DNA-controlled excitonic switches.
Ontology highlight
ABSTRACT:
SUBMITTER: Graugnard E
PROVIDER: S-EPMC3324986 | biostudies-literature | 2012 Apr
REPOSITORIES: biostudies-literature
Publications
DNA-controlled excitonic switches.
Graugnard Elton E Kellis Donald L DL Bui Hieu H Bui Hieu H Barnes Stephanie S Kuang Wan W Lee Jeunghoon J Hughes William L WL Knowlton William B WB Yurke Bernard B
Nano letters 20120315 4
Fluorescence resonance energy transfer (FRET) is a promising means of enabling information processing in nanoscale devices, but dynamic control over exciton pathways is required. Here, we demonstrate the operation of two complementary switches consisting of diffusive FRET transmission lines in which exciton flow is controlled by DNA. Repeatable switching is accomplished by the removal or addition of fluorophores through toehold-mediated strand invasion. In principle, these switches can be networ ...[more]
Similar Datasets
Project description:Controlled non-local energy and coherence transfer enables light harvesting in photosynthesis and non-local logical operations in quantum computing. This process is intuitively pictured by a pair of mechanical oscillators, coupled by a spring, allowing for a reversible exchange of excitation. On a microscopic level, the most relevant mechanism of coherent coupling of distant quantum bits--like trapped ions, superconducting qubits or excitons confined in semiconductor quantum dots--is coupling via the electromagnetic field. Here we demonstrate the controlled coherent coupling of spatially separated quantum dots via the photon mode of a solid state microresonator using the strong exciton-photon coupling regime. This is enabled by two-dimensional spectroscopy of the sample's coherent response, a sensitive probe of the coherent coupling. The results are quantitatively understood in a rigorous description of the cavity-mediated coupling of the quantum dot excitons. This mechanism can be used, for instance in photonic crystal cavity networks, to enable a long-range, non-local coherent coupling.
| S-EPMC3644086 | biostudies-other
Project description:A promising application of DNA self-assembly is the fabrication of chromophore-based excitonic devices. DNA brick assembly is a compelling method for creating programmable nanobreadboards on which chromophores may be rapidly and easily repositioned to prototype new excitonic devices, optimize device operation, and induce reversible switching. Using DNA nanobreadboards, we have demonstrated each of these functions through the construction and operation of two different excitonic AND logic gates. The modularity and high chromophore density achievable via this brick-based approach provide a viable path toward developing information processing and storage systems.
| S-EPMC4370369 | biostudies-literature
Project description:We report a combined theoretical/experimental study of dynamic screening of excitons in media with frequency-dependent dielectric functions. We develop an analytical model showing that interparticle interactions in an exciton are screened in the range of frequencies from zero to the characteristic binding energy depending on the symmetries and transition energies of that exciton. The problem of the dynamic screening is then reduced to simply solving the Schrodinger equation with an effectively frequency-independent potential. Quantitative predictions of the model are experimentally verified using a test system: neutral, charged and defect-bound excitons in two-dimensional monolayer WS2, screened by metallic, liquid, and semiconducting environments. The screening-induced shifts of the excitonic peaks in photoluminescence spectra are in good agreement with our model.
| S-EPMC5768700 | biostudies-literature
Project description:DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
| S-EPMC10642627 | biostudies-literature
Project description:Spiropyran dyes were attached to fluorescent core-shell CdSe/ZnS nanocrystals via thiol-containing linkers. Photoisomerization of the dye to its merocyanine form by UV irradiation caused a dramatic loss in the intrinsic nanoparticle fluorescence, which was regained upon reversing the isomerization with visible light. The fluorescence quenching efficiency increased with increasing spectral overlap of fluorescence emission and merocyanine adsorption bands, consistent with FRET as the quenching mechanism. Typically, complete quenching required at least 80 bound dye molecules per particle.
| S-EPMC1435833 | biostudies-literature
Project description:Nucleosidic diarylethenes (DAEs) are an emerging class of photochromes but have rarely been used in materials science. Here, we have developed doubly methylated DAEs derived from 2'-deoxyuridine with high thermal stability and fatigue resistance. These new photoswitches not only outperform their predecessors but also rival classical non-nucleosidic DAEs. To demonstrate the utility of these new DAEs, we have designed an all-optical excitonic switch consisting of two oligonucleotides: one strand containing a fluorogenic double-methylated 2'-deoxyuridine as a fluorescence donor and the other a tricyclic cytidine (tC) as acceptor, which together form a highly efficient conditional Förster-Resonance-Energy-Transfer (FRET) pair. The system was operated in liquid and solid phases and showed both strong distance- and orientation-dependent photochromic FRET. The superior ON/OFF contrast was maintained over up to 100 switching cycles, with no detectable fatigue.
| S-EPMC9305942 | biostudies-literature
Project description:A 1,2,3-triazole-based chemosensor is used for selective switching in logic gate operations through colorimetric and fluorometric response mechanisms. The molecular probe synthesized via "click chemistry" resulted in a non-fluorescent 1,4-diaryl-1,2,3-triazole with a phenol moiety (PTP). However, upon sensing fluoride, it TURNS ON the molecule's fluorescence. The TURN-OFF order occurs through fluorescence quenching of the sensor when metal ions, e.g., Cu2+, and Zn2+, are added to the PTP-fluoride ensemble. A detailed characterization using Nuclear Magnetic Resonance (NMR) spectroscopy in a sequential titration study substantiated the photophysical characteristics of PTP through UV-Vis absorption and fluorescence profiles. A combination of fluorescence OFF-ON-OFF sequences provides evidence of 1,2,3-triazoles being controlled switches applicable to multimodal logic operations. The "INH" gate was constructed based on the fluorescence output of PTP when the inputs are F- and Zn2+. The "IMP" and "OR" gates were created on the colorimetric output responses using the probe's absorption with multiple inputs (F- and Zn2+ or Cu2+). The PTP sensor is the best example of the "Write-Read-Erase-Read" mimic.
| S-EPMC10422406 | biostudies-literature
Project description:Circumventing the limitations of current bioassays, we introduce a light-controlled assay, OptoAssay, toward wash- and pump-free point-of-care diagnostics. Extending the capabilities of standard bioassays with light-dependent and reversible interaction of optogenetic switches, OptoAssays enable a bidirectional movement of assay components, only by changing the wavelength of light. Demonstrating exceptional versatility, the OptoAssay showcases its efficacy on various substrates, delivering a dynamic bioassay format. The applicability of the OptoAssay is successfully demonstrated by the calibration of a competitive model assay, resulting in a superior limit of detection of 8 pg ml-1, which is beyond those of conventional ELISA tests. In the future, combined with smartphones, OptoAssays could obviate the need for external flow control systems such as pumps or valves and signal readout devices, enabling on-site analysis in resource-limited settings.
| S-EPMC11423887 | biostudies-literature
Project description:Control over the strength of excitonic coupling in molecular dye aggregates is a substantial factor for the development of technologies such as light harvesting, optoelectronics, and quantum computing. According to the molecular exciton model, the strength of excitonic coupling is inversely proportional to the distance between dyes. Covalent DNA templating was proved to be a versatile tool to control dye spacing on a subnanometer scale. To further expand our ability to control photophysical properties of excitons, here, we investigated the influence of dye hydrophobicity on the strength of excitonic coupling in squaraine aggregates covalently templated by DNA Holliday Junction (DNA HJ). Indolenine squaraines were chosen for their excellent spectral properties, stability, and diversity of chemical modifications. Six squaraines of varying hydrophobicity from highly hydrophobic to highly hydrophilic were assembled in two dimer configurations and a tetramer. In general, the examined squaraines demonstrated a propensity toward face-to-face aggregation behavior observed via steady-state absorption, fluorescence, and circular dichroism spectroscopies. Modeling based on the Kühn-Renger-May approach quantified the strength of excitonic coupling in the squaraine aggregates. The strength of excitonic coupling strongly correlated with squaraine hydrophobic region. Dimer aggregates of dichloroindolenine squaraine were found to exhibit the strongest coupling strength of 132 meV (1065 cm-1). In addition, we identified the sites for dye attachment in the DNA HJ that promote the closest spacing between the dyes in their dimers. The extracted aggregate geometries, and the role of electrostatic and steric effects in squaraine aggregation are also discussed. Taken together, these findings provide a deeper insight into how dye structures influence excitonic coupling in dye aggregates covalently templated via DNA, and guidance in design rules for exciton-based materials and devices.
| S-EPMC8883467 | biostudies-literature
Project description:Here we demonstrate the rational design of allosterically controllable, metal-ion-triggered molecular switches. Specifically, we designed DNA sequences that adopt two low energy conformations, one of which does not bind to the target ion and the other of which contains mismatch sites serving as specific recognition elements for mercury(II) or silver(I) ions. Both switches contain multiple metal binding sites and thus exhibit homotropic allosteric (cooperative) responses. As heterotropic allosteric effectors we employ single-stranded DNA sequences that either stabilize or destabilize the nonbinding state, enabling dynamic range tuning over several orders of magnitude. The ability to rationally introduce these effects into target-responsive switches could be of value in improving the functionality of DNA-based nanomachines.
| S-EPMC3831027 | biostudies-literature