Site-specific assembly of DNA-based photonic wires by using programmable polyamides.
Ontology highlight
ABSTRACT:
SUBMITTER: Su W
PROVIDER: S-EPMC3210824 | biostudies-literature | 2011 Mar
REPOSITORIES: biostudies-literature
Publications
Site-specific assembly of DNA-based photonic wires by using programmable polyamides.
Su Wu W Schuster Markus M Bagshaw Clive R CR Rant Ulrich U Burley Glenn A GA
Angewandte Chemie (International ed. in English) 20110225 12
Similar Datasets
Project description:Three-dimensional dielectric photonic crystals have well-established enhanced light-matter interactions via high Q factors. Their plasmonic counterparts based on arrays of nanoparticles, however, have not been experimentally well explored owing to a lack of available synthetic routes for preparing them. However, such structures should facilitate these interactions based on the small mode volumes associated with plasmonic polarization. Herein we report strong light-plasmon interactions within 3D plasmonic photonic crystals that have lattice constants and nanoparticle diameters that can be independently controlled in the deep subwavelength size regime by using a DNA-programmable assembly technique. The strong coupling within such crystals is probed with backscattering spectra, and the mode splitting (0.10 and 0.24 eV) is defined based on dispersion diagrams. Numerical simulations predict that the crystal photonic modes (Fabry-Perot modes) can be enhanced by coating the crystals with a silver layer, achieving moderate Q factors (∼10(2)) over the visible and near-infrared spectrum.
| S-EPMC4313827 | biostudies-literature
Project description:DNA demonstrates a remarkable capacity for creating designer nanostructures and devices. A growing number of these structures utilize Förster resonance energy transfer (FRET) as part of the device's functionality, readout or characterization, and, as device sophistication increases so do the concomitant FRET requirements. Here we create multi-dye FRET cascades and assess how well DNA can marshal organic dyes into nanoantennae that focus excitonic energy. We evaluate 36 increasingly complex designs including linear, bifurcated, Holliday junction, 8-arm star and dendrimers involving up to five different dyes engaging in four-consecutive FRET steps, while systematically varying fluorophore spacing by Förster distance (R0). Decreasing R0 while augmenting cross-sectional collection area with multiple donors significantly increases terminal exciton delivery efficiency within dendrimers compared with the first linear constructs. Förster modelling confirms that best results are obtained when there are multiple interacting FRET pathways rather than independent channels by which excitons travel from initial donor(s) to final acceptor.
| S-EPMC4275599 | biostudies-literature
Project description:Our ability to synthesize nanometre-scale chemical species, such as nanoparticles with desired shapes and compositions, offers the exciting prospect of generating new functional materials and devices by combining them in a controlled fashion into larger structures. Self-assembly can achieve this task efficiently, but may be subject to thermodynamic and kinetic limitations: reactants, intermediates and products may collide with each other throughout the assembly time course to produce non-target species instead of target species. An alternative approach to nanoscale assembly uses information-containing molecules such as DNA to control interactions and thereby minimize unwanted cross-talk between different components. In principle, this method should allow the stepwise and programmed construction of target products by linking individually selected nanoscale components-much as an automobile is built on an assembly line. Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and are attached in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo. As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an 'ON' state, allowing its cargo to be transferred to the walker, and an 'OFF' state, in which no transfer occurs. We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.
| S-EPMC2872101 | biostudies-literature
Project description:Combining surface-initiated, TdT (terminal deoxynucleotidyl transferase) catalyzed enzymatic polymerization (SI-TcEP) with precisely engineered DNA origami nanostructures (DONs) presents an innovative pathway for the generation of stable, polynucleotide brush-functionalized DNA nanostructures. We demonstrate that SI-TcEP can site-specifically pattern DONs with brushes containing both natural and non-natural nucleotides. The brush functionalization can be precisely controlled in terms of the location of initiation sites on the origami core and the brush height and composition. Coarse-grained simulations predict the conformation of the brush-functionalized DONs that agree well with the experimentally observed morphologies. We find that polynucleotide brush-functionalization increases the nuclease resistance of DONs significantly, and that this stability can be spatially programmed through the site-specific growth of polynucleotide brushes. The ability to site-specifically decorate DONs with brushes of natural and non-natural nucleotides provides access to a large range of functionalized DON architectures that would allow for further supramolecular assembly, and for potential applications in smart nanoscale delivery systems.
| S-EPMC8511278 | biostudies-literature
Project description:Magnetic iron oxide nanoparticles (IONPs) have received significant interest for the use in biomedical applications. The assembly of IONPs into larger superstructures has been used to modify the properties and functionality of these particles. For example, the clustering of IONPs can lead to improvements in MRI contrast generation, changes in heat generation during magnetic fluid hyperthermia, and alterations to pharmacokinetics and biodistribution. Nevertheless, the IONP clustering leads to significant heterogeneity in the assembly. Here, we demonstrate a method for using DNA origami to precisely control the number and positions of IONPs. We also showed how this technique can be used to module the functionality of IONP clusters by showing how MRI contrast generation efficiency can be tuned by altering the number and spacing of IONPs. Finally, we show that these property changes can be dynamically regulated, demonstrating the possibility for this technology to be used in biosensing applications.
