2D DNA Lattices Research Articles

2D DNA lattices assembled from DX-coupled tiles

HypothesisFormation of coupled double crossovers (DXs) in a circular 106-mer oligonucleotide (c106nt) could generate stable tiles with the tile core span of 10 half turns. The large-span tiles with complicated curvatures and mechanics could assemble 2D lattices under different environments. Hence, 2D DNA lattice structures based on tile types and sequences, tile packing modes of corrugation and non-corrugation, and assembly media of solution and the substrate-solution interface are yet to be explored. ExperimentsTwo c106nt scaffold strands with different sequences were synthesized. Four types of tiles, two rectilinear and two triangular tiles, were designed and their 2D assemblies were examined by atomic force microscopy (AFM). FindingsThe DX-coupled tiles provided fair strength and rigidity to assemble 2D lattices. Due to the complicated curvature and mechanics of tiles, the two-tile assemblies in solution displayed a few ripe lattices of ribbons, tubes, or polycrystalline aggregates as the minor products and tile oligomers as the major products; whereas the one-tile assemblies via substrate mediation exhibited well-organized monolayer lattices covering the whole mica disk. The herringbone packing patterns were first observed in DNA nanostructures. Based on the lattice constants and the surface coverages of lattices, we estimated the lattice yields for the substrate-mediated assemblies.

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules.

This article presents a detailed protocol for synthesis of small circular DNA molecules, annealing of circular DNA motifs, and construction of 1D and 2D DNA nanostructures. Over decades, the rapid development of DNA nanotechnology is attributed to the use of linear DNAs as the source materials. For example, the DAO (double crossover, antiparallel, odd half-turns) tile is well-known as a building block for construction of 2D DNA lattices; the core structure of DAO is made from two linear single-stranded (ss) oligonucleotides, like two ropes making a right hand grannyknot. Herein, a new type of DNA tiles called cDAO (coupled DAO) are built using a small circular ss-DNA of c64nt or c84nt (circular 64 or 84 nucleotides) as the scaffold strand and several linear ss-DNAs as the staple strands. Perfect 1D and 2D nanostructures are assembled from cDAO tiles: infinite nanowires, nanospirals, nanotubes, nanoribbons; and finite nano-rectangles. Detailed protocols are described: 1) preparation by T4 ligase and purification by denaturing PAGE (polyacrylamide gel electrophoresis) of small circular oligonucleotides, 2) annealing of stable circular tiles, followed by native PAGE analysis, 3) assembling of infinite 1D nanowires, nanorings, nanospirals, infinite 2D lattices of nanotubes and nanoribbons, and finite 2D nano-rectangles, followed by AFM (Atomic Force Microscopy) imaging. The method is simple, robust, and affordable for most labs.

2D DNA lattice arrays assembled from DNA dumbbell tiles using poly(A-T)-rich stems

Poly(A-T)-rich sequences have been applied as stems of DNA dumbbell tiles for construction of single crystalline 2D DNA lattice arrays in slightly acidic solutions. These arrays show much higher stability and better organised crystalline lattice structures than those assembled from DNA dumbbell tiles with randomly sequenced stems in slightly alkaline environments. DNA nanotechnology probably provides a useful platform to study the mechanical properties of DNA duplexes with specific sequences.

2D DNA lattices constructed from two-tile DAE-O systems possessing circular central strands.

We reported a classical two-tile system of DAE-O (doublecrossover, antiparallel, and even half-turns tiles with odd half-turns connection) to construct regular single crystalline 2D (two dimensional) DNA lattices, using pre-circularised oligonucleotides of 42-, 64-, and 84-nt (nucleotides) as the central looped strands in DAE tiles respectively. DAE tiles with 42- and 64-nt as central strands, either in circular form or in linear form, grew regular single crystalline lattices well. However DAE tiles including a circular 84-nt as the central strand grew single crystalline lattices, those including a linear 84-nt as the central strand grew polycrystalline 2D lattices. A subtle difference in the lateral rigidity of DAE tiles with regard to the duplex axis was suggested to be the cause of the morphological difference.

Substrate-assisted 2D DNA lattices and algorithmic lattices from single-stranded tiles.

We present a simple route to circumvent kinetic traps which affect many types of DNA nanostructures in their self-assembly process. Using this method, a new 2D DNA lattice made up of short, single-stranded tile (SST) motifs was created. Previously, the growth of SST DNA assemblies was restricted to 1D (tubes and ribbons) or finite-sized 2D (molecular canvases). By utilizing the substrate-assisted growth method, sets of SSTs were designed as unit cells to self-assemble into periodic and aperiodic 2D lattices which continuously grow both along and orthogonal to the helical axis. Notably, large-scale (∼1 μm(2)) fully periodic 2D lattices were fabricated using a minimum of just 2 strand species. Furthermore, the ability to create 2D lattices from a few motifs enables certain rules to be encoded into these SSTs to carry out algorithmic self-assembly. A set of these motifs was designed to execute simple 1-input 1-output COPY and NOT algorithms, the space-time manifestations which were aperiodic 2D algorithmic SST lattices. The methodology presented here can be straightforwardly applied to other motifs which fall into this type of kinetic trap to create novel DNA crystals.

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, (90)Sr-(90)Y. 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.

The label free DNA sensor using a silicon nanowire array

Biosensors based on silicon nanowire (Si-NW) promise highly sensitive dynamic label free electrical detection of various biological molecules. Here we report Si-NW array electronic devices that function as sensitive and selective detectors of as synthesized 2D DNA lattices with biotins. The Si-NW array was fabricated using top-down approach consists of 250 nanowires of 20 μm in length, equally spaced with an interval of 3.2 μm. Measurements of photoresistivity of the Si-NW array device with streptavidin (SA) attached on biotinylated DNA lattices at different concentration were observed and analyzed.. The conductivity in the DNA lattices with protein SA shows significant change in the photoresistivity of Si-NW array device. This Si-NW based DNA sensor would be one of very efficient devices for direct, label free DNA detection and could provide a pathway to immunological assays, DNA forensics and toxin detection in modern biotechnology.

NMR Studies of Artificial Double-Crossover DNA Tiles

This report documents the design and characterization of DNA molecular nanoarchitectures consisting of artificial double crossover DNA tiles with different geometry and chemistry. The Structural characterization of the unit tiles, including normal, biotinylated and hairpin loop structures, are morphologically studied by atomic force microscopy. The specific proton resonance of the individual tiles and their intra/inter nucleotide relationships are verified by proton nuclear magnetic resonance spectroscopy and 2-dimensional correlation spectral studies, respectively. Significant up-field and down-field shifts in the resonance signals of the individual residues at various temperatures are discussed. The results suggest that with artificially designed DNA tiles it is feasible to obtain structural information of the relative base sequences. These tiles were later fabricated into 2D DNA lattice structures for specific applications such as protein arrangement by biotinylated bulged loops or pattern generation using a hairpin structure.

Photoresistivity and optical switching of graphene with DNA lattices

We present the photon induced conductivity of 2D DNA lattices with and without graphene and demonstrate the switching current responses controlled by light irradiation. The conductivity in the DNA lattices with protein streptavidin controlled by blue and white lights shows significant enhancement with the addition of graphene. An optical pulse response of a graphene immobilized DNA lattice is encouraging and may lead to various bio-sensing applications such as immunological assays, DNA forensics, and toxin detection.

Assembly of Fullerene Arrays Templated by DNA Scaffolds

A water-soluble fullerene, C60-N,N-dimethylpyrrolidinium iodide, was dispersed in aqueous media in the form of vesicles. By mixing and incubating the fullerene vesicle and a 2D DNA lattice bearing a phosphate-labeled protruded strand together, pearl-like arrays of fullerene domains can be obtained on the DNA template.