<i>M</i>‑State and <i>N</i>‑Color (<i>M</i>–<i>N</i> = 1–1, 2–1, and 1–2) Turing Algorithms Demonstrated via DNA Self-Assembly

The fast and extensive generation of patterns using specific algorithms is a major challenge in the field of DNA algorithmic self-assembly. Turing machines (TMs) are simple computable machines that execute certain algorithms using carefully designed logic gates. We investigate Turing algorithms for the generation of patterns on algorithmic lattices using specific logic gates. Logic gates can be implemented into Turing building blocks. We discuss comprehensive methods for designing Turing building blocks to demonstrate an M-state and N-color Turing machine (M–N TM). The M-state and N-color (M–N = 1–1, 2–1, and 1–2) TMs generate Turing patterns that can be fabricated via DNA algorithmic self-assembly. The M–N TMs require two-input and three-output logic gates. We designed the head, tape, and transition rule tiles to demonstrate TMs for the 1–1, 2–1, and 1–2 Turing algorithms. By analyzing the characteristics of the Turing patterns, we classified them into two classes (DL and DR for states grown diagonally to the left and right, respectively) for the 1–1 TM, three for the 2–1 TM, and nine for the 1–2 TM. Among these, six representative Turing patterns generated using rules R11-0 and R11-1 for 1–1 TM, R21-01 and R21-09 for 2–1 TM, and R12-02 and R12-08 for 1–2 TM were constructed with DNA building blocks. Turing patterns on the DNA lattices were visualized by atomic force microscopy. The Turing patterns on the DNA lattices were similar to those simulated patterns. Implementing the Turing algorithms into DNA building blocks, as demonstrated via DNA algorithmic self-assembly, can be extended to a higher order of state and color to generate more complicated patterns, compute arithmetic operations, and solve mathematical functions

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 <i>M</i>-input/<i>N</i>-output logic gate implemented into simple DNA building blocks. To date, no experimental demonstrations have been reported with <i>M</i> > 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%

Morphological and Optoelectronic Characteristics of Double and Triple Lanthanide Ion-Doped DNA Thin Films

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

Multidimensional Honeycomb-like DNA Nanostructures Made of C‑Motifs

Thanks to its remarkable properties of self-assembly and molecular recognition, DNA can be used in the construction of various dimensional nanostructures to serve as templates for decorating nanomaterials with nanometer-scale precision. Accordingly, this study discusses a design strategy for fabricating such multidimensional DNA nanostructures made of simple C-motifs. One-dimensional (1D) honeycomb-like tubes (1HTs) and two-dimensional (2D) honeycomb-like lattices (2HLs) were constructed using a C-motif with an arm length of 14 nucleotides (nt) at an angle of 240° along the counterclockwise direction. We designed and fabricated four different types of 1HTs and three different 2HLs. The study used atomic force microscopy to characterize the distinct topologies of the 1D and 2D DNA nanostructures (i.e., 1HTs and 2HLs, respectively). The width deviation of the 1HTs and height suppression percentage of the 2HLs were calculated and discussed. Our study can be provided to construct various dimensional DNA nanostructures easily with high efficiency

n- and p‑Type Doping Phenomenon by Artificial DNA and M‑DNA on Two-Dimensional Transition Metal Dichalcogenides

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 (<i>V</i>_TH, 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

Energy Band Gap and Optical Transition of Metal Ion Modified Double Crossover DNA Lattices

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

A 2D DNA Lattice as an Ultrasensitive Detector for Beta Radiations

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

Combining Protein-Shelled Platinum Nanoparticles with Graphene to Build a Bionanohybrid Capacitor

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

Long dsRNA-Mediated RNA Interference and Immunostimulation: A Targeted Delivery Approach Using Polyethyleneimine Based Nano-Carriers

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

Nature-Inspired Construction of Two-Dimensionally Self-Assembled Peptide on Pristine Graphene

Peptide assemblies have received significant attention because of their important role in biology and applications in bionanotechnology. Despite recent efforts to elucidate the principles of peptide self-assembly for developing novel functional devices, peptide self-assembly on two-dimensional nanomaterials has remained challenging. Here, we report nature-inspired two-dimensional peptide self-assembly on pristine graphene via optimization of peptide–peptide and peptide–graphene interactions. Two-dimensional peptide self-assembly was designed based on statistical analyses of >10⁴ protein structures existing in nature and atomistic simulation-based structure predictions. We characterized the structures and surface properties of the self-assembled peptide formed on pristine graphene. Our study provides insights into the formation of peptide assemblies coupled with two-dimensional nanomaterials for further development of nanobiocomposite devices