Junyoung Son

Quantitative analysis of molecular-level DNA crystal growth on a 2D surface

Crystallization is an essential process for understanding a molecules 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.

Ternary and senary representations using DNA double-crossover tiles

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.

Manipulation of graphene work function using a self-assembled monolayer

We report an effective and reliable method to increase the work function of graphene to as high as 5.50 eV by applying a self-assembled monolayer on its surface. The work function of pristine graphene (4.56 eV) was increased by approximately +0.94 eV following trichlorosilane (HDF-S) self-assembly. This increase in the work function was confirmed by ab initio calculations. HDF-S self-assembled graphene exhibited no significant changes in structural, optical, or electrical characteristics compared with pristine graphene. In addition, we verified that the modified work function of HDF-S self-assembled graphene was not affected by the underlying substrates.

Vibrational characteristics of DNA nanostructures obtained through a mass-weighted chemical elastic network model

Using the programmable and self-assembly characteristics of DNA, various DNA nanostructures have been designed and synthesized for specific applications, such as nanomachinery and chemical/biological sensors. Although their physical features and feasibility in engineering applications can be conjectured using experimental techniques such as atomic force microscopy and Raman spectroscopy, their vibration characteristics at low frequency states, which are the most dominant factors that determine their structural functions, are difficult to observe experimentally because it is almost impossible to capture the real-time atomic motion of DNA nanostructures. Here, we propose a novel method to elucidate the vibration characteristics of DNA nanostructures in atomic detail using a normal mode analysis based on a mass-weighted chemical elastic network model (MWCENM). Because the MWCENM is a precise method for modeling molecular structures that considers both chemical bond information and inertia effects, it can calculate both vibration frequencies and the corresponding mode shapes in atomic detail. In terms of vibration frequencies, our simulation results show good agreement, within an error deviation of 4.0%, with experimental data measured by Raman spectroscopy. Therefore, the proposed theoretical approach is a feasible method for understanding DNA nanostructures vibration characteristics, including both frequencies and mode shapes, in atomic detail, adding to the molecular fingerprint provided by the conventional Raman spectrum.

Fabrication of multi-layered DNA nanostructures using single-strand and double-crossover tile connectors

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 methods. 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.

Topological, chemical and electro-optical characteristics of riboflavin-doped artificial and natural DNA thin films

DNA is considered as a useful building bio-material, and it serves as an efficient template to align functionalized nanomaterials. Riboflavin (RF)-doped synthetic double-crossover DNA (DX-DNA) lattices and natural salmon DNA (SDNA) thin films were constructed using substrate-assisted growth and drop-casting methods, respectively, and their topological, chemical and electro-optical characteristics were evaluated. The critical doping concentrations of RF ([RF]C, approx. 5 mM) at given concentrations of DX-DNA and SDNA were obtained by observing the phase transition (from crystalline to amorphous structures) of DX-DNA and precipitation of SDNA in solution above [RF]C. [RF]C are verified by analysing the atomic force microscopy images for DX-DNA and current, absorbance and photoluminescence (PL) for SDNA. We study the physical characteristics of RF-embedded SDNA thin films, using the Fourier transform infrared spectrum to understand the interaction between the RF and DNA molecules, current to evaluate the conductance, absorption to understand the RF binding to the DNA and PL to analyse the energy transfer between the RF and DNA. The current and UV absorption band of SDNA thin films decrease up to [RF]C followed by an increase above [RF]C. By contrast, the PL intensity illustrates the reverse trend, as compared to the current and UV absorption behaviour as a function of the varying [RF]. Owing to the intense PL characteristic of RF, the DNA lattices and thin films with RF might offer immense potential to develop efficient bio-sensors and useful bio-photonic devices.

Magneto-optical and thermal characteristics of magnetite nanoparticle-embedded DNA and CTMA-DNA thin films

Recently, DNA molecules embedded with magnetite (Fe3O4) nanoparticles (MNPs) drew much attention for their wide range of potential usage. With specific intrinsic properties such as low optical loss, high transparency, large band gap, high dielectric constant, potential for molecular recognition, and their biodegradable nature, the DNA molecule can serve as an effective template or scaffold for various functionalized nanomaterials. With the aid of cetyltrimethylammonium (CTMA) surfactant, DNA can be used in organic-based applications as well as water-based ones. Here, DNA and CTMA-DNA thin films with various concentrations of MNPs fabricated by the drop-casting method have been characterized by optical absorption, refractive index, Raman, and cathodoluminescence measurements to understand the binding, dispersion, chemical identification/functional modes, and energy transfer mechanisms, respectively. In addition, magnetization was measured as a function of either applied magnetic field or temperature in field cooling and zero field cooling. Saturation magnetization and blocking temperature demonstrate the importance of MNPs in DNA and CTMA-DNA thin films. Finally, we examine the thermal stabilities of MNP-embedded DNA and CTMA-DNA thin films through thermogravimetric analysis, derivative thermogravimetry, and differential thermal analysis. The unique optical, magnetic, and thermal characteristics of MNP-embedded DNA and CTMA-DNA thin films will prove important to fields such as spintronics, biomedicine, and function-embedded sensors and devices.

3-Input/1-Output Logic Implementation Demonstrated by DNA Algorithmic Self-Assembly

Although structural DNA nanotechnology is a well-established field, computations performed using DNA algorithmic self-assembly is still in the primitive stages in terms of its adaptability of rule implementation and experimental complexity. Here, we discuss the feasibility of constructing an M-input/ N-output logic gate implemented into simple DNA building blocks. To date, no experimental demonstrations have been reported with M > 2 owing to the difficulty of tile design. To overcome this problem, we introduce a special tile referred to as an operator. We design appropriate binding domains in DNA tiles, and we demonstrate the growth of DNA algorithmic lattices generated by eight different rules from among 256 rules in a 3-input/1-output logic. The DNA lattices show simple, linelike, random, and mixed patterns, which we analyze to obtain errors and sorting factors. The errors vary from 0.8% to 12.8% depending upon the pattern complexity, and sorting factors obtained from the experiment are in good agreement with simulation results within a range of 1-18%.