Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime

Microwave analogy of Förster resonance energy transfer and effect of finite antenna length

The near-field interaction between quantum emitters, governed by Förster resonance energy transfer (FRET), plays a pivotal role in nanoscale energy transfer mechanisms. However, FRET measurements in the optical regime are challenging as they require nanoscale control of the position and orientation of the emitters. To overcome these challenges, microwave measurements were proposed for enhanced spatial resolution and precise orientation control. However, unlike in optical systems for which the dipole can be taken to be infinitesimal in size, the finite size of microwave antennas can affect energy transfer measurements, especially at short distances. This highlights the necessity to consider the finite antenna length to obtain accurate results. In this study, we advance the understanding of dipole-dipole energy transfer in the microwave regime by developing an analytical model that explicitly considers finite antennas. Unlike previous works, our model calculates the mutual impedance of finite-length thin-wire dipole antennas without assuming a uniform current distribution. We validate our analytical model through experiments investigating energy transfer between antennas placed adjacent to a perfect electric conductor mirror. This allows us to provide clear guidelines for designing microwave experiments, distinguishing conditions where finite-size effects can be neglected and where they must be taken into account. Our study not only contributes to the fundamental physics of energy transfer but also opens avenues for microwave antenna impedance-based measurements to complement optical FRET experiments and quantitatively explore dipole-dipole energy transfer in a wider range of conditions.

Giant enhancement of fluorescence resonance energy transfer based on nanoporous gold with small amount of residual silver

Fluorescence resonance energy transfer (FRET) was found strongly enhanced by plasmon resonance. In this work, Nanoporous Gold with small amount of residual silver was used to form nanoporous gold/organic molecular layer compound with PSS and PAH. The ratio of its specific gold and silver content is achieved by controlling the time of its dealloying. Layered films of polyelectrolyte multilayers were assembled between the donor-acceptor pairs and NPG films to control distance. The maximum of FRET enhancement of 80-fold on the fluorescence intensity between the donor-acceptor pairs (CFP-YFP) is observed at a distance of ∼10.5 nm from the NPG film. This Nanoporous Gold with small amount of residual silver not only enhanced FRET 4-fold more than nanoporous gold of only gold content almost, but also effectively realized the regulation of FRET enhancement. The ability to precisely measure and regulate the enhancement of FRET enables the rational selection of plasmonic nanotransducer dimensions for the particular biosensing application.

Single-Molecule FRET at 10 MHz Count Rates

A bottleneck in many studies utilizing single-molecule Förster resonance energy transfer is the attainable photon count rate, as it determines the temporal resolution of the experiment. As many biologically relevant processes occur on time scales that are hardly accessible with currently achievable photon count rates, there has been considerable effort to find strategies to increase the stability and brightness of fluorescent dyes. Here, we use DNA nanoantennas to drastically increase the achievable photon count rates and observe fast biomolecular dynamics in the small volume between two plasmonic nanoparticles. As a proof of concept, we observe the coupled folding and binding of two intrinsically disordered proteins, which form transient encounter complexes with lifetimes on the order of 100 μs. To test the limits of our approach, we also investigated the hybridization of a short single-stranded DNA to its complementary counterpart, revealing a transition path time of 17 μs at photon count rates of around 10 MHz, which is an order-of-magnitude improvement compared to the state of the art. Concomitantly, the photostability was increased, enabling many seconds long megahertz fluorescence time traces. Due to the modular nature of the DNA origami method, this platform can be adapted to a broad range of biomolecules, providing a promising approach to study previously unobservable ultrafast biophysical processes.

DNA-Based Gold Nanoparticle Assemblies: From Structure Constructions to Sensing Applications

Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. In this review, we focus on the progress in the DNA-mediated assembly of Au NPs and their application in sensing in the past five years. Firstly, we highlight the strategies used for the orderly organization of Au NPs with DNA. Then, we describe the DNA-based assembly of Au NPs for sensing applications and representative research therein. Finally, we summarize the advantages of DNA nanotechnology in assembling complex Au NPs and outline the challenges and limitations in constructing complex gold nanoparticle assembly structures with tailored functionalities.

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

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.

