345 research outputs found
Experimental Progress in Computation by Self-Assembly of DNA Tilings
Approaches to DNA-based computing by self-assembly require the
use of D. T A nanostructures, called tiles, that have efficient chemistries, expressive
computational power: and convenient input and output (I/O) mechanisms.
We have designed two new classes of DNA tiles: TAO and TAE, both
of which contain three double-helices linked by strand exchange. Structural
analysis of a TAO molecule has shown that the molecule assembles efficiently
from its four component strands. Here we demonstrate a novel method for
I/O whereby multiple tiles assemble around a single-stranded (input) scaffold
strand. Computation by tiling theoretically results in the formation of structures
that contain single-stranded (output) reported strands, which can then
be isolated for subsequent steps of computation if necessary. We illustrate the
advantages of TAO and TAE designs by detailing two examples of massively
parallel arithmetic: construction of complete XOR and addition tables by linear
assemblies of DNA tiles. The three helix structures provide flexibility for
topological routing of strands in the computation: allowing the implementation
of string tile models
Is J 133658.3-295105 a Radio Source at z >= 1.0 or at the Distance of M 83?
We present Gemini optical imaging and spectroscopy of the radio source J
133658.3-295105. This source has been suggested to be the core of an FR II
radio source with two detected lobes. J 133658.3-295105 and its lobes are
aligned with the optical nucleus of M 83 and with three other radio sources at
the M 83 bulge outer region. These radio sources are neither supernova remnants
nor H II regions. This curious configuration prompted us to try to determine
the distance to J 133658.3-295105. We detected H_alpha emission redshifted by ~
130 km s^-1 with respect to an M 83 H II region 2.5" east-southeast of the
radio source. We do not detect other redshifted emission lines of an optical
counterpart down to m_i = 22.2 +/- 0.8. Two different scenarios are proposed:
the radio source is at z >= 2.5, a much larger distance than the previously
proposed lower limit z >= 1.0, or the object was ejected by a gravitational
recoil event from the M 83 nucleus. This nucleus is undergoing a strong
dynamical evolution, judging from previous three-dimensional spectroscopy.Comment: 6 pages, 4 figure
Coupling Strategies for the Synthesis of Peptide-Oligonucleotide Conjugates for Patterned Synthetic Biomineralization
This work describes preparation strategies for peptide-oligonucleotide conjugates that combine the self-assembling behavior of DNA oligonucleotides with the molecular recognition capabilities of peptides. The syntheses include a solution-phase fragment coupling reaction and a solid-phase fragment coupling strategy where the oligonucleotide has been immobilized on DEAE Sepharose. The yield of four coupling reagents is evaluated, two reagents in water, EDC (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride) and DMTMM (4-(4,6-dimethoxy[1,3,5]triazin-2-yl)-4-methyl-morpholinium chloride), and two in dimethylformamide (DMF), PyBOP ((Benzotriazol-1-yloxy) tripyrrolidinophosphonium hexafluorophosphate) and HBTU (O-benzotriazole-N,N,N′,N′-tetramethyluronium hexafluorophosphate), while the oligonucleotide fragment is either in solution or immobilized on DEAE. These coupling strategies rely on an unprotected 5′ amino linker on the oligonucleotide reacting with the peptide C-terminus. The peptide, selected from a combinatorial library for its gold-binding behavior, was 12 amino acids long with an N-terminus acetyl cap. Formation of the conjugates was confirmed by gel electrophoresis and mass spectrometry while molecular recognition functionality of the peptide portion was verified using atomic force microscopy. Solution-phase yields were superior to their solid-phase counterparts. EDC resulted in the highest yield for both solution-phase (95%) and solid-phase strategies (24%), while the DMF-based reagents, PyBOP and HBTU, resulted in low yields with reduced recovery. All recoverable conjugates demonstrated gold nanoparticle templating capability
Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes
This paper extends the study and prototyping of unusual DNA motifs, unknown in nature, but founded
on principles derived from biological structures. Artificially designed DNA complexes show promise as building
blocks for the construction of useful nanoscale structures, devices, and computers. The DNA triple crossover
(TX) complex described here extends the set of experimentally characterized building blocks. It consists of
four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by
strand exchange at four immobile crossover points. The topology selected for this TX molecule allows for the
presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of
DNA-based computation. Nucleotide sequence design for the synthetic strands was assisted by the application
of algorithms that minimize possible alternative base-pairing structures. Synthetic oligonucleotides were purified,
stoichiometric mixtures were annealed by slow cooling, and the resulting DNA structures were analyzed by
nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical
autofootprinting provide strong evidence for the assembly of the strands to the target TX structure. Ligation
of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded
two-dimensional crystals in two different arrangements. Future applications of TX units include the construction
of larger structures from multiple TX units, and DNA-based computation. In addition to the presence of reporter
strands, potential advantages of TX units over other DNA structures include space for gaps in molecular arrays,
larger spatial displacements in nanodevices, and the incorporation of well-structured out-of-plane components
in two-dimensional arrays
Programming DNA Tube Circumferences
Synthesizing molecular tubes with monodisperse, programmable circumferences is an important goal shared by nanotechnology, materials science, and supermolecular chemistry. We program molecular tube circumferences by specifying the complementarity relationships between modular domains in a 42-base single-stranded DNA motif. Single-step annealing results in the self-assembly of long tubes displaying monodisperse circumferences of 4, 5, 6, 7, 8, 10, or 20 DNA helices
Self-replication and evolution of DNA crystals
Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required
Stepwise Self-Assembly of DNA Tile Lattices Using dsDNA Bridges
The simple helical motif of double-strand DNA (dsDNA) has typically been judged to be uninteresting for assembly in DNA-based nanotechnology applications. In this letter, we demonstrate construction of superstructures consisting of heterogeneous DNA motifs using dsDNA in conjunction with more complex, cross-tile building blocks. Incorporation of dsDNA bridges in stepwise assembly processes can be used for controlling length and directionality of superstructures and is analogous to the “reprogramming” of sticky-ends displayed on the DNA tiles. Two distinct self-assembled DNA lattices, fixed-size nanoarrays, and extended 2D crystals of nanotracks with nanobridges, are constructed and visualized by high-resolution, liquid-phase atomic force microscopy
Sensitization of Transforming Growth Factor-β Signaling by Multiple Peptides Patterned on DNA Nanostructures
We report sensitization of a cellular signaling pathway by addition of functionalized DNA nanostructures. Signaling by transforming growth factor β (TGFβ) has been shown to be dependent on receptor clustering. By patterning a DNA nanostructure with closely spaced peptides that bind to TGFβ we observe increased sensitivity of NMuMG cells to TGFβ ligand. This is evidenced by translocation of secondary messenger proteins to the nucleus and stimulation of an inducible luciferase reporter at lower concentrations of TGFβ ligand. We believe this represents an important initial step towards realization of DNA as a self assembling and biologically compatible material for use in tissue engineering and drug delivery
The Emergence of Complexity: Lessons from DNA
The same molecular qualities that endowed DNA with its capacity to carry hereditary information make it a powerful tool to explore the self-assembly of complex nanostructure
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