Pb2+ Ion Sensors Employing Gold Etching Process: Comparative Investigation on Au Nanorods and Au Nanotriangles.

The leaching phenomenon of gold (Au) nanomaterials by Pb2+ ions in the presence of 2-mercaptoethanol (2-ME) and thiosulfate (S2O32- ion) has been systematically applied to a Pb2+ ion sensor. To further investigate the role of Pb2+ ions in sensors containing Au nanomaterials, we revisited the leaching conditions for Au nanorods and compared them with the results for Au nanotriangles. By monitoring the etching rate, it was revealed that Pb2+ ions were important for the acceleration of the etching rate mainly driven by 2-ME and S2O32- pairs, and nanomolar detection of Pb2+ ions were shown to be promoted through this catalytic effect. Using the etchant, the overall size of the Au nanorods decreased but showed an unusual red-shift in UV-Vis spectrum indicating increase of aspect ratio. Indeed, the length of Au nanorods decreased by 9.4% with the width decreasing by 17.4% over a 30-min reaction time. On the other hand, the Au nanotriangles with both flat sides surrounded mostly by dense Au{111} planes showed ordinary blue-shift in UV-Vis spectrum as the length of one side was reduced by 21.3%. By observing the changes in the two types of Au nanomaterials, we inferred that there was facet-dependent alloy formation with lead, and this difference resulted in Au nanotriangles showing good sensitivity, but lower detection limits compared to the Au nanorods.

Covalent and Oriented Immobilization of Antibodies through Systematic Modification of Photoactivatable RNA Hybrid Aptamers.

We report a covalent and well-oriented strategy of immobilization of antibodies using photoactivatable Fc-binding RNA aptamers (FcBAs). We prepared several types of FcBAs that were further modified with photoaffinity probes (i.e., benzophenone or diazirine), and evaluated the binding capabilities and the photo-crosslinking efficiency of them via pull-down assays and fluorescence analyses, respectively. Initial moderate photo-crosslinking efficiency (Kd ∼ 110 nM) was substantially improved by multivalent association of FcBAs and structural modification of FcBAs. For a conceptual proof, covalent crosslinking of human IgG on FcBA-tethered solid chips was fabricated and investigated by scanometry, which eventually proved real applicability of the present scheme toward immunoassays.

Ternary representation of N (N = 1 or 2)-input and 1-output algorithmic self-assembly demonstrated by DNA.

Deoxyribonucleic acid (DNA) is effective for molecular computation because of its high energy efficiency, high information density, and parallel-computing capability. Although logic implementation using DNA molecules is well established in binary systems (base value of 2) via decoration of hairpin structures on DNA duplexes, systems with base values of >2 (e.g. 3, corresponding to a ternary system) are rarely discussed owing to the complexity of the design and the experimental difficulties with DNA. In this study, DNA rule tiles that participate to form algorithmic DNA crystals exhibiting the ternary representation of an N (N = 1 or 2)-input and 1-output algorithmic assembly are conceived. The number of possible algorithmic patterns is [Formula: see text] in the ternary N-input and 1-output logic gate. Thus, the number of possible rules is 27 (=33) for a 1-input and 1-output algorithmic logic gate and 19 638 (=39) for a 2-input and 1-output algorithmic logic gate. Ternary bit information (i.e. 0-, 1-, and 2-bit) is encoded on rule tiles without hairpins and with short and long hairpins. We construct converged, line-like, alternating, and commutative patterns by implementing specific rules (TR00, TR05, TR07, and TR15, respectively) for the 1-input and 1-output gate and an ascending line-like pattern (with the rule of TR3785) for the 2-input and 1-output gate. Specific patterns generated on ternary-representing rule-embedded algorithmic DNA crystals are visualized via atomic force microscopy, and the errors during the growth of the crystals are analyzed (average error rates obtained for all experimental data are <4%). Our method can easily be extended to a system having base values of >3.

Growth and Detachment of 5 Helix DNA Ribbons.

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.

Highly stable colorimetric aptamer sensors for detection of ochratoxin A through optimizing the sequence with the covalent conjugation of hemin.

Optimization of hairpin DNA is introduced to detect ochratoxin A (OTA) by chemically conjugating its cofactor, hemin, toward the 5'-end. The newly designed OTA aptasensor showed enhanced stability and sensitivity, thereby lowering the detection limit to an ~1 nM level. Furthermore, an optimal spacer for hemin conjugation was investigated for stable responses toward very diluted OTA solutions.

