DNA lattice growth with single, double, and triple double-crossover boundaries by stepwise self-assembly.

Construction of various nanostructures with nanometre-scale precision through various DNA building blocks depends upon self-assembly, base-pair complementarity and sequence programmability. During annealing, unit tiles are formed by the complementarity of base pairs in each strand. Enhancement of growth of target lattices is expected if seed lattices (i.e. boundaries for growth of target lattices) are initially present in a test tube during annealing. Although most processes for annealing DNA nanostructures adopt a one-step high temperature method, multi-step annealing provides certain advantages such as reusability of unit tiles and tuneability of lattice formation. We can construct target lattices effectively (through multi-step annealing) and efficiently (via boundaries) by multi-step annealing and combining boundaries. Here, we construct efficient boundaries made of single, double, and triple double-crossover DNA tiles for growth of DNA lattices. Two unit double-crossover DNA tile-based lattices and copy-logic implemented algorithmic lattices were introduced to test the growth of target lattices on boundaries. We used multi-step annealing to tune the formation of DNA crystals during fabrication of DNA crystals comprised of boundaries and target lattices. The formation of target DNA lattices was visualized using atomic force microscopy (AFM). The borders between boundaries and lattices in a single crystal were clearly differentiable from AFM images. Our method provides way to construct various types of lattices in a single crystal, which might generate various patterns and enhance the information capacity in a given crystal.

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.

DNA foams constructed by freeze drying and their optoelectronic characteristics.

The distinctive properties of DNA make it a promising biomaterial to use in nanoscience and nanotechnology. In the present study, DNA foam was fabricated into multi-dimensional shapes using a freeze drying process with liquid nitrogen and 3D printed molds. The physicochemical and optoelectronic properties of the fabricated DNA foams were investigated using Fourier transform infrared (FTIR) spectrum, X-ray photoelectron spectrum (XPS), thermogravimetric analysis (TGA), ultraviolet-visible (UV-Vis) absorption spectrum, and current-voltage (I-V) characteristics to understand the changes formed in the DNA structure and their effect on properties during the fabrication of DNA foam. The FTIR and XPS analyses confirmed that nitrogen was diffusing into the DNA structure during the DNA foam fabrication. The diffused nitrogen caused a decrease in bond lengths, strong chemical bonds, compaction of DNA structure, existence of additional carbon-nitrogen bonds, and variation in the electron density of the base elements in DNA. These changes in the DNA structure of the DNA foam were reflected in their chemical, optical, and electrical properties. Furthermore, the proper utilization of DNA foams as a template for functional materials by embedding carbon nanotubes (CNTs) and thermocolor was demonstrated.

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.

Fibres and films made from DNA and CTMA-modified DNA embedded with gold nanorods and organic light-emitting materials.

The scaffolding of deoxyribonucleic acid (DNA) makes DNA molecules effective templates for hosting various types of nanomaterials. Recently, electrospun fibres formed by a variety of polymers have begun to see use in a number of applications, such as filtration in energy applications, insulation in thermodynamics and protein scaffolding in biomedicine. In this study, we constructed electrospun fibres and thin films made of DNA and cetyltrimethylammonium chloride (CTMA)-modified DNA (CDNA) embedded with dyes, organic light-emitting materials (OLEMs), and gold nanorods (GNRs). These materials provide significant advantages, including selectivity of dimensionality, solubility in organic and inorganic solvents, and functionality enhancement. In addition, coaxial fibres made of CDNA were constructed to demonstrate the feasibility of constructing relatively complex fibres with an electrospinner. To determine the basic physical characteristics of the fibres and thin films containing GNRs and OLEMs, we conducted current measurements, photoluminescence (PL) measurements, X-ray photoelectron spectroscopy (XPS), and ultraviolet-visible (UV-Vis) spectroscopy. The currents in DNA and CDNA were found to exhibit Ohmic behaviour, while the PL emission could be controlled by OLEMs. In addition, the XPS provided the chemical configuration of samples, and the UV-Vis spectra revealed the plasmon resonance of GNR. Due to their simple fabrication and enhanced functionality, these DNA and CDNA fibres and thin films could be used in various devices (e.g., filters or blocking layers) and sensors (e.g., gas detectors and bio sensors) in a number of industries.

Multi-Domains in a Single Lattice Formed by DNA Self-Assembly.

