Fluorescence Anisotropy Reloaded-Emerging Polarization Microscopy Methods for Assessing Chromophores' Organization and Excitation Energy Transfer in Single Molecules, Particles, Films, and Beyond

Boosting Excited-State Energy Transfer by Anchoring Dipole Orientation in Binary Thermally Activated Delayed Fluorescence/J-Aggregate Assemblies

Förster resonance energy transfer (FRET) has been widely applied in fluorescence imaging, sensing and so on, while developing useful strategy of boosting FRET efficiency becomes a key issue that limits the application. Except optimizing spectral properties, promoting orientation factor (κ2) has been well discussed but rarely utilized for boosting FRET. Herein, we constructed binary nano-assembling of two thermally activated delayed fluorescence (TADF) emitters (2CzPN and DMAC-DPS) with J-type aggregate of cyanine dye (C8S4) as doping films by taking advantage of their electrostatic interactions. Time-resolved spectroscopic measurements indicated that 2CzPN/Cy-J films exhibit an order of magnitude higher kFRET than DMAC-DPS/Cy-J films. Further quantitative analysing on kFRET and kDET indicated higher orientation factor (κ2) in 2CzPN/Cy-J films play a key role for achieving fast kFRET, which was subsequently confirmed by anisotropic measurements. Corresponding DFT/TDDFT calculation revealed strong "two-point" electrostatic anchoring in 2CzPN/Cy-J films that is responsible for highly orientated transitions. We provide a new strategy for boosting FRET in nano-assemblies, which might be inspired for designing FRET-based devices of sensing, imaging and information encryption.

Expanded single-color barcoding in microspheres with fluorescence anisotropy for multiplexed biochemical detection

Single-color barcoding strategies could break the limits of spectral crosstalk in conventional intensity-based fluorescence barcodes. Fluorescence anisotropy (FA), a self-referencing quantity able to differentiate spectrally similar fluorophores, is highly attractive in designing fluorescent barcodes within a limited emission window. In this study, FA-based encoding of polystyrene (PS) microspheres was realized for the first time. The FA signals of fluorophores were stabilized inside PS microspheres owing to hampered rotational motion. Fluorescent labels were incorporated with similar emission but different structures, symmetries, and lifetimes. On the one hand, Förster Resonance Energy Transfer (FRET) including homo-FRET and hetero-FRET resulted in a decrease of steady-state FA with increasing dye loading, converting conventional intensity-based codes into FA-based codes. On the other hand, mixing dyes with different intrinsic FA values generated different FA values at the same fluorescence intensity level. Single color 5-plex FA-encoded microspheres were demonstrated and decoded on a homemade microscopic FA imaging platform in real time. The FA-encoded microspheres were successfully applied to detect the oligonucleotide of the foodborne bacterium, Bacillus cereus, without spectral crosstalk between the encoding and reporting dyes. Overall, FA-based encoding with an expanded coding capacity in the FA dimension holds great potential in multiplexed high-throughput chemical and biological analyses.

Multiparametric Remote Investigation in the near-IR through Optical Fiber for In Situ Measurements

Diffuse reflectance spectroscopy (DRS) has proven to be a powerful, reliable, and non-invasive optical method for characterizing a specimen. Nevertheless, these methods are based on a rudimentary interpretation of the spectral response and can be irrelevant to understanding 3D structures. In this work, we proposed adding optical modalities into a customized handheld probe head in order to increase the number of parameters in DRS acquired from the light/matter interaction. It consists of (1) placing the sample in a reflectance manual rotation stage to collect spectral backscattered angularly resolved light and (2) illuminating it with two sequential linear polarization orientations. We demonstrate that this innovative approach leads to a compact instrument, capable of performing fast polarization-resolved spectroscopic analysis. Due to the significant amount of data available with this technique in a short time, we observe sensitive quantitative discrimination between two types of biological tissue provided by a raw rabbit leg. We believe that this technique can pave the way for rapid meat quality check or biomedical diagnosis of pathological tissues in situ at an early stage.