| S-EPMC7252324 | biostudies-literature
Project description:Programmable site-specific nucleases promise to unlock myriad applications in basic biology research, biotechnology and gene therapy. Gene-editing systems have revolutionized our ability to engineer genomes across diverse eukaryotic species. However, key challenges, including delivery, specificity and targeting organellar genomes, pose barriers to translational applications. Here, we use peptide nucleic acids (PNAs) to facilitate precise DNA strand invasion and unwinding, enabling prokaryotic Argonaute (pAgo) proteins to specifically bind displaced single-stranded DNA and introduce site-specific double-strand breaks (DSBs) independent of the target sequence. We named this technology PNA-assisted pAgo editing (PNP editing) and determined key parameters for designing PNP editors to efficiently generate programable site-specific DSBs. Our design allows the simultaneous use of multiple PNP editors to generate multiple site-specific DSBs, thereby informing design considerations for potential in vitro and in vivo applications, including genome editing.
| S-EPMC10516665 | biostudies-literature
Project description:Natural systems display sophisticated control of light-matter interactions at multiple length scales for light harvesting, manipulation, and management, through elaborate photonic architectures and responsive material formats. Here, we combine programmable photonic function with elastomeric material composites to generate optomechanical actuators that display controllable and tunable actuation as well as complex deformation in response to simple light illumination. The ability to topographically control photonic bandgaps allows programmable actuation of the elastomeric substrate in response to illumination. Complex three-dimensional configurations, programmable motion patterns, and phototropic movement where the material moves in response to the motion of a light source are presented. A "photonic sunflower" demonstrator device consisting of a light-tracking solar cell is also illustrated to demonstrate the utility of the material composite. The strategy presented here provides new opportunities for the future development of intelligent optomechanical systems that move with light on demand.
| S-EPMC7955034 | biostudies-literature
Project description:Site-specific nucleases are crucial for genome engineering applications in medicine and agriculture. The ideal site-specific nucleases are easily reprogrammable, highly specific in target site recognition, and robust in nuclease activities. Prokaryotic Argonaute (pAgo) proteins have received much attention as biotechnological tools due to their ability to recognize specific target sequences without a protospacer adjacent motif, but their lack of intrinsic dsDNA unwinding activity limits their utility in key applications such as gene editing. Recently, we developed a pAgo-based system for site-specific DNA cleavage at physiological temperatures independently of the DNA form, using peptide nucleic acids (PNAs) to facilitate unwinding dsDNA targets. Here, we fused catalytically dead pAgos with the nuclease domain of the restriction endonuclease FokI and named this modified platform PNA-assisted FokI-(d)pAgo (PNFP) editors. In the PNFP system, catalytically inactive pAgo recognizes and binds to a specific target DNA sequence based on a programmable guide DNA sequence; upon binding to the target site, the FokI domains dimerize and introduce precise dsDNA breaks. We explored key parameters of the PNFP system including the requirements of PNA and guide DNAs, the specificity of PNA and guide DNA on target cleavage, the optimal concentration of different components, reaction time for invasion and cleavage, and ideal temperature and reaction buffer, to ensure efficient DNA editing in vitro. The results demonstrated robust site-specific target cleavage by PNFP system at optimal conditions in vitro. We envision that the PNFP system will provide higher editing efficiency and specificity with fewer off-target effects in vivo.
| S-EPMC11421335 | biostudies-literature
Project description:Controlling topological phases of light allows the observation of abundant topological phenomena and the development of robust photonic devices. The prospect of more sophisticated control with topological photonic devices for practical implementations requires high-level programmability. Here we demonstrate a fully programmable topological photonic chip with large-scale integration of silicon photonic nanocircuits and microresonators. Photonic artificial atoms and their interactions in our compound system can be individually addressed and controlled, allowing the arbitrary adjustment of structural parameters and geometrical configurations for the observation of dynamic topological phase transitions and diverse photonic topological insulators. Individual programming of artificial atoms on the generic chip enables the comprehensive statistical characterization of topological robustness against relatively weak disorders, and counterintuitive topological Anderson phase transitions induced by strong disorders. This generic topological photonic chip can be rapidly reprogrammed to implement multifunctionalities, providing a flexible and versatile platform for applications across fundamental science and topological technologies.
| S-EPMC11230904 | biostudies-literature
Project description:Programmable photonic integrated circuits (PICs) are emerging as powerful tools for control of light, with applications in quantum information processing, optical range finding, and artificial intelligence. Low-power implementations of these PICs involve micromechanical structures driven capacitively or piezoelectrically but are often limited in modulation bandwidth by mechanical resonances and high operating voltages. Here we introduce a synchronous, micromechanically resonant design architecture for programmable PICs and a proof-of-principle 1×8 photonic switch using piezoelectric optical phase shifters. Our design purposefully exploits high-frequency mechanical resonances and optically broadband components for larger modulation responses on the order of the mechanical quality factor Qm while maintaining fast switching speeds. We experimentally show switching cycles of all 8 channels spaced by approximately 11 ns and operating at 4.6 dB average modulation enhancement. Future advances in micromechanical devices with high Qm, which can exceed 10000, should enable an improved series of low-voltage and high-speed programmable PICs.
| S-EPMC10673894 | biostudies-literature