Enhanced resonance energy transfer in gold nanoparticles bifunctionalized by tryptophan and riboflavin and its application in fluorescence bioimaging

Gold nanoparticles were functionalized by amino acid tryptophan and vitamin riboflavin - a resonance energy transfer (RET) pair of biomolecules. The presence of the gold nanoparticles resulted in 65% increase in RET efficiency. Because of enhanced RET efficiency, the photobleaching dynamics of the fluorescent molecules at the surface of the nanoparticles is different from that of molecules in solution. The observed effect was used for detection of the functionalized nanoparticles within biological material rich with autofluorescent species. Synchrotron radiation deep-ultraviolet fluorescence microscopy is used to study the photobleaching dynamics of the fluorescence centers within human hepatocellular carcinoma Huh7.5.1 cells incubated with the nanoparticles. The fluorescent centers were classified according to their photobleaching dynamics, which enabled the discrimination of the cell areas where the accumulation of the nanoparticles takes place, even though the particles were smaller than the spatial resolution of the images.

Controllable Aggregation-Induced Emission and Förster Resonance Energy Transfer Behaviors of Bistable [c2] Daisy Chain Rotaxanes for White-Light Emission and Temperature-Sensing Applications

Bistable [c2] daisy chain rotaxanes with respective extended and contracted forms of [c2]A and [c2]B containing a blue-emissive anthracene (AN) donor and orange-emissive indandione-carbazole (IC) acceptor were successfully synthesized via click reaction. Tunable-emission bistable [c2] daisy chain rotaxanes with fluorescence changes from blue to orange, including bright-white-light emissions, could be modulated by the aggregation-induced emission (AIE) characteristics and Förster resonance energy transfer (FRET) processes through altering water fractions and shuttling processes (i.e., acid/base controls). Accordingly, as a result of excellent fine-tuning AIE (at 60% water content of H₂O/THF) and FRET (with a compatible energy transfer of E_FRET = 33.2%) behaviors after the shuttling process (by adding base), the brightest white-light emission at CIE (0.31, 0.37) with a quantum yield of Φ = 15.64% was obtained in contracted [c2]B with good control of molecular shuttling to possess higher photoluminescence (PL) quantum yields and better energy transfer efficiencies (i.e., the manipulation of reduced PET and enhanced FRET processes) due to their intramolecular aggregations of blue AN donors and orange IC acceptors with a proper water content of 60% H₂O. Furthermore, dynamic light-scattering (DLS) and time-resolved photoluminescence (TRPL) measurements, along with theoretical calculations, were utilized to investigate and confirm AIE and FRET phenomena of bistable [c2] daisy chain rotaxanes. Especially, both bistable [c2] daisy chain rotaxanes [c2]A and [c2]B and noninterlocked monomer M could be exploited for the applications of ratiometric fluorescence temperature sensing due to the temperature effects on the AIE and FRET features. Based on these desirable bistable [c2] daisy chain rotaxane structures, this work provides a potential strategy for the future applications of tunable multicolor emission and ratiometric fluorescence temperature-sensing materials.

DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation

An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control, and well-defined orientation. The DNA origami technique has evolved into a highly versatile bottom-up nanofabrication methodology that fulfils almost all of these features. It enables the nanometric positioning of molecules and nanoparticles with stoichiometric control, and even the orientation of asymmetrical nanoparticles along predefined directions. However, orienting individual molecules has been a standing challenge. Here, we show how single molecules, namely, Cy5 and Cy3 fluorophores, can be incorporated in a DNA origami with controlled orientation by doubly linking them to oligonucleotide strands that are hybridized while leaving unpaired bases in the scaffold. Increasing the number of bases unpaired induces a stretching of the fluorophore linkers, reducing its mobility freedom, and leaves more space for the fluorophore to accommodate and find different sites for interaction with the DNA. Particularly, we explore the effects of leaving 0, 2, 4, 6, and 8 bases unpaired and find extreme orientations for 0 and 8 unpaired bases, corresponding to the molecules being perpendicular and parallel to the DNA double-helix, respectively. We foresee that these results will expand the application field of DNA origami toward the fabrication of nanodevices involving a wide range of orientation-dependent molecular interactions, such as energy transfer, intermolecular electron transport, catalysis, exciton delocalization, or the electromagnetic coupling of a molecule to specific resonant nanoantenna modes.