Self-Assembly of Multivalent Aptamer-Tethered DNA Monolayers Dedicated to a Fluorescence Polarization-Responsive Circular Isothermal Strand Displacement Amplification for Salmonella Assay

Pathogenic bacteria are pathogens widely spread that are capable of causing mild to life-threatening diseases in human beings or other organisms. Rationally organizing the simple helical motif of double-stranded DNA (dsDNA) tiles into designed ensemble structures with architecturally defined collective properties could lead to promising biosensing applications for pathogen detection. In this work, we facilely engineered multivalent hairpin aptamer probe-tethered DNA monolayers (MHAP-DNA monolayers) and applied them to build a fluorescence polarization-responsive circular isothermal strand displacement amplification (FP-CSDA) for Salmonella assay. In this system, the MHAP-DNA monolayers were constructed based on a dsDNA tile-directed self-assembly. A FAM-labeled reporting probe (RP^FAM) with an inherent low FP signal serves as the signaling unit. The presence of target Salmonella leads to the trapping of F RP^FAM into the super DNA monolayers via a target-triggered CSDA to peel off the tethered hairpin-structured aptamer probes (HAPs) responsible for the binding of RP^FAM. As a result, the FP signal of the FAM fluorophore can be remarkably amplified due to the recycling of target Salmonella and the capacity of structural DNA materials to strongly restrict the free rotation of the FAM fluorophore but without a fluorescence quenching effect. Experimental results demonstrate that the FP assay is able to detect Salmonella with a low limit of detection (LOD) of 7.2 × 10⁰ CFU/mL and high specificity. As a proof-of-concept study, we envision our study using DNA nanoarchitecture as the foundation to modulate CSDA-based FP assays, promising to open up a new avenue for disease diagnosis, food safety detection, and biochemical studies.

Disentangling the Orientations of Spectrally Overlapping Transition Dipoles in Dense Dye Layers

The transition dipole orientations of dye assemblies in heterostructures have a crucial impact on the efficiency of novel optoelectronic devices such as organic thin-film transistors and light-emitting diodes. These devices are frequently based on heterojunctions and tandem structures featuring multiple optical transitions. Precise knowledge of preferred orientations, spatial order, and spatial variations is highly relevant. We present a fast and universal large-area screening method to determine the transition dipole orientations in dye assemblies with diffraction-limited spatial resolution. Moreover, our hyperspectral imaging approach disentangles the orientations of different chromophores. As a demonstration, we apply our technique to dye monolayers with two optical transitions sandwiched between two ultrathin silicate nanosheets. A comprehensive model for dipole orientation distributions in monolayers reveals a long-range orientational order and a strong correlation between the two transitions.

Probing size variations of molecular aggregates inside chlorosomes using single-object spectroscopy

We theoretically investigate the possibility to use single-object spectroscopy to probe size variations of the bacteriochlorophyll aggregates inside chlorosomes. Chlorosomes are the light-harvesting organelles of green sulfur and non-sulfur bacteria. They are known to be the most efficient light-harvesting systems in nature. Key to this efficiency is the organization of bacteriochlorophyll molecules in large self-assembled aggregates that define the secondary structure inside the chlorosomes. Many studies have been reported to elucidate the morphology of these aggregates and the molecular packing inside them. It is widely believed that tubular aggregates play an important role. Because the size (radius and length) of these aggregates affects the optical and excitation energy transport properties, it is of interest to be able to probe these quantities inside chlorosomes. We show that a combination of single-chlorosome linear polarization resolved spectroscopy and single-chlorosome circular dichroism spectroscopy may be used to access the typical size of the tubular aggregates within a chlorosome and, thus, probe possible variations between individual chlorosomes that may result, for instance, from different stages in growth or different growth conditions.

Split-HaloTag imaging assay for sophisticated microscopy of protein-protein interactions in planta

An ever-increasing number of intracellular multi-protein networks have been identified in plant cells. Split-GFP-based protein-protein interaction assays combine the advantages of in vivo interaction studies in a native environment with additional visualization of protein complex localization. Because of their simple protocols, they have become some of the most frequently used methods. However, standard fluorescent proteins present several drawbacks for sophisticated microscopy. With the HaloTag system, these drawbacks can be overcome, as this reporter forms covalent irreversible bonds with synthetic photostable fluorescent ligands. Dyes can be used in adjustable concentrations and are suitable for advanced microscopy methods. Therefore, we have established the Split-HaloTag imaging assay in plants, which is based on the reconstitution of a functional HaloTag protein upon protein-protein interaction and the subsequent covalent binding of an added fluorescent ligand. Its suitability and robustness were demonstrated using a well-characterized interaction as an example of protein-protein interaction at cellular structures: the anchoring of the molybdenum cofactor biosynthesis complex to filamentous actin. In addition, a specific interaction was visualized in a more distinctive manner with subdiffractional polarization microscopy, Airyscan, and structured illumination microscopy to provide examples of sophisticated imaging. Split-GFP and Split-HaloTag can complement one another, as Split-HaloTag represents an alternative option and an addition to the large toolbox of in vivo methods. Therefore, this promising new Split-HaloTag imaging assay provides a unique and sensitive approach for more detailed characterization of protein-protein interactions using specific microscopy techniques, such as 3D imaging, single-molecule tracking, and super-resolution microscopy.

Bulky Barbiturates as Non-Toxic Ionic Dye Insulators for Enhanced Emission in Polymeric Nanoparticles

Bulky hydrophobic counterions (weakly coordinating anions) can insulate ionic dyes against aggregation-caused quenching (ACQ) and enable preparation of highly fluorescent dye-loaded nanoparticles (NPs) for bioimaging, biosensing and light harvesting. Here, we introduce a family of hydrophobic anions based on fluorinated C-acyl barbiturates with delocalized negative charge and bulky non-polar groups. Similarly to fluorinated tetraphenylborates, these barbiturates prevent ACQ of cationic dye alkyl rhodamine B inside polymer NPs made of biodegradable poly(lactic-co-glycolic acid) (PLGA). Their efficiency to prevent ACQ increases for analogues with higher acidity and bulkiness. Their structure controls dye-dye communication, yielding bright NPs with on/off switching or stable emission. They enhance dye encapsulation inside NPs, allowing intracellular imaging without dye leakage. Compared to fluorinated tetraphenylborates known as cytotoxic transmembrane ion transporters, the barbiturates display a significantly lower cytotoxicity. These chemically available and versatile barbiturate derivatives are promising counterion scaffolds for preparation of bright non-toxic fluorescent nanomaterials.

Anisotropy in fifth-order exciton-exciton-interaction two-dimensional spectroscopy

Exciton-exciton-interaction two-dimensional (EEI2D) spectroscopy is a fifth-order variant of 2D electronic spectroscopy. It can be used to probe biexciton dynamics in molecular systems and to observe exciton diffusion in extended systems such as polymers or light-harvesting complexes. The exciton transport strongly depends on the geometrical and energetic landscape and its perturbations. These can be of both local character, such as molecular orientation and energetic disorder, and long-range character, such as polymer kinks and structural domains. In the present theoretical work, we investigate the anisotropy in EEI2D spectroscopy. We introduce a general approach for how to calculate the anisotropy by using the response-function formalism in an efficient way. In numerical simulations, using a Frenkel exciton model with Redfield-theory dynamics, we demonstrate how the measurement of anisotropy in EEI2D spectroscopy can be used to identify various geometrical effects on exciton transport in dimers and polymers. Investigating a molecular heterodimer as an example, we demonstrate the utility of anisotropy in EEI2D spectroscopy for disentangling dynamic localization and annihilation. We further calculate the annihilation in extended systems such as conjugated polymers. In a polymer, a change in the anisotropy provides a unique signature for exciton transport between differently oriented sections. We analyze three types of geometry variations in polymers: a kink, varying geometric and energetic disorder, and different geometric domains. Our findings underline that employing anisotropy in EEI2D spectroscopy provides a way to distinguish between different geometries and can be used to obtain a better understanding of long-range exciton transport.

Advances of super-resolution fluorescence polarization microscopy and its applications in life sciences

Fluorescence polarization microscopy (FPM) analyzes both intensity and orientation of fluorescence dipole, and reflects the structural specificity of target molecules. It has become an important tool for studying protein organization, orientational order, and structural changes in cells. However, suffering from optical diffraction limit, conventional FPM has low orientation resolution and observation accuracy, as the polarization information is averaged by multiple fluorescent molecules within a diffraction-limited volume. Recently, novel super-resolution FPMs have been developed to break the diffraction barrier. In this review, we will introduce the recent progress to achieve sub-diffraction determination of dipole orientation. Biological applications, based on polarization analysis of fluorescence dipole, are also summarized, with focus on chromophore-target molecule interaction and molecular organization.

Enhanced reconstruction of structured illumination microscopy on a polarized specimen

Structured illumination microscopy (SIM) requires polarization control to guarantee the high-contrast illumination pattern. However, this modulated polarization will induce artifacts in SIM when imaging fluorescent dipoles. Here we proposed the polarization weighted recombination of frequency components to reconstruct SIM data with suppressed artifacts and better resolving power. Both the simulation results and experimental data demonstrate that our algorithm can obtain isotropic resolution on dipoles and resolve a clearer structure in high-density sections compared to the conventional algorithm. Our work reinforces the SIM theory and paves the avenue for the application of SIM on a polarized specimen.

Parallel Polarization Illumination with a Multifocal Axicon Metalens for Improved Polarization Imaging

Polarization imaging is an important branch of the microscopy technique that can provide additional information and enhanced contrast. The illumination system of a polarization microscope enables many different polarizations but makes the setup bulky, complicated, and slow. Here, we design and fabricate an ultrathin planar axicon metalens that also enables parallel illumination with different polarizations. Our results reveal a diffraction-limited size and high degree of linear polarization. To verify our approach, we accurately map the polarization angle of an aluminum grating, which is used as a polarizer. Furthermore, we demonstrate that elliptical polarization can be generated without additional design. A single metalens has the same capabilities as a conventional illumination module containing a polarizer, compensator, and rotation-stage/optical modulator. In addition, our device has the potential to enable rapid super-resolution polarization imaging. The new method could be useful in many applications and areas, including, e.g., materials research and biomedicine.

Control of Intrachain Morphology in the Formation of Polyfluorene Aggregates on the Single-Molecule Level

Controlling the morphology of π-conjugated polymers for organic optoelectronic devices has long been a goal in the field of materials science. Since the morphology of a polymer chain is closely intertwined with its photophysical properties, it is desirable to be able to change the arrangement of the polymers at will. We investigate the π-conjugated polymer poly(9,9-dioctylfluorene) (PFO), which can exist in three distinctly different structural phases: the α-, β-, and γ-phase. Every phase has a different chain structure and a unique photoluminescence (PL) spectrum. Due to its unique properties and the pronounced spectral structure-property relations, PFO can be used as a model system to study the morphology of π-conjugated polymers. To avoid ensemble averaging, we examine the PL spectrum of single PFO chains embedded in a non-fluorescent matrix. With single-molecule spectroscopy the structural phase of every single chain can be determined, and changes can be monitored very easily. To manipulate the morphology, solvent vapor annealing (SVA) was applied, which leads to a diffusion of the polymer chains in the matrix. The β- and γ-phases appear during the self-assembly of single α-phase PFO chains into mesoscopic aggregates. The extent of β- and γ-phase formation is directed by the solvent-swelling protocol used for aggregation. Aggregation unequivocally promotes formation of the more planar β- and γ-phases. Once these lower-energy more ordered structural phases are formed, SVA cannot return the polymer chain to the less ordered phase by aggregate swelling.

Endogenous alpha-synuclein monomers, oligomers and resulting pathology: let's talk about the lipids in the room

Alpha-synuclein is an intrinsically disordered, highly dynamic protein that pathogenically aggregates into inclusion structures called Lewy bodies, in several neurogenerative diseases termed synucleinopathies. Despite its importance for understanding disease, the oligomerization status of alpha-synuclein in healthy cells remains unclear. Alpha-synuclein may exist predominantly as either a monomer or a variety of oligomers of different molecular weights. There is solid evidence to support both theories. Detection of apparent endogenous oligomers are intimately dependent on vesicle and lipid interactions. Here we consider the possibility that apparent endogenous alpha-synuclein oligomers are in fact conformations of membrane-bound alpha-synuclein and not a bona fide stable soluble species. This perspective posits that the formation of any alpha-synuclein oligomers within the cell is likely toxic and interconversion between monomer and oligomer is tightly controlled. This differs from the hypothesis that there is a continuum of endogenous non-toxic oligