Water-Soluble, Thermostable, Photomodulated Color-Switching Quantum Dots

Hybrid Nucleic Acid-Quantum Dot Assemblies as Multiplexed Reporter Platforms for Cell-Free Transcription Translation-Based Biosensors

Cell-free synthetic biology has emerged as a valuable tool for the development of rapid, portable biosensors that can be readily transported in the freeze-dried form to the point of need eliminating cold chain requirements. One of the challenges associated with cell-free sensors is the ability to simultaneously detect multiple analytes within a single reaction due to the availability of a limited set of fluorescent and colorimetric reporters. To potentially provide multiplexing capabilities to cell-free biosensors, we designed a modular semiconductor quantum dot (QD)-based reporter platform that is plugged in downstream of the transcription-translation functionality in the cell-free reaction and which converts enzymatic activity in the reaction into distinct optical signals. We demonstrate proof of concept by converting restriction enzyme activity, utilized as our prototypical sensing output, into optical changes across several distinct spectral output channels that all use a common excitation wavelength. These hybrid Förster resonance energy transfer (FRET)-based QD peptide PNA-DNA-Dye reporters (QD-PDDs) are completely self-assembled and consist of differentially emissive QD donors paired to a dye-acceptor displayed on a unique DNA encoding a given enzyme's cleavage site. Three QD-based PDDs, independently activated by the enzymes BamHI, EcoRI, and NcoI, were prototyped in mixed enzyme assays where all three demonstrated the ability to convert enzymatic activity into fluorescent output. Simultaneous monitoring of each of the three paired QD-donor dye-acceptor spectral channels in cell-free biosensing reactions supplemented with added linear genes encoding each enzyme confirmed robust multiplexing capabilities for at least two enzymes when co-expressed. The modular QD-PDDs are easily adapted to respond to other restriction enzymes or even proteases if desired.

Construction of a photo-controlled fluorescent switching with diarylethene modified carbon dots

Photo-controlled fluorescent switching is of great utility in fluorescence sensors, reversible data storage, and logic circuit, based on their modifiable emission intensity and spectra. In this work, a novel photo-controlled reversible fluorescent switching system was constructed based on photochromic diarylethene (DT) molecular modified fluorescent carbon dots (CDs). The fluorescent CDs acted as fluorescent donors and the photochromic diarylethene molecular functioned as acceptors in this fluorescent switching system. The fluorescence modulation efficiency of the fluorescent switching was determined to be 97.1%. The result was attributable to Förster resonance energy transfer between the CDs and the diarylethene molecular. The fluorescent switching could undergo 20 cycles without significant decay.

Photofluorochromic water-dispersible nanoparticles for single-photon-absorption upconversion cell imaging

Photofluorochromic diarylethene (DAE) molecules have been widely investigated due to their excellent fatigue resistance and thermal stability. However, the poor water solubility of DAEs limits their biological applications to some extent. Herein, we reported two kinds of water-dispersible DAE nanoparticles (DAEI-NPs and DAEB-NPs), in which DAE molecules were stabilized by the amphiphilic polymer DSPE-mPEG2000 using the nanoprecipitation approach. The fabricated nanoparticles retain well-controlled luminescence and fluorescence photoswitching properties in aqueous solution, which could be reversibly switched on and off under the alternating irradiation of ultraviolet (UV) and visible light. In addition, the closed-ring isomers of DAEB-NPs performed hot-band-absorption-based photon upconversion when excited by a 593.5 nm laser. Bearing excellent photophysical properties and low cytotoxicity, DAEB-NPs were applicable for upconversion cell imaging without high-excitation power density and free from oxygen removal. Additionally, the imaging process could be switched on by regulating the photofluorochromic nanoparticles.

Switchable Circularly Polarized Luminescence in Supramolecular Gels through Photomodulated FRET

While the tremendous deal of efforts has been dedicated to the design and fabrication of materials with circularly polarized luminescence (CPL), the development of the chiroptical switch between different CPL signals is one of the important routes toward its application. Here, we prepared a supramolecular gel from the coassemblies containing a chiral gelator (9-fluoren-methoxycarbonyl-functionalized glutamate derivatives, FLG), a fluorescent molecule [(rhodamine B, RhB) or (2',7'-dichlorofluorescein sodium salt, DCF)], and a photochromic molecule [1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)-3,3,4,4,5,5-hexafluoro-1-cyclopentene, DAE], thus constructing photomodulated switchable CPL soft materials. It was found that FLG could form supramolecular gel in ethanol and self-assemble into left-handed twisted nanostructures. During the formation of a co-gel with RhB (or DCF) and DAE, the chirality of FLG could be effectively transferred to both the fluorescent and photochromic components, which induced them with chiroptical properties including CPL and circular dichroism (CD). DAE undergoes a reversible transition between the achromatous open state and the dark purple closed state in the co-gel under alternating irradiation with UV and visible light. During such a process, an intermolecular Förster resonance energy transfer (FRET) behavior from fluorescent RhB to ring-closed DAE caused the emission quenching of RhB, which led to CPL silence of RhB in the co-gel. Subsequent irradiation with visible light caused the restoration of the emission and CPL activity with the restored open state. These changes could be repeated many times upon alternate UV and visible irradiation. Therefore, a reversible CPL switch was fabricated in supramolecular gels through the photomodulated FRET process.

Temperature and pH Responsive Light-Harvesting System Based on AIE-Active Microgel for Cell Imaging

A highly emissive microgel is synthesized by polymerizing tetraphenylethene (TPE) based comonomers, acrylic acid, NIPAM, and permanent crosslinker ethylenebisacrylamide (BIS) (named as TPE microgel), which exhibited temperature responsive fluorescence emission. Rhodamine B (RhB), a positively charged molecule, is then inserted onto the surface of fabricated microgels through electrostatic interaction. As a result, a novel artificial light harvesting system with high energy transfer efficiency is constructed (named as TPE microgel-RhB light harvesting system), which is the first light harvesting system based on TPE microgels presenting dual response to pH and temperature. MTT assay indicates the fabricated TPE microgel and TPE microgel-RhB light harvesting system has good cytocompatibility. The strong fluorescence and good cytocompatibility make them perfect candidates for cell imaging. The prepared emissive microgel and light-harvesting system with desirable fluorescent property not only provide a new strategy for the fabrication of tunable luminescent nanomaterials, but also expand potential applications in the fields of stomach recognition, temperature sensors, and drug delivery.

Light-Triggered Switching of Quantum Dot Photoluminescence through Excited-State Electron Transfer to Surface-Bound Photochromic Molecules

This paper describes reversible "on-off" switching of the photoluminescence (PL) intensity of CdSe quantum dots (QDs), mediated by photochromic furylfulgide carboxylate (FFC) molecules chemisorbed to the surfaces of the QDs. Repeated cycles of UV and visible illumination switch the FFC between "closed" and "open" isomers. Reversible switching of the QDs' PL intensity by >80% is enabled by different rates and yields of PL-quenching photoinduced electron transfer (PET) from the QDs to the respective isomers. This difference is consistent with cyclic voltammetry measurements and density functional calculations of the isomers' frontier orbital energies. This work demonstrates fatigue-resistant modulation of the PL of a QD-molecule complex through remote control of PET. Such control potentially enables applications, such as all-optical memory, sensing, and imaging, that benefit from a fast, tunable, and reversible response to light stimuli.

A simplicity-guided cocktail approach toward multicolor fluorescent systems

A molecular cocktail containing two photochromic diarylethene derivatives that displays multicolor emission spanning blue-green to orange in a color-correlated fashion has been devised. The function does not rely on excited state communication such as energy transfer reactions, which is the typical case for similar systems. Instead, harnessing the intrinsic fluorescent and photochromic properties of the two individual diarylethene derivatives run in parallel is enough to realize the color changes. This offers an extremely flexible situation as for the choice of the fluorophores and their respective concentrations. The function is conveniently demonstrated in bulk solution at μM concentrations, where a single light source serves as the color changing stimulus.

Multi-color emission with orthogonal input triggers from a diarylethene pyrene-OTHO organogelator cocktail

A cocktail combination of stimuli responsive materials, a photoswitch and gelator, is used for multicolored emission tuning.

An all-photonic full color RGB system based on molecular photoswitches

On-command changes in the emission color of functional materials is a sought-after property in many contexts. Of particular interest are systems using light as the external trigger to induce the color changes. Here we report on a tri-component cocktail consisting of a fluorescent donor molecule and two photochromic acceptor molecules encapsulated in polymer micelles and we show that the color of the emitted fluorescence can be continuously changed from blue-to-green and from blue-to-red upon selective light-induced isomerization of the photochromic acceptors to the fluorescent forms. Interestingly, isomerization of both acceptors to different degrees allows for the generation of all emission colors within the red-green-blue (RGB) color system. The function relies on orthogonally controlled FRET reactions between the blue emitting donor and the green and red emitting acceptors, respectively.

Stimuli-responsive multicolor luminescent materials typically react on external triggers of physical nature, but photonically controlled systems which allow for remote operation were not realized. Here the authors use light as the stimulus of a responsive luminescent material which eliminates the need for physical access.

Post-Modification of the Ethene Bridge in the Rational Design of Photochromic Diarylethenes

Fine-tuning of the molecular structure of organic bistable compounds to improve their photochromic performance or to introduce additional functions remains an important issue in the development of photoresponsive materials. Diarylethenes bearing heterocyclic moieties belong to the most intensively studied class of organic photochromes due to their excellent photochemical properties. A huge number of diarylethenes have been synthesized so far. Analysis of the literature data shows that there are very worthy examples of diarylethenes developed by the Irie and Feringa groups, which can be the common starting material for a number of diarylethenes functionalized in hetaryl moieties. We refer to these structures as photochromic diarylethene precursors. These diarylethenes have proved to be very useful in the construction of functional molecules with desired properties. On the other hand, in our groups, we have elaborated on diarylethene precursors with modifiable ethene bridges. In this review, we have collected examples of such structures and their chemical modifications, leading to the improvement or fine-tuning of photochromic switching.

The Growing Development of DNA Nanostructures for Potential Healthcare-Related Applications

DNA self-assembly has proven to be a highly versatile tool for engineering complex and dynamic biocompatible nanostructures from the bottom up with a wide range of potential bioapplications currently being pursued. Primary among these is healthcare, with the goal of developing diagnostic, imaging, and drug delivery devices along with combinatorial theranostic devices. The path to understanding a role for DNA nanotechnology in biomedical sciences is being approached carefully and systematically, starting from analyzing the stability and immune-stimulatory properties of DNA nanostructures in physiological conditions, to estimating their accessibility and application inside cellular and model animal systems. Much remains to be uncovered but the field continues to show promising results toward developing useful biomedical devices. This review discusses some aspects of DNA nanotechnology that makes it a favorable ingredient for creating nanoscale research and biomedical devices and looks at experiments undertaken to determine its stability in vivo. This is presented in conjugation with examples of state-of-the-art developments in biomolecular sensing, imaging, and drug delivery. Finally, some of the major challenges that warrant the attention of the scientific community are highlighted, in order to advance the field into clinically relevant applications.

Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors

DNA can process information through sequence-based reorganization but cannot typically receive input information from most biological processes and translate that into DNA compatible language. Coupling DNA to a substrate responsive to biological events can address this limitation. A two-component sensor incorporating a chimeric peptide-DNA substrate is evaluated here as a protease-to-DNA signal convertor which transduces protease activity through DNA gates that discriminate between different input proteases. Acceptor dye-labeled peptide-DNAs are assembled onto semiconductor quantum dot (QD) donors as the input gate. Addition of trypsin or chymotrypsin cleaves their cognate peptide sequence altering the efficiency of Förster resonance energy transfer (FRET) with the QD and frees a DNA output which interacts with a tetrahedral output gate. Downstream output gate rearrangement results in FRET sensitization of a new acceptor dye. Following characterization of component assembly and optimization of individual steps, sensor ability to discriminate between the two proteases is confirmed along with effects from joint interactions where potential for cross-talk is highest. Processing multiple bits of information for a sensing outcome provides more confidence than relying on a single change especially for the discrimination between different targets. Coupling other substrates to DNA that respond similarly could help target other types of enzymes.

Reversible regulation of CdTe quantum dots fluorescence intensity based on Prussian blue with high anti-fatigue performance

A fluorescence switching device with excellent anti-fatigue performance based on the electrochromic material Prussian blue and fluorophore CdTe quantum dots was realized. The fluorescence switching device ultimately demonstrated a high fluorescence contrast, short response time and superior anti-fatigue property. Notably, the fluorescence contrast remains unchanged after 133 cycles.

Increased Transfer Efficiency from Molecular Photonic Wires on Solid Substrates and Cryogenic Conditions

Molecular photonic wires (MPWs) are tunable nanophotonic structures capable of capturing and directing light with high transfer efficiencies. DNA-based assembly techniques provide a simple and economical preparation method for MPWs that allows precise positioning of the molecular transfer components. Unfortunately, the longest DNA-based MPWs (∼30 nm) report only modest transfer efficiencies of ∼2% and have not been demonstrated on solid-state platforms. Here, we demonstrate that DNA-based MPWs can be spin-coated in a polymer matrix onto silicon wafers and exhibit a 5-fold increase in photonic transfer efficiency over solution-phase MPWs. Cooling these MPWs to 5 K led to further efficiency increases ranging from ∼40 to 240% depending on the length of the MPW. The improvement of MPW energy transport efficiencies advances prospects for their incorporation in a variety of optoelectronics technologies and makes them an ideal test bed for further exploration of nanoscale energy transfer.

Inorganic Nanoparticles as Donors in Resonance Energy Transfer for Solid-Phase Bioassays and Biosensors

Bioassays for the rapid detection and quantification of specific nucleic acids, proteins, and peptides are fundamental tools in many clinical settings. Traditional optical emission methods have focused on the use of molecular dyes as labels to track selective binding interactions and as probes that are sensitive to environmental changes. Such dyes can offer good detection limits based on brightness but typically have broad emission bands and suffer from time-dependent photobleaching. Inorganic nanoparticles such as quantum dots and upconversion nanoparticles are photostable over prolonged exposure to excitation radiation and tend to offer narrow emission bands, providing a greater opportunity for multiwavelength multiplexing. Importantly, in contrast to molecular dyes, nanoparticles offer substantial surface area and can serve as platforms to carry a large number of conjugated molecules. The surface chemistry of inorganic nanoparticles offers both challenges and opportunities for the control of solubility and functionality for selective molecular interactions by the assembly of coatings through coordination chemistry. This report reviews advances in the compositional design and methods of conjugation of inorganic quantum dots and upconversion nanoparticles and the assembly of combinations of nanoparticles to achieve energy exchange. Our interest is the exploration of configurations where the modified nanoparticles can be immobilized to solid substrates for the development of bioassays and biosensors that operate by resonance energy transfer (RET).

Kinetic enhancement in high-activity enzyme complexes attached to nanoparticles

Accumulating studies by many groups have found consistent enhancement in a wide variety of enzyme activities when they are displayed around nanoparticles. However, the underlying mechanism(s) that give rise to this phenomenon are still largely unknown. Herein, we develop a detailed reaction scheme that considers many of the various possible interactions between a substrate and a given enzyme-nanoparticle bioconjugate. The properties and some functional predictions that emanate from the reaction scheme were then tested using a model system where the homotetrameric beta-galactosidase enzyme complex was assembled with luminescent semiconductor nanocrystalline quantum dots displayed around its periphery. This type of assembly occurs as the ∼465 kDa enzyme complex is significantly larger than the 4.2 nm diameter green emitting quantum dots utilized. This unique architecture, in conjunction with the fact that this enzyme functions at or near the diffusion limit, provided a unique opportunity to selectively probe certain aspects of enzyme enhancement when attached to a nanoparticle with minimal potential perturbations to the native enzyme structure. Experimental assays were conducted where both free enzymes and quantum dot-decorated enzymes were compared directly in side-by-side samples and included formats where the kinetic processes were challenged with increasing viscosity and competitive inhibitors. The results strongly suggest that it is possible for there to be significant enhancements in an enzyme's catalytic rate or k_cat after attachment to a nanoparticle even when it is apparently diffusion limited without requiring any gross changes to the enzyme's structure. A discussion of how this reaction scheme and model can be applied to other systems is provided.

ESIPT and FRET probes for monitoring nanoparticle polymer coating stability

Coating strategies of inorganic nanoparticles (NPs) can provide properties unavailable to the NP core alone, such as targeting, specific sensing, and increased biocompatibility. Non-covalent amphiphilic NP capping polymers function via hydrophobic interactions with surface ligands and are extensively used to transfer NPs to aqueous media. For applications of coated NPs as actuators (sensors, markers, or for drug delivery) in a complex environment, such as biological systems, it is important to achieve a deep understanding of the factors affecting coating stability and behavior. We have designed a system that tests the coating stability of amphiphilic polymers through a simple fluorescent readout using either polarity sensing ESIPT (excited state intramolecular proton transfer) dyes or NP FRET (Förster resonance energy transfer). The stability of the coating was determined in response to changes in polarity, pH and ionic strength in the medium. Using the ESIPT system we observed linear changes in signal up to ∼20-25% v/v of co-solvent addition, constituting a break point. Based on such data, we propose a model for coating instability and the important adjustable parameters, such as the electrical charge distribution. FRET data provided confirmatory evidence for the model. The ESIPT dyes and FRET based methods represent new, simple tools for testing NP coating stability in complex environments.

Fluorescent Photoswitchable Diarylethenes for Biolabeling and Single-Molecule Localization Microscopies with Optical Superresolution

A modular assembly of water-soluble diarylethenes (DAEs), applicable as biomarkers for optical nanoscopy, is reported. Reversibly photoswitchable 1,2-bis(2-alkyl-6-phenyl-1-benzothiophene-1,1-dioxide-3-yl)perfluorocyclopentenes possessing a fluorescent "closed" form were decorated with one or two methoxy group(s) attached to the para-position(s) of phenyl ring(s) and two, four, or eight carboxylic acid groups. Antibody conjugates of these DAEs feature low aggregation, efficient photoswitching in aqueous buffers, specific staining of cellular structures, and photophysical properties (high emission efficiencies and low cycloreversion quantum yields) enabling their application in superresolution microscopy. Images of tubulin, vimentin, and nuclear pore complexes are presented. The superresolution images can also be acquired by using solely 488 nm light without additional photoactivation with UV light. These DAEs exhibit reversible photoswitching without requiring any additives to the imaging media and open new paths toward the modular design of fluorescent dyes for bioimaging with optical superresolution.

Photoswitchable fluorescent polymeric nanoparticles for rewritable fluorescence patterning and intracellular dual-color imaging with AIE-based fluorogens as FRET donors

Photoswitchable fluorescent polymeric nanoparticles with AIE-based fluorogens as FRET donors were prepared for rewritable fluorescence patterning and intracellular dual-color imaging.

Wavelength-selective and high-contrast multicolour fluorescence photoswitching in a mixture of photochromic nanoparticles

Wavelength-selective and high-contrast multicolour fluorescence photoswitching was successfully demonstrated based on the nonlinear fluorescence quenching in photochromic nanoparticles.