Using sequence programmability and the characteristics of self-assembly, DNA has been utilized in the construction of various nanostructures and the placement of specific patterns on lattices. Even though many complex structures and patterns formed by DNA assembly have been reported, the fabrication of multi-domain patterns in a single lattice has rarely been discussed. Multi-domains possessing specifically designed patterns in a single lattice provide the possibility to generate multiple patterns that enhance the pattern density in a given single lattice. Here, we introduce boundaries to construct double- and quadruple-domains with specific patterns in a single lattice and verify them with atomic force microscopy. ON, OFF, and ST (stripe) patterns on a lattice are made of DNA tiles with hairpins (ON), without hairpins (OFF), and alternating DNA tiles without and with hairpins (formed as a stripe, ST). For double- and quadruple-domain lattices, linear and cross boundaries were designed to fabricate two (e.g., ON and OFF, ON and ST, and OFF and ST) and four (OFF, ST, OFF, and ON) different types of patterns in single lattices, respectively. In double-domain lattices, each linear boundary is placed between two different domains. Similarly, four linear boundaries connected with a seed tile (i.e., a cross boundary) can separate four domains in a single lattice in quadruple-domain lattices. Due to the presence of boundaries, the pattern growth directions are different in each domain. The experimentally obtained multi-domain patterns agree well with our design. Lastly, we propose the possibility of the construction of a hexadomain lattice through the mapping from hexagonal to square grids converted by using an axial coordinate system. By proposing a hexadomain lattice design, we anticipate the possibility to extend to higher numbers of multi-domains in a single lattice, thereby further increasing the information density in a given lattice.

Nanomaterial-Embedded DNA Films on 2D Frames.

Recently, 3D printing has provided opportunities for designing complex structures with ease. These printed structures can serve as molds for complex materials such as DNA and cetyltrimethylammonium chloride (CTMA)-modified DNA that have easily tunable functionalities via the embedding of various nanomaterials such as ions, nanoparticles, fluorophores, and proteins. Herein, we develop a simple and efficient method for constructing DNA flat and curved films containing water-soluble/thermochromatic dyes and di/trivalent ions and CTMA-modified DNA films embedded with organic light-emitting molecules (OLEM) with the aid of 2D/3D frames made by a 3D printer. We study the Raman spectra, current, and resistance of Cu2+-doped and Tb3+-doped DNA films and the photoluminescence of OLEM-embedded CTMA-modified DNA films to better understand the optoelectric characteristics of the samples. Compared to pristine DNA, ion-doped DNA films show noticeable variation of Raman peak intensities, which might be due to the interaction between the ion and phosphate backbone of DNA and the intercalation of ions in DNA base pairs. As expected, ion-doped DNA films show an increase of current with an increase in bias voltage. Because of the presence of metallic ions, DNA films with embedded ions showed relatively larger current than pristine DNA. The photoluminescent emission peaks of CTMA-modified DNA films with OLEMRed, OLEMGreen, and OLEMBlue were obtained at the wavelengths of 610, 515, and 469 nm, respectively. Finally, CIE color coordinates produced from CTMA-modified DNA films with different OLEM color types were plotted in color space. It may be feasible to produce multilayered DNA films as well. If so, multilayered DNA films embedded with different color dyes, ions, fluorescent materials, nanoparticles, proteins, and drug molecules could be used to realize multifunctional physical devices such as energy harvesting and chemo-bio sensors in the near future.

The Effects of Forest Therapy on Immune Function.

We conducted a systematic review of the effects of a forest therapy program on adults' immune function. We used PICO-SD (participants, interventions, comparisons, outcomes, study design) to identify key items. The participants were adults over the age of 18 and the intervention was forest therapy. Our comparisons included studies that comparatively analyzed urban groups or groups that did not participate in forest therapy intervention. Cases without control groups were also included. Immunological outcome measures were included in measuring intervention outcomes. All experimental studies, such as randomized controlled trials (RCTs), non-equivalent control group designs (non-RCTs), and one-group pretest-posttest design were included in the study design. A total of 13 studies were included for comparison. Forest therapy programs were divided into lodging-type and session-type programs. The representative measures for evaluating the effects of immune function were the number of NK cells, the cytotoxic activity of NK cells, and cytotoxic effector molecules. Most studies reported improvement in these measures when comparing values after intervention with values before the forest therapy intervention. Therefore, forest therapy has been found to be effective in improving immune function. More RCT studies on the effects of forest therapy on immune function are necessary.

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.

Demonstration of elementary functions via DNA algorithmic self-assembly.

Target-oriented cellular automata with computation are the primary challenge in the field of DNA algorithmic self-assembly in connection with specific rules. We investigate the feasibility of using the principle of cellular automata for mathematical subjects by using specific logic gates that can be implemented into DNA building blocks. Here, we connect the following five representative elementary functions: (i) enumeration of multiples of 2, 3, and 4 (demonstrated via R094, R062, and R190 in 3-input/1-output logic rules); (ii) the remainder of 0 and 1 (R132); (iii) powers of 2 (R129); (iv) ceiling function for n/2 and n/4 (R152 and R144); and (v) analogous pattern of annihilation (R184) to DNA algorithmic patterns formed by specific rules. After designing the abstract building blocks and simulating the generation of algorithmic lattices, we conducted an experiment as follows: designing of DNA tiles with specific sticky ends, construction of DNA lattices via a two-step annealing method, and verification of expected algorithmic patterns on a given DNA lattice using an atomic force microscope (AFM). We observed representative patterns, such as horizontal and diagonal stripes and embedded triangles, on the given algorithmic lattices. The average error rates of individual rules are in the range of 8.8% (R184) to 11.9% (R062), and the average error rate for all the rules was 10.6%. Interpretation of elementary functions demonstrated through DNA algorithmic patterns could be extended to more complicated functions, which may lead to new insights for achieving the final answers of functions with experimentally obtained patterns.

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.

Use of the Bispectral Index to Predict Eye Position of Children during General Anesthesia.

PURPOSE: To assess the relationship between eye position and anesthesia depth using the bispectral index (BIS) value, a parameter derived from electroencephalography data. METHODS: We investigated the relationship between BIS value and eye position in 32 children who underwent surgery for epiblepharon under general anesthesia. BIS values were recorded continuously throughout the procedure (from induction to awakening). Eye positions were video-recorded and analyzed after surgery. The vertical position of each eye was scored according to its height in relation to the medial canthus. An eye position in which the upper eyelid covered one-third of the cornea was defined as a significant ocular elevation. RESULTS: The BIS value correlated inversely with the end-tidal concentration of each anesthetic agent, whereas it correlated positively with the eye elevation score (eye position = 0.014 × BIS + 0.699, p = 0.011). The mean eye position score was significantly greater in patients whose BIS values were over 65. Eleven patients (34.4%) had significant ocular elevation; their mean concurrent BIS value was 61.6. Two of these patients had elevation during surgery and 9 had elevation during emergence from anesthesia. CONCLUSIONS: We found that high BIS values were correlated with low levels of anesthetic concentration and high eye position, suggesting that BIS monitoring may be useful for predicting eye position during anesthesia. Particular attention must be given to eye position during ophthalmic surgery. Anesthesia depth can be maintained by assuring that the BIS value remains below 65.

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%.

Technical approaches of a natural dye extracted from Phytolacca americana L.-berries with chemical mordants.

Phytolacca americana L. is a large semi-succulent herbaceous plant which reaches three meters in height. It is native to eastern North America, the Midwest, and the Gulf Coast, with more scattered populations in the far West. It is imported into Korea and has been frequently used as a traditional natural drug for diseases such as systemic edema and nephritis. Its berries, that is, fruits are shiny dark purple held in racemous clusters on pink pedicels with a pink peduncle. They are round with a flat indented top and bottom. Immature berries are green, maturing into white and then blackish purple. It is not well known how the berries are used for a natural staining yet. In this study, using Phytolacca americana L.-berries, a natural staining was analyzed. Moreover, due to the broad use of chemical mordants, five different mordants including copper acetate, aluminum potassium sulfate, sodium tartrate plus citric acid, Iron II sulfate and potassium dichromate were combined. Extracted dye from the berries stained silk fabrics with ivory. The original purple color from the berries disappeared and transformed into ivory. Although the silk fabrics were differentially stained by the berries that were combined with mordants of aluminum potassium sulfate, sodium tartrate plus citric acid and potassium dichromate, only differences in lightness and darkness were observed. Interestingly, the combination of the dye from the berries with a mordant of copper acetate and Iron II sulfate induced the staining of the silk fabrics into khaki and dark khaki, respectively. This study is the first systemic report on staining silk fabrics with Phytolacca americana L.-berries and chemical mordants and suggests application of natural products to the fiber industry.