Role of GO and Photoinitiator Concentration on Curing Behavior of PEG-Based Polymer for DLP 3D Printing.

Photocuring kinetics in photopolymerization-based three-dimensional (3D) printing processes have gained significant attention because they determine the final dimension accuracy of the printed structures. In this study, the curing kinetics of liquid-light-curable resins, including water-dispersed graphene oxide (GO) and ultraviolet (UV)-cured acrylic resins, were investigated during digital light processing (DLP) 3D printing. Various stable composites of water-dispersed GO and UV-cured acrylic resin were prepared to fabricate 3D structures for cure-depth measurements. Several factors, including the UV-exposure conditions, photoinitiator concentration, and composition of the photopolymer resin, were found to significantly affect the cure-depth characteristics of the printed structures. The photocuring depth of the polymeric resin system was investigated as a function of the photoinitiator concentration. In addition, the study showed that the introduction of GO played a significant role in controlling the performance of the highly cross-linked network and the thickness of the cured layer. The curing characteristics of functional photocurable polymer-based DLP 3D printing contribute to process development and improvement of the quality of printed microstructures for industrial applications.

Construction and Configuration Analysis of Zelkova Serrata Lenticel-Like Patterns Generated through DNA Algorithmic Self-Assembly.

Multiple models and simulations have been proposed and performed to understand the mechanism of the various pattern formations existing in nature. However, the logical implementation of those patterns through efficient building blocks such as nanomaterials and biological molecules is rarely discussed. This study adopts a cellular automata model to generate simulation patterns (SPs) and experimental patterns (EPs) obtained from DNA lattices similar to the discrete horizontal brown-color line-like patterns on the bark of the Zelkova serrata tree, known as lenticels [observation patterns (OPs)]. SPs and EPs are generated through the implementation of six representative rules (i.e., R004, R105, R108, R110, R126, and R218) in three-input/one-output algorithmic logic gates. The EPs obtained through DNA algorithmic self-assembly are visualized by atomic force microscopy. Three different modules (A, B, and C) are introduced to analyze the similarities between the SPs, EPs, and OPs of Zelkova serrata lenticels. Each module has unique configurations with specific orientations allowing the calculation of the deviation of the SPs and the EPs with respect to the OPs within each module. The findings show that both the SP and the EP generated under R105 and R126 and analyzed with module B provide a higher similarity of Zelkova serrata lenticel-like patterns than the other four rules. This study provides a perspective regarding the use of DNA algorithmic self-assembly for the construction of various complex natural patterns.

Configuration Analysis of a Lizard Skin-like Pattern Formed by DNA Self-Assembly.

Nature manifests diverse and complicated patterns through efficient physical, chemical, and biological processes. One of the approaches to generate complex patterns, as well as simple patterns, is the use of the cellular automata algorithm. However, there are certain limitations to produce such patterns experimentally due to the difficulty of finding candidate programmable building blocks. Here, we demonstrated the feasibility of generating an ocellated lizard skin-like pattern by simulation considering the probabilistic occurrence of cells and constructed the simulation results on DNA lattices via bottom-up self-assembly. To understand the similarity between the simulated pattern (SP) and the observed pattern (OP) of lizard skin, a unique configuration scheme (unit configuration was composed of 7 cells) was conceived. SPs were generated through a computer with a controlling population of gray and black cells in a given pattern. Experimental patterns (EPs) on DNA lattices, consisting of double-crossover (DX) tiles without and with protruding hairpins, were fabricated and verified through atomic force microscopy (AFM). For analyzing the similarity of the patterns, we introduced deviation of the average configuration occurrence for SP and EP with respect to OP, i.e., σα(SO) and σα(EO). The configuration and deviation provide characteristic information of patterns. We recognized that the minimum values of <σα(SO)> and <σα(EO)> occurred when 50% (55%) of black cells in given SPs (DX tiles with hairpins in given EPs) appeared to be most similar to the OP. Our study provides a novel platform for the applicability of DNA molecules to systematically demonstrate other naturally existing complex patterns or processes with ease.

Cathepsin B-Responsive Liposomes for Controlled Anticancer Drug Delivery in Hep G2 Cells.