Resonance mode analysis of DNA self-assembled metamolecules with an effective refractive index model

We investigated the feasibility of a simple effective refractive index model based on the finite-difference time-domain method for DNA self-assembled metamolecules. Metamolecules were fabricated with Au nanoparticles (AuNPs) and a two-layer rectangular DNA template. Simulated scattering spectra for AuNPs placed on the template (n_eff= 1.3), self-assembled DNA dimers (n_eff= 1.34), and quadrumers (n_eff= 1.5) matched well with experimental results. Dipolar and Fano-like resonances were predicted from the calculated field distribution. These results indicate that we can easily estimate the resonance mode of fabricated metamolecules on a glass substrate, even when they are surrounded by complex materials such as DNA, by using a simple refractive index model.

Colloidal Self-Assembly Approaches to Smart Nanostructured Materials

Colloidal self-assembly refers to a solution-processed assembly of nanometer-/micrometer-sized, well-dispersed particles into secondary structures, whose collective properties are controlled by not only nanoparticle property but also the superstructure symmetry, orientation, phase, and dimension. This combination of characteristics makes colloidal superstructures highly susceptible to remote stimuli or local environmental changes, representing a prominent platform for developing stimuli-responsive materials and smart devices. Chemists are achieving even more delicate control over their active responses to various practical stimuli, setting the stage ready for fully exploiting the potential of this unique set of materials. This review addresses the assembly of colloids into stimuli-responsive or smart nanostructured materials. We first delineate the colloidal self-assembly driven by forces of different length scales. A set of concepts and equations are outlined for controlling the colloidal crystal growth, appreciating the importance of particle connectivity in creating responsive superstructures. We then present working mechanisms and practical strategies for engineering smart colloidal assemblies. The concepts underpinning separation and connectivity control are systematically introduced, allowing active tuning and precise prediction of the colloidal crystal properties in response to external stimuli. Various exciting applications of these unique materials are summarized with a specific focus on the structure-property correlation in smart materials and functional devices. We conclude this review with a summary of existing challenges in colloidal self-assembly of smart materials and provide a perspective on their further advances to the next generation.

Few-Molecule Strong Coupling with Dimers of Plasmonic Nanoparticles Assembled on DNA

Hybrid nanostructures, in which a known number of quantum emitters are strongly coupled to a plasmonic resonator, should feature optical properties at room temperature such as few-photon nonlinearities or coherent superradiant emission. We demonstrate here that this coupling regime can only be reached with dimers of gold nanoparticles in stringent experimental conditions, when the interparticle spacing falls below 2 nm. Using a short transverse DNA double-strand, we introduce five dye molecules in the gap between two 40 nm gold particles and actively decrease its length down to sub-2 nm values by screening electrostatic repulsion between the particles at high ionic strengths. Single-nanostructure scattering spectroscopy then evidence the observation of a strong-coupling regime in excellent agreement with electrodynamic simulations. Furthermore, we highlight the influence of the planar facets of polycrystalline gold nanoparticles on the probability of observing strongly coupled hybrid nanostructures.

DNA Origami Nanoantennas for Fluorescence Enhancement

The possibility to increase fluorescence by plasmonic effects in the near-field of metal nanostructures was recognized more than half a century ago. A major challenge, however, was to use this effect because placing single quantum emitters in the nanoscale plasmonic hotspot remained unsolved for a long time. This not only presents a chemical problem but also requires the nanostructure itself to be coaligned with the polarization of the excitation light. Additional difficulties arise from the complex distance dependence of fluorescence emission: in contrast to other surface-enhanced spectroscopies (such as Raman spectroscopy), the emitter should not be placed as close as possible to the metallic nanostructure but rather needs to be at an optimal distance on the order of a few nanometers to avoid undesired quenching effects.Our group addressed these challenges almost a decade ago by exploiting the unique positioning ability of DNA nanotechnology and reported the first self-assembled DNA origami nanoantennas. This Account summarizes our work spanning from this first proof-of-principle study to recent advances in utilizing DNA origami nanoantennas for single DNA molecule detection on a portable smartphone microscope.We summarize different aspects of DNA origami nanoantennas that are essential for achieving strong fluorescence enhancement and discuss how single-molecule fluorescence studies helped us to gain a better understanding of the interplay between fluorophores and plasmonic hotspots. Practical aspects of preparing the DNA origami nanoantennas and extending their utility are also discussed.Fluorescence enhancement in DNA origami nanoantennas is especially exciting for signal amplification in molecular diagnostic assays or in single-molecule biophysics, which could strongly benefit from higher time resolution. Additionally, biophysics can greatly profit from the ultrasmall effective detection volumes provided by DNA nanoantennas that allow single-molecule detection at drastically elevated concentrations as is required, e.g., in single-molecule DNA sequencing approaches.Finally, we describe our most recent progress in developing DNA NanoAntennas with Cleared HOtSpots (NACHOS) that are fully compatible with biomolecular assays. The developed DNA origami nanoantennas have proven robustness and remain functional after months of storage. As an example, we demonstrated for the first time the single-molecule detection of DNA specific to antibiotic-resistant bacteria on a portable and battery-driven smartphone microscope enabled by DNA origami nanoantennas. These recent developments mark a perfect moment to summarize the principles and the synthesis of DNA origami nanoantennas and give an outlook of new exciting directions toward using different nanomaterials for the construction of nanoantennas as well as for their emerging applications.

Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization

Cellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule fluorescence resonance energy transfer and molecular simulations on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.

Graphene Energy Transfer for Single-Molecule Biophysics, Biosensing, and Super-Resolution Microscopy

Graphene is considered a game-changing material, especially for its mechanical and electrical properties. This work exploits that graphene is almost transparent but quenches fluorescence in a range up to ≈40 nm. Graphene as a broadband and unbleachable energy-transfer acceptor without labeling, is used to precisely determine the height of molecules with respect to graphene, to visualize the dynamics of DNA nanostructures, and to determine the orientation of Förster-type resonance energy transfer (FRET) pairs. Using DNA origami nanopositioners, biosensing, single-molecule tracking, and DNA PAINT super-resolution with <3 nm z-resolution are demonstrated. The range of examples shows the potential of graphene-on-glass coverslips as a versatile platform for single-molecule biophysics, biosensing, and super-resolution microscopy.

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices.

Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures

We present a technique to determine the orientation of single fluorophores attached to DNA origami structures based on two measurements. First, the orientation of the absorption transition dipole of the molecule is determined through a polarization-resolved excitation measurement. Second, the orientation of the DNA origami structure is obtained from a DNA-PAINT nanoscopy measurement. Both measurements are performed consecutively on a fluorescence wide-field microscope. We employed this approach to study the orientation of single ATTO 647N, ATTO 643, and Cy5 fluorophores covalently attached to a 2D rectangular DNA origami structure with different nanoenvironments, achieved by changing both the fluorophores' binding position and immediate vicinity. Our results show that when fluorophores are incorporated with additional space, for example, by omitting nucleotides in an elsewise double-stranded environment, they tend to stick to the DNA and to adopt a preferred orientation that depends more on the specific molecular environment than on the fluorophore type. With the aid of all-atom molecular dynamics simulations, we rationalized our observations and provide insight into the fluorophores' probable binding modes. We believe this work constitutes an important step toward manipulating the orientation of single fluorophores in DNA origami structures, which is vital for the development of more efficient and reproducible self-assembled nanophotonic devices.

Recent advances in plasmonic nanocavities for single-molecule spectroscopy

Plasmonic nanocavities are able to engineer and confine electromagnetic fields to subwavelength volumes. In the past decade, they have enabled a large set of applications, in particular for sensing, optical trapping, and the investigation of physical and chemical phenomena at a few or single-molecule levels. This extreme sensitivity is possible thanks to the highly confined local field intensity enhancement, which depends on the geometry of plasmonic nanocavities. Indeed, suitably designed structures providing engineered local optical fields lead to enhanced optical sensing based on different phenomena such as surface enhanced Raman scattering, fluorescence, and Förster resonance energy transfer. In this mini-review, we illustrate the most recent results on plasmonic nanocavities, with specific emphasis on the detection of single molecules.

Efficient FRET Approaches toward Copper(II) and Cyanide Detections via Host-Guest Interactions of Photo-Switchable [2]Pseudo-Rotaxane Polymers Containing Naphthalimide and Merocyanine Moieties

A supramolecular [2]pseudo-rotaxane containing a naphthalimide-based pillararene host and a spiropyran-based imidazole guest was synthesized and investigated in a semiaqueous solution with 90% water fraction. Upon UV exposure, the close-form structure of nonemissive spiropyran guest could be transformed into the open-form structure of red-emissive merocyanine guest reversibly, which was utilized as a monofluorophoric sensor to detect copper(II) and cyanide ions. Moreover, the naphthalimide host as an energy donor with green photoluminescence (PL) emission at 505 nm was complexed with the merocyanine guest as an energy acceptor with red PL emission at 650 nm in 1:1 molar ratio to generate a [2]pseudo-rotaxane polymer, which was further verified by the diffusion coefficients of DOSY nuclear magnetic resonance (NMR) measurements. Due to the Förster resonance energy transfer (FRET) processes, the bifluorophoric [2]pseudo-rotaxane produced more efficient ratiometric PL behavior to induce a stronger red PL emission than that of the monofluorophoric guest; therefore, the PL sensor responses of the supramolecular [2]pseudo-rotaxane toward copper(II) and cyanide ions could be further amplified via the FRET-OFF processes to turn off red PL emission of the reacted merocyanine acceptor and to recover green PL emission of the naphthalimide donor. Accordingly, the best and prominent values of the limit of detection (LOD) for the host-guest detections toward Cu²⁺ and CN^- were 0.53 and 1.34 μM, respectively. The highest red MC emission with the optimum FRET processes of [2]pseudo-rotaxane was maintained around room temperature (20-40 °C) in wide pH conditions (pH = 3-13), which can be utilized in the cell viability tests to prove the nontoxic and remarkable biomarker of [2]pseudo-rotaxane to detect Cu²⁺ and CN^- in living cells. The developed FRET-OFF processes with ratiometric PL behavior of the bifluorophoric supramolecular [2]pseudo-rotaxane polymer will open a new avenue to the future applications of chemo- and biosensors.

Highly Efficient Förster Resonance Energy Transfer Modulations of Dual-AIEgens between a Tetraphenylethylene Donor and a Merocyanine Acceptor in Photo-Switchable [2]Rotaxanes and Reversible Photo-Patterning Applications

A series of novel photo-switchable [2]rotaxanes (i.e., Rot-A-SP and Rot-B-SP before and after shuttling controlled by acid-base, respectively) containing one spiropyran (SP) unit (as a photochromic stopper) on the axle and two tetraphenylethylene (TPE) units on the macrocycle were synthesized via click reaction. Upon UV/visible light exposure, both mono-fluorophoric rotaxanes Rot-A-SP and Rot-B-SP with the closed form (i.e., non-emissive SP unit) could be transformed into the open form (i.e., red-emissive merocyanine (MC) unit) to acquire their respective bi-fluorophoric Rot-A-MC and Rot-B-MC reversibly. The aggregation-induced emission (AIE) properties of bi-fluorophoric TPE combined with MC AIEgens of these designed rotaxanes and mixtures in semi-aqueous solutions induced interesting ratiometric photoluminescence (PL) and Förster resonance energy transfer (FRET) behaviors, which were further investigated and verified by dynamic light scattering (DLS), X-ray diffraction (XRD), and time-resolved photoluminescence (TRPL) measurements along with theoretical studies. Accordingly, in contrast to the model axle (Axle-MC) and the analogous mixture (Mixture-MC, containing the axle and macrocycle components in a 1:1 molar ratio), more efficient FRET behaviors and stronger red PL emissions were obtained from dual-AIEgens between a blue-emissive TPE donor (PL emission at 468 nm) and a red-emissive MC acceptor (PL emission at 668 nm) in both novel photo-switchable [2]rotaxanes Rot-A-MC and Rot-B-MC under various external modulations, including water content, UV/Vis irradiation, pH value, and temperature. Furthermore, the reversible fluorescent photo-patterning applications of Rot-A-SP in a powder form and a solid film with excellent photochromic and fluorescent behaviors are first investigated in this report.

Controllable Frequency Dependence of Resonance Energy Transfer Coupled with Localized Surface Plasmon Polaritons

We investigate the intrinsic characteristics of resonance energy transfer (RET) coupled with localized surface plasmon polaritons (LSPPs) from the perspective of macroscopic quantum electrodynamics. To quantify the effect of LSPPs, we propose a numerical scheme that allows us to accurately calculate the rate of RET between a donor-acceptor pair near a nanoparticle. Our study shows that LSPPs can be used to enhance the RET rate significantly and control its frequency dependence by modifying a core/shell structure, which indicates the possibility of RET rate optimization. Moreover, we systematically explore the angle (distance) dependence of the RET rate and analyze its origin. According to different frequency regimes, the angle dependence of RET is dominated by different mechanisms, such as LSPPs, surface plasmon polaritons (SPPs), and anti-resonance. For the proposed core/shell structure, the characteristic distance of RET coupled with LSPPs (approximately 0.05 emission wavelength) is shorter than that of RET coupled with SPPs (approximately 0.1 emission wavelength), which may provide promising applications in energy science.

