A surface‐assisted fabrication scheme enables direct surface coverage control of functionalized DNA nanostructures on centimeter‐scaled silica (SiO2) substrates from 0 to 100 % (see picture). Electrostatic interactions between the DNA structures and the surface lead to dramatic topological changes of the structures, thereby creating novel formations of the crystals.
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-replication and derive a quantitative metric of the self-replicability of the rings.
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.
We report on the energy band gap and optical transition of a series of divalent metal ion (Cu(2+), Ni(2+), Zn(2+), and Co(2+)) 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 Ni(2+), 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.
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.
DNA has become a promising resource for self-organized material and has provided a particular degree of freedom to current nanotechnology for several decades. [1] The exceptional programmability of DNA, i.e., the ability to artificially design the DNA base sequence, allows highly selective binding for creating complex DNA nanostructures in all dimensions. [2][3][4][5] Additionally, since these DNA nanostructures can be easily conjugated with various heteromaterials, such as proteins, [3,6] nanoparticles [7,8] or nanowires, [6,9] by simple molecular modification, it makes DNA nanostructures one of the most viable biomaterials for use with current techniques. Although many developments took advantage of these characteristics, what has been lacking in DNA nanotechnology is sufficient investigation into specific interactions between DNA nanostructures and metal ions. Due to DNA's poor conductivity, [10] many scientists have been tried to enhance its electrical properties by metal modification on a single duplex DNA. [11,12] Since a modified single duplex DNA shows improved electric characteristics compared with bare DNA, the metal-modifying process on artificially designed DNA nanostructures should not be overlooked when trying to utilize DNA's full potential. If any mechanisms for metal-ion modification of DNA nanostructures were found, it would facilitate research into fields such as bioelectronics and biophotonics. In light of this, we report on the fabrication of size-controllable DNA structures using non-cross-over DNA motifs and the interaction mechanism between DNA structures and divalent copper ions (Cu 2+ ) used for metal modification.Three different sizes of DNA rings-named 'ringn', where n denotes the relative size of structures-were designed from non-cross-over-based DNA motifs. [13] Two different types of DNA motifs, core and extension, were used for structure fabrication, and each DNA motif had three duplex DNAs connected by single-stranded regions. Each motif has two single-stranded bulged sections in the body and complementary single-stranded segments at both ends of the helix, which take on the role of 'sticky-end' base pairs, as shown in Figure 1a. When two complementary parts are hybridized during the annealing process, the Watson-Crick base paring results in bending of the adjacent duplex perpendicularly and forms a DNA junction. The schematic diagrams of the building blocks and ring-1, -2, and -3 are shown in Figure 1. During assembly, the building blocks are grown unidirectionally with different duplex lengths of the core motif, which leads to the polydispersion of the building blocks with an extrinsic angle change. Typically 12 × n building blocks are required to fabricate the rings, and each building block comprised 1 core and (n-1) extension motifs. The final three ringn rings have diameters of about 21, 48, and 75 nm. Figure 2a-c shows the atomic force microscopy (AFM) images of ring-1 to -3 with size analyses in the inset images clearly showing the different sizes of each ring. Although the...
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.
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.
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