In recent decades, several types of anticancer drugs that inhibit cancer cell growth and cause cell death have been developed for chemotherapeutic application. However, these agents are usually associated with side effects resulting from nonspecific delivery, which may induce cytotoxicity in healthy cells. To reduce the nonspecific delivery issue, nanoparticles have been successfully used for the delivery of anticancer drugs to specific target sites. In this study, a functional polymeric lipid, PEG-GLFG-K(C16)2 (PEG-GLFG, polyethylene glycol-Gly-Leu-Phe-Gly-Lys(C16)2), was synthesized to enable controlled anticancer drug delivery using cathepsin B enzyme-responsive liposomes. The liposomes composed of PEG-GLFG/DOTAP (1,2-dioleoyl-3-trimethylammonium-propane (chloride salt))/DPPC (dipalmitoylphosphatidylcholine)/cholesterol were prepared and characterized at various ratios. The GLFG liposomes formed were stable liposomes and were degraded when acted upon by cathepsin B enzyme. Doxorubicin (Dox) loaded GLFG liposomes (GLFG/Dox) were observed to exert an effective anticancer effect on Hep G2 cells in vitro and inhibit cancer cell proliferation in a zebrafish model.

Visualization of unstained homo/heterogeneous DNA nanostructures by low-voltage scanning transmission electron microscopy.

Three-dimensional (3D) homo/heterogeneous DNA nanostructures were studied with low-voltage scanning transmission electron microscopy (LV-STEM). Four types of 3D DNA nanostructures were designed and fabricated by the origami method including newly proposed protocols. The low-energy electron probe and optimized dark-field STEM detector enabled individual unstained DNA nanostructures to be clearly imaged by the single acquisition without the averaging process. For the vertically stacked double structures, assembled through modified single-stranded domains, and the structures containing a square opening (i.e., a hole) in the center, the LV-STEM successfully reveals the vertical information of these 3D structures as the contrast differences compared to the reference. For the heterogeneous structures, the LV-STEM visualized both regions of the functionalized gold nanoparticles and the DNA base structure with distinct contrasts. This study introduces a straightforward method to fabricate stackable DNA nanostructures or nanoparticles by replacing a relatively small number of incumbent DNA strands, which could realize the simple and sophisticated fabrication of higher-order 3D DNA homo/hetero nanostructures. Together with these design techniques of DNA nanostructures, this study has demonstrated that the LV-STEM is the swift and simple method for visualizing the 3D DNA nanostructures and certifying the fabricated products as the specified design, which is applicable to various research fields on soft materials including DNA nanotechnology.

Demonstration of Arithmetic Calculations by DNA Tile-Based Algorithmic Self-Assembly.

Owing to its high information density, energy efficiency, and massive parallelism, DNA computing has undergone several advances and made significant contributions to nanotechnology. Notably, arithmetic calculations implemented by multiple logic gates such as adders and subtractors have received much attention because of their well-established logic algorithms and feasibility of experimental implementation. Although small molecules have been used to implement these computations, a DNA tile-based calculator has been rarely addressed owing to complexity of rule design and experimental challenges for direct verification. Here, we construct a DNA-based calculator with three types of building blocks (propagator, connector, and solution tiles) to perform addition and subtraction operations through algorithmic self-assembly. An atomic force microscope is used to verify the solutions. Our method provides a potential platform for the construction of various types of DNA algorithmic crystals (such as flip-flops, encoders, and multiplexers) by embedding multiple logic gate operations in the DNA base sequences.

Calculation of π and Classification of Self-avoiding Lattices via DNA Configuration.

Numerical simulation (e.g. Monte Carlo simulation) is an efficient computational algorithm establishing an integral part in science to understand complex physical and biological phenomena related with stochastic problems. Aside from the typical numerical simulation applications, studies calculating numerical constants in mathematics, and estimation of growth behavior via a non-conventional self-assembly in connection with DNA nanotechnology, open a novel perspective to DNA related to computational physics. Here, a method to calculate the numerical value of π, and way to evaluate possible paths of self-avoiding walk with the aid of Monte Carlo simulation, are addressed. Additionally, experimentally obtained variation of the π as functions of DNA concentration and the total number of trials, and the behaviour of self-avoiding random DNA lattice growth evaluated through number of growth steps, are discussed. From observing experimental calculations of π (πexp) obtained by double crossover DNA lattices and DNA rings, fluctuation of πexp tends to decrease as either DNA concentration or the number of trials increases. Based upon experimental data of self-avoiding random lattices grown by the three-point star DNA motifs, various lattice configurations are examined and analyzed. This new kind of study inculcates a novel perspective for DNA nanostructures related to computational physics and provides clues to solve analytically intractable problems.

Kinetic Trans-Assembly of DNA Nanostructures.

The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic paradigms of DNA nanotechnology, we present a rationally designed synthetic platform that functions in an analogous manner to create complex DNA nanostructures. Starting from one type of DNA nanostructure, DNA strand displacement circuits were designed to interact and pass along the information encoded in the initial structure to mediate the self-assembly of a different type of structure, the final output structure depending on the type of circuit triggered. Using this concept of a DNA structure "trans-assembling" a different DNA structure through nonlocal strand displacement circuitry, four different schemes were implemented. Specifically, 1D ladder and 2D double-crossover (DX) lattices were designed to kinetically trigger DNA circuits to activate polymerization of either ring structures or another type of DX lattice under enzyme-free, isothermal conditions. In each scheme, the desired multilayer reaction pathway was activated, among multiple possible pathways, ultimately leading to the downstream self-assembly of the correct output structure.

Streptavidin-Decorated Algorithmic DNA Lattices Constructed by Substrate-Assisted Growth Method.

The ultimate goal of DNA computing is to store information at higher density and solve complex problems with less computational time and minimal error. Most algorithmic DNA lattices have been constructed using the free-solution growth (FSG) annealing method, and hairpin-embedded DNA rule tiles have been introduced in most algorithmic implementations to differentiate 0- and 1-bit information. Here, we developed streptavidin (SA)-decorated algorithmic COPY (produced line-like patterns with biotinylated 1-bit rule tiles) and XOR (triangle-like patterns) lattices constructed by a substrate-assisted growth (SAG) method and FSG. SA decoration in algorithmic lattices provides an efficient platform for visualizing bit information, and the SAG method in algorithmic assembly offers full coverage of algorithmic lattices on a substrate with a relatively lower DNA concentration than previous methods. The algorithmic COPY and XOR lattices assembled with various ratios of 0- and 1-bit rule tiles were verified by atomic force microscopy. We found that even asymmetric DNA patterns produced by certain algorithmic logic gates could be easily constructed by SAG. Finally, we evaluated sorting factors and error rates of algorithmic COPY and XOR lattices to determine the bit population and quality of the algorithmic assembly. Because of the catalytic effect of the substrate, the sorting factor of algorithmic DX-DNA lattices did not greatly influence the specific rules (i.e., COPY and XOR logic gates) annealed by SAG. Additionally, we found that the overall error rates of algorithmic DX-DNA lattices prepared by the FSG and SAG methods were low, within the range of 1-3%. Hence, the self-assembled algorithmic patterns generated with DNA molecules may serve as a scaffold for molecular demultiplexing circuits and computing.

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%.

Long-Term Stability and Integrity of Plasmid-Based DNA Data Storage.

Validation of long-term DNA stability and integrity are essential for the use of DNA in data storage applications. Because of this, we evaluated the plasmid-based DNA data storage in a manner that preserves DNA stability and integrity. A document consisting of 2046 words was encoded with DNA sequences using Perl script, and the encoded DNA sequences were synthesized for information storage. The DNA comprised a total of 22 chemically synthesized DNA fragments with 400 nucleotides each, which were incorporated into a plasmid vector. A long-term DNA stability study demonstrated that 3-year stored plasmid containing text information showed DNA stability at controlled conditions of -20 °C. The plasmid DNA under accelerated aging conditions (AAC) up to 65 °C for 20 days, which corresponds to approximately 20 years of storage at -20 °C, also exhibited no significant differences in DNA stability compared to newly produced plasmid. Also, the 3-year old plasmid stored at -20 °C and the AAC-tested plasmid stored up to 65 °C for 20 days had functional integrity and nucleotide integrity comparable to control sample, thereby allowing for retrieval of the original error-free text data. Finally, the nucleotides were sequenced, and then decoded to retrieve the original data, thereby allowing us to read the text with 100% accuracy, and amplify the DNA with a simple and quick bacterial transformation. To the best of our knowledge, this is the first report on examining the long-term stability and integrity of plasmid-based DNA data storage. Taken together, our results indicate that plasmid DNA data storage can be useful for long-term archival storage to recover the source text in a reproducible and accountable manner.

Fluorescent polydopamine nanoparticles as a probe for zebrafish sensory hair cells targeted in vivo imaging.