Long-Range Single-Molecule Förster Resonance Energy Transfer between Alexa Dyes in Zero-Mode Waveguides

Zero-mode waveguide (ZMW) nano-apertures milled in metal films were proposed to improve the Förster resonance energy transfer (FRET) efficiency and enable single-molecule FRET detection beyond the 10 nm barrier, overcoming the restrictions of diffraction-limited detection in a homogeneous medium. However, the earlier ZMW demonstrations were limited to the Atto 550-Atto 647N fluorophore pair, asking the question whether the FRET enhancement observation was an artifact related to this specific set of fluorescent dyes. Here, we use Alexa Fluor 546 and Alexa Fluor 647 to investigate single-molecule FRET at large donor-acceptor separations exceeding 10 nm inside ZMWs. These Alexa fluorescent dyes feature a markedly different chemical structure, surface charge, and hydrophobicity as compared to their Atto counterparts. Our single molecule data on Alexa 546-Alexa 647 demonstrate enhanced FRET efficiencies at large separations exceeding 10 nm, extending the spatial range available for FRET and confirming the earlier conclusions. By showing that the FRET enhancement inside a ZMW does not depend on the set of fluorescent dyes, this report is an important step to establish the relevance of ZMWs to extend the sensitivity and detection range of FRET, while preserving its ability to work on regular fluorescent dye pairs.

A Self-Assembled Plasmonic Substrate for Enhanced Fluorescence Resonance Energy Transfer

Fluorescence resonance energy transfer (FRET) has found widespread uses in biosensing, molecular imaging, and light harvesting. Plasmonic metal nanostructures offer the possibility of engineering photonic environment of specific fluorophores to enhance the FRET efficiency. However, the potential of plasmonic nanostructures to enable tailored FRET enhancement on planar substrates remains largely unrealized, which are of considerable interest for high-performance on-surface bioassays and photovoltaics. The main challenge lies in the necessitated concurrent control over the spectral properties of plasmonic substrates to match that of fluorophores and the fluorophore-substrate spacing. Here, a self-assembled plasmonic substrate based on polydopamine (PDA)-coated plasmonic nanocrystals is developed to effectively address this challenge. The PDA coating not only drives interfacial self-assembly of the nanocrystals to form closely packed arrays with customized optical properties, but also can serve as a tailored nanoscale spacer between the fluorophores and plasmonic nanocrystals, which collectively lead to optimized fluorescence enhancement. The biocompatible plasmonic substrate that allows convenient bioconjugation imparted by PDA has afforded improved FRET efficiency in DNA microarray assay and FRET imaging of live cells. It is envisioned that the self-assembled plasmonic substrates can be readily integrated into fluorescence-based platforms for diverse biomedical and photoconversion applications.

Gold nanocap-supported upconversion nanoparticles for fabrication of a solid-phase aptasensor to detect ochratoxin A

Solid-phase, single-step biosensors are crucial for the development of portable, reusable, and convenient biosensors, otherwise known as point-of-care (POC) testing. Although high-performance single-step biosensors based on the principle of Förster resonance energy transfer (FRET) and using upconversion nanoparticles (UCNPs) functionalized with aptamers have been suggested as easy-to-use platforms, they lack portability and reusability when used for solution-phase biosensing. In this study, we describe a solid-phase, single-step aptasensor that showed higher performance than those of solution-phase aptasensors, as well as promising reusability. The solid-phase, single-step aptasensor was developed based on Au nanocap-supported UCNPs (Au/UCNPs), which were partially embedded in a solid substrate (e.g. polydimethylsiloxane, PDMS). The Au nanocaps allowed the UCNPs to emit upconverted light only from the restricted areas of the UCNPs, i.e., where they were not covered by the nanocaps and PDMS. Functionalization of an aptamer labeled with a quencher on the restricted area enabled the effective quenching of upconverted light from Au/UCNP via FRET after target (ochratoxin A, OTA) detection. The solid-phase, single-step aptasensor showed a linear range of 0.1-1000 ng mL^-1 and limit of detection of 0.022 ng mL^-1 within 30 min toward OTA. Furthermore, reusability of the solid-phase aptasensor was evaluated for three cycles of detection and regeneration, establishing its apparent reusability via heat treatment. Hence, such solid-phase, single-step aptasensors pave the path to the development of a portable and reusable biosensor platform for POC testing.

