motifs. Chemical reduction and current measurements are adopted for verifying Cu2+ modification, and the results provide clear evidence for the co-ordination of Cu2+ in DNA structures.

Title : The restoration of DNA structures by the dry–wet method
Authors : Junwye Lee , Rashid Amin , Byeonghoon Kim , Sang Jung Ahn , Keun Woo Lee , Hyun Jae Kim and Sung Ha Park
Published Date : Nov, 2011. (online) Jan, 2012. (offline)
Journal Reference : Soft Matter, 2012,8, 619-622

Abstract :
Since DNA nanotechnology often requires water-based solution annealing processes, there are certain limitations on applying the results directly to physical devices which should be protected from the water treatment process during sample preparation. In an effort to overcome this problem, we develop a solution substitution technique, which we call the dry–wet method. These results may help facilitate integrating the DNA structures in current technologies.

Title : Fabrication of zigzag and folded DNA nanostructures by an angle control scheme
Authors : Junwye Lee, Rashid Amin, Byeonghoon Kim, Soyeon Kim, Chang-Won Lee, Jong Min Kim, Thomas H. LaBean and Sung Ha Park
Published Date : Nov, 2011.
Journal Reference : Soft Matter, 2012, Advance Article

Abstract :
We fabricated zigzag and folded DNA nanostructures by an angle control scheme. In order to give a solid verification of its operation, an open tube structure was also designed and it shows drastic dimensional changes compared with 2 dimensional zigzag and folded structures. These self-assembled artificial DNA structures would provide nanoscale-resolution templates for the alignment of various functional materials.

Title : RKKY Interaction in Disordered Graphene
Authors : Hyunyong Lee, Junghoon Kim, E. R. Mucciolo, Georges Bouzerar, S. Kettemann
Published Date : Feb, 2012.
Journal Reference : Physical Review B 85, 075420 (2012)
arXiv : arXiv:1110.6272v1 [cond-mat.mes-hall]

Abstract :
We investigate the effects of nonmagnetic disorder on the Ruderman-Kittel-Kasuya-Yoshida (RKKY) interaction in graphene by studying numerically the Anderson model with on-site and hopping disorder on a honeycomb lattice at half filling. We evaluate the strength of the interaction as a function of the distance R between two magnetic ions, as well as their lattice positions and orientations. In the clean limit, we find that the strength of the interaction decays as 1/R^3, with its sign and oscillation amplitude showing strong anisotropy. With increasing on-site disorder, the mean amplitude decreases exponentially at distances exceeding the elastic mean free path. At smaller distances, however, the oscillation amplitude increases strongly and its sign changes on the same sublattice for all directions but the armchair direction. For random hopping disorder, no sign change is observed. No significant changes to the geometrical average values of the RKKY interaction are found at small distances, while exponential suppression is observed at distances exceeding the localization length.

2011

Title : DNA thin film coated optical fiber biosensor
Authors : Rashid Amin, Atul Kulkarni, Taesung Kim and Sung Ha Park
Published Date : Nov, 2011.(online)
Journal Reference : Current Applied Physics 11 (2012) 841-845

Abstract :
We present a simple but highly sensitive biotinylated DNA double crossover thin film coated fiber optic reflectance biosensor (DTF FORS) for the detection of streptavidin aerosols as a building block towards sensing bio-aerosols. The DNA double crossover lattice with biotin was dropped on the polymer optical fiber end face to prepare DNA Thin Film. The streptavidin aerosols were prepared using conventional aerosol technology. The DTF FORS response to streptavidin aerosol was few seconds and the sensor repeatability for air and streptavidin aerosol was found to be excellent. The presented FORS sensing approach, where the film can be changed on the end face of the optical fiber, is expected to detect atmospheric bio-aerosols with great sensitivity and effective specificity.

Title : Growth and restoration of a T-tile-based 1D DNA nanotrack
Authors : Byeonghoon Kim, Rashid Amin, Junwye Lee, Kyusik Yun and Sung Ha Park
Published Date : Sep, 2011.
Journal Reference : Chem. Commun., 2011, 47, 11053-11055

Abstract :
We designed an artificial one-dimensional DNA nanotrack that contains two T-motifs. It can be fabricated in a free solution and with a mica-assisted growth process. Also, we introduced a dry and wet method for the restoration of DNA nanostructures in order for them to be used in multiple applications.

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 : Coverage Control of DNA Crystals Grown by Silica Assistance
Authors : Junwye Lee, Sunho Kim, Junghoon Kim, Chang-Won Lee, Yonghan Roh, and Sung Ha Park
Published Date : Aug 26, 2011.
Journal Reference : Angew. Chem. Int. Ed., Vol. 50, 9145-9149
arXiv : 1111.2960 [cond-mat.mtrl-sci]

Abstract :
One of the main goals of DNA nanotechnology is to provide a viable solution to the limitations of top-down approaches in microfabrication schemes. Although a completely practical bottom-up approach is yet to be realized, there has been great progress in integrating the two approaches in the past few years. In this vein, we present a novel surface assisted fabrication scheme able to directly control the coverage rate, from 0 to 100%, of functionalized DNA nanostructures on centimeter-scaled silica (SiO_2) substrates which is one key to harnessing DNA's unique properties in electronics and photonics. Furthermore, electrostatic interactions between the DNA structures and the surface lead to dramatic topological changes of the structures, creating novel formations of the crystals. These results provide a direct route to applying fully functionalized layers of DNA nanostructures to current technologies in SiO_2-based electronics and photonics.

Title : A two-dimensional DNA lattice implanted polymer solar cell
Authors : Keun Woo Lee, Kyung Min Kim, Junwye Lee, Rashid Amin, Byeonghoon Kim, Sung Kye Park, Seok Kiu Lee, Sung Ha Park and Hyun Jae Kim
Published Date : Aug 18, 2011.
Journal Reference : Nanotechnology 22 375202

Abstract :
A double crossover tile based artificial two-dimensional (2D) DNA lattice was fabricated and the dry–wet method was introduced to recover an original DNA lattice structure in order to deposit DNA lattices safely on the organic layer without damaging the layer. The DNA lattice was then employed as an electron blocking layer in a polymer solar cell causing an increase of about 10% up to 160% in the power conversion efficiency. Consequently, the resulting solar cell which had an artificial 2D DNA blocking layer showed a significant enhancement in power conversion efficiency compared to conventional polymer solar cells. It should be clear that the artificial DNA nanostructure holds unique physical properties that are extremely attractive for various energy-related and photonic applications.

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 : 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 : 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

2010 and before

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

Abstract :

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

Abstract :

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 Switched by DNA Nanoactuator
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

Abstract :

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.