Fluorescent polydopamine nanoparticles (FPNPs) are prepared via the ethylenediamine (EDA)-induced degradation of as-prepared non-fluorescent polydopamine (PDA) and used for targeted bioimaging. The reductive treatment of PDA in the presence of EDA yields fluorescent precipitates, inspiring us to seek various biological approaches to preparing FPNPs with excellent optical and biocompatible properties. Moreover, we firstly found that FPNPs selectively label neuromast hair cells in the lateral line of zebrafish, their applications as a reliable fluorescent indicator to investigate the neuromast hair cells, to in turn determine the viability of hair cells, was demonstrated. FPNPs also provided a minimal toxicity enable to assay the number of functional hair cells per neuromast in live animals as development proceeds. Upon combined incubation with TO-PRO-3, a well-established hair cell marker, all hair cells that were rapidly labeled with FPNPs were observed to be also completely labeled with the TO-PRO-3, labeling hair cells in neuromasts positioned in the supraorbital, otic and occipital lateral line as well as in posterior lateral line of living zebrafish larvae. Their potential efficacy for biological applications was demonstrated by their excellent optical and biocompatible properties, offering new opportunities in cancer research, real-time monitoring of stem cell transplantation and other cell-based therapies.

On-Chip Fluorescence Switching System for Constructing a Rewritable Random Access Data Storage Device.

We report the development of on-chip fluorescence switching system based on DNA strand displacement and DNA hybridization for the construction of a rewritable and randomly accessible data storage device. In this study, the feasibility and potential effectiveness of our proposed system was evaluated with a series of wet experiments involving 40 bits (5 bytes) of data encoding a 5-charactered text (KRIBB). Also, a flexible data rewriting function was achieved by converting fluorescence signals between "ON" and "OFF" through DNA strand displacement and hybridization events. In addition, the proposed system was successfully validated on a microfluidic chip which could further facilitate the encoding and decoding process of data. To the best of our knowledge, this is the first report on the use of DNA hybridization and DNA strand displacement in the field of data storage devices. Taken together, our results demonstrated that DNA-based fluorescence switching could be applicable to construct a rewritable and randomly accessible data storage device through controllable DNA manipulations.

Atomistic evolution during the phase transition on a metastable single NaYF4:Yb,Er upconversion nanoparticle.

The phase evolution of as-prepared NaYF4:Yb,Er upconversion nanoparticles (UCNPs) with a metastable cubic structure is studied based on in situ heating experiments via transmission electron microscopy (TEM). The atomistic behavior on the single NaYF4:Yb,Er UCNP is observed during the phase transition. The formation and evolution of voids on the NaYF4:Yb,Er UCNP appear at a temperature below 420 °C. Small circular voids are transformed at the initial stage to a large, hexagonal-pillar shaped single void. Two different routes to reach the stable α-phase from the metastable cubic structure are identified on a single NaYF4:Yb,Er UCNP. The first is via a stable ß-phase and the second is a direct change via a liquid-like phase. The specific orientation relationships, [110]cubic//[11[Formula: see text]0]hexagonal and {002}cubic//{2[Formula: see text]00}hexagonal, between the cubic and hexagonal structures are confirmed. Additionally, a few extra-half planes terminated in the cubic structures are also observed at the cubic/hexagonal interface.

Fast and sensitive near-infrared fluorescent probes for ALP detection and 3d printed calcium phosphate scaffold imaging in vivo.

Alkaline phosphatase (ALP) is a critical biological marker for osteoblast activity during early osteoblast differentiation, but few biologically compatible methods are available for its detection. Here, we describe the discovery of highly sensitive and rapidly responsive novel near-infrared (NIR) fluorescent probes (NIR-Phos-1, NIR-Phos-2) for the fluorescent detection of ALP. ALP cleaves the phosphate group from the NIR skeleton and substantially alters its photophysical properties, therefore generating a large "turn-on" fluorescent signal resulted from the catalytic hydrolysis on fluorogenic moiety. Our assay quantified ALP activity from 0 to 1.0UmL-1 with a 10-5-10-3UmL-1 limit of detection (LOD), showing a response rate completed within 1.5min. A potentially powerful approach to probe ALP activity in biological systems demonstrated real-time monitoring using both concentration- and time-dependent variations of endogenous ALP in live cells and animals. Based on high binding affinity to bone tissue of phosphate moiety, bone-like scaffold-based ALP detection in vivo was accessed using NIR probe-labeled three-dimensional (3D) calcium deficient hydroxyapatite (CDHA) scaffolds. They were subcutaneously implanted into mice and monitored ALP signal changes using a confocal imaging system. Our results suggest the possibility of early-stage ALP detection during neo-bone formation inside a bone defect, by in vivo fluorescent evaluation using 3D CDHA scaffolds.