Off-Resonance Control and All-Optical Switching: Expanded Dimensions in Nonlinear Optics

The theory of non-resonant optical processes with intrinsic optical nonlinearity, such as harmonic generation, has been widely understood since the advent of the laser. In general, such effects involve multiphoton interactions that change the population of each input optical mode or modes. However, nonlinear effects can also arise through the input of an off-resonant laser beam that itself emerges unchanged. Many such effects have been largely overlooked. Using a quantum electrodynamical framework, this review provides detail on such optically nonlinear mechanisms that allow for a controlled increase or decrease in the intensity of linear absorption and fluorescence and in the efficiency of resonance energy transfer. The rate modifications responsible for these effects were achieved by the simultaneous application of an off-resonant beam with a moderate intensity, acting in a sense as an optical catalyst, conferring a new dimension of optical nonlinearity upon photoactive materials. It is shown that, in certain configurations, these mechanisms provide the basis for all-optical switching, i.e., the control of light-by-light, including an optical transistor scheme. The conclusion outlines other recently proposed all-optical switching systems.

Directing Single-Molecule Emission with DNA Origami-Assembled Optical Antennas

We demonstrate the capability of DNA self-assembled optical antennas to direct the emission of an individual fluorophore, which is free to rotate. DNA origami is used to fabricate optical antennas composed of two colloidal gold nanoparticles separated by a predefined gap and to place a single Cy5 fluorophore near the gap center. Although the fluorophore is able to rotate, its excitation and far-field emission is mediated by the antenna, with the emission directionality following a dipolar pattern according to the antenna main resonant mode. This work is intended to set out the basis for manipulating the emission pattern of single molecules with self-assembled optical antennas based on colloidal nanoparticles.

Resonance energy transfer and quantum entanglement mediated by epsilon-near-zero and other plasmonic waveguide systems

The resonance energy transfer and entanglement between two-level quantum emitters are typically limited to sub-wavelength distances due to the inherently short-range nature of the dipole-dipole interactions. Moreover, the entanglement of quantum systems is hard to preserve for a long time period due to decoherence and dephasing mainly caused by radiative and nonradiative losses. In this work, we outperform the aforementioned limitations by presenting efficient long-range inter-emitter entanglement and large enhancement of resonance energy transfer between two optical qubits mediated by epsilon-near-zero (ENZ) and other plasmonic waveguide types, such as V-shaped grooves and cylindrical nanorods. More importantly, we explicitly demonstrate that the ENZ waveguide resonant energy transfer and entanglement performance drastically outperforms the other waveguide systems. Only the excited ENZ mode has an infinite phase velocity combined with a strong and homogeneous electric field distribution, which leads to a giant energy transfer and efficient entanglement independent of the emitters' separation distances and nanoscale positions in the ENZ nanowaveguide, an advantageous feature that can potentially accommodate multi-qubit entanglement. Moreover, the transient entanglement can be further improved and become almost independent of the detrimental decoherence effect when an optically active (gain) medium is embedded inside the ENZ waveguide. We also present that efficient steady-state entanglement can be achieved by using a coherent external pumping scheme. Finally, we report a practical way to detect the steady-state entanglement by computing the second-order correlation function. The presented findings stress the importance of plasmonic ENZ waveguides in the design of the envisioned on-chip quantum communication and information processing plasmonic nanodevices.

Extending Single-Molecule Förster Resonance Energy Transfer (FRET) Range beyond 10 Nanometers in Zero-Mode Waveguides

Single-molecule Förster resonance energy transfer (smFRET) is widely used to monitor conformations and interaction dynamics at the molecular level. However, conventional smFRET measurements are ineffective at donor-acceptor distances exceeding 10 nm, impeding the studies on biomolecules of larger size. Here, we show that zero-mode waveguide (ZMW) apertures can be used to overcome the 10 nm barrier in smFRET. Using an optimized ZMW structure, we demonstrate smFRET between standard commercial fluorophores up to 13.6 nm distance with a significantly improved FRET efficiency. To further break into the classical FRET range limit, ZMWs are combined with molecular constructs featuring multiple acceptor dyes to achieve high FRET efficiencies together with high fluorescence count rates. As we discuss general guidelines for quantitative smFRET measurements inside ZMWs, the technique can be readily applied for monitoring conformations and interactions on large molecular complexes with enhanced brightness.