Modular self-assembly of DNA lattices with tunable periodicity.
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Buffers↗
Biomedical subjects
Hao Yan
Publications and source records attributed to Hao Yan.
Three-helix bundle DNA tiles self-assemble into 2D lattice or 1D templates for silver nanowires.
We present a DNA nanostructure, the three-helix bundle (3HB), which consists of three double helical DNA domains connected by six immobile crossover junctions such that the helix axes are not coplanar. The 3HB motif presents a triangular cross-section with one helix lying in the groove formed by the other two. By differential programming of sticky-ends, 3HB tiles can be arrayed in two distinct lattice conformations: one-dimensional filaments and two-dimensional lattices. Filaments and lattices have been visualized by high-resolution, tapping mode atomic force microscopy (AFM) under buffer. Their dimensions are shown to be in excellent agreement with designed structures. We also demonstrate an electroless chemical deposition for fabricating metallic nanowires templated on self-assembled filaments. The metallized nanowires have diameters down to 20 nm and display Ohmic current-voltage characteristic.
DNA↗
Programmable DNA self-assemblies for nanoscale organization of ligands and proteins.
We demonstrate the precise control of periodic spacing between individual protein molecules by programming the self-assembly of DNA tile templates. In particular, we report the application of two self-assembled periodic DNA structures, two-dimensional nanogrids, and one-dimensional nanotrack, as template for programmable self-assembly of streptavidin protein arrays with controlled density.
DNA↗
Materials science. Nucleic acid nanotechnology.
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Algorithms↗
A unidirectional DNA walker that moves autonomously along a track.
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DNA↗
Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology.
Paranemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.
Circular Dichroism↗
DNA-templated self-assembly of protein and nanoparticle linear arrays.
Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Here we report an experiment using a linear array of DNA triple crossover tiles to controllably template the self-assembly of single-layer or double-layer linear arrays of streptavidin molecules and streptavidin-conjugated nanogold particles through biotin-streptavidin interaction. The organization of streptavidin and its conjugated gold nanoparticles into periodic arrays was visualized by atomic force microscopy and scanning electron microscopy.
Biotin↗
Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly.
Self-assembling DNA nanostructures are an efficient means of executing parallel molecular computations. However, previous experimental demonstrations of computations by DNA tile self-assembly only allowed for one set of distinct input to be processed at a time. Here, we report the multibit, parallel computation of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. A set of DNA tiles encoding the truth table for the XOR logical operation was constructed. Parallel tile self-assembly and ligation led to the formation of reporter DNA strands which encoded both the input and the output of the computations. These reporter strands provided a molecular look-up table containing all possible pairwise XOR calculations up to a certain input size. The computation was readout by sequencing the cloned reporter strands. This is the first experimental demonstration of a parallel computation by DNA tile self-assembly in which a large number of distinct input were simultaneously processed.
DNA↗
DNA-templated self-assembly of protein arrays and highly conductive nanowires.
A DNA nanostructure consisting of four four-arm junctions oriented with a square aspect ratio was designed and constructed. Programmable self-assembly of 4 x 4 tiles resulted in two distinct lattice morphologies: uniform-width nanoribbons and two-dimensional nanogrids, which both display periodic square cavities. Periodic protein arrays were achieved by templated self-assembly of streptavidin onto the DNA nanogrids containing biotinylated oligonucleotides. On the basis of a two-step metallization procedure, the 4 x 4 nanoribbons acted as an excellent scaffold for the production of highly conductive, uniform-width, silver nanowires.
Biotinylation↗
A two-state DNA lattice switched by DNA nanoactuator.
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DNA↗
Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices.
The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.
Base Sequence↗
[Interferon alpha-2b inhibits rabbit corneal haze induced by PRK].
OBJECTIVES: To evaluate the effect of interferon alpha-2b on the treatment of corneal haze after PRK. METHODS: 36 rabbits were divided into three groups (A.B.C). The refractive degree of ablation was -4.00 D, -8.00 D, -10.00 D in each group respectively. The treatment given in group A was 1 x 10(5) IU/ml interferon alpha-2b, in group B 0.1% dexamethasone and placebo eyedrops for group C after PRK 2 months. Corneal haze, histopathologic response, intraocular pressure (IOP) were investigated. RESULTS: Less corneal haze was observed in group A and B. Postoperative IOP was higher than that of preoperation in group B. Keratocytes and fibrotic response in corneal stroma were active up to 2 months in group C. CONCLUSIONS: Interferon alpha-2b was effective on inhibition of corneal haze after PRK.
Animals↗
Paranemic cohesion of topologically-closed DNA molecules.
Specific cohesion of DNA molecules is key to the success of work in biotechnology, DNA nanotechnology and DNA-based computation. The most common form of intermolecular cohesion between double helices is by sticky ends, but sticky ends generated by naturally occurring restriction enzymes may often be too short to bind large constructs together. An alternative form of binding is available through the paranemic crossover (PX) motif. Each of the two components of a PX motif can be a DNA dumbbell or other topologically closed species. Alternate half-turns of the dumbbell are paired intramolecularly. The intervening half-turns are paired with those of the opposite component. We demonstrate the efficacy of PX cohesion by showing that it can result in the 1:1 binding of two triangle motifs, each containing nearly 500 nucleotides. The cohesion goes to completion, demonstrating an alternative to binding nucleic acid molecules through sticky ends.
DNA↗
A robust DNA mechanical device controlled by hybridization topology.
Controlled mechanical movement in molecular-scale devices has been realized in a variety of systems-catenanes and rotaxanes, chiroptical molecular switches, molecular ratchets and DNA-by exploiting conformational changes triggered by changes in redox potential or temperature, reversible binding of small molecules or ions, or irradiation. The incorporation of such devices into arrays could in principle lead to complex structural states suitable for nanorobotic applications, provided that individual devices can be addressed separately. But because the triggers commonly used tend to act equally on all the devices that are present, they will need to be localized very tightly. This could be readily achieved with devices that are controlled individually by separate and device-specific reagents. A trigger mechanism that allows such specific control is the reversible binding of DNA strands, thereby 'fuelling' conformational changes in a DNA machine. Here we improve upon the initial prototype system that uses this mechanism but generates by-products, by demonstrating a robust sequence-dependent rotary DNA device operating in a four-step cycle. We show that DNA strands control and fuel our device cycle by inducing the interconversion between two robust topological motifs, paranemic crossover (PX) DNA and its topoisomer JX2 DNA, in which one strand end is rotated relative to the other by 180 degrees. We expect that a wide range of analogous yet distinct rotary devices can be created by changing the control strands and the device sequences to which they bind.
Base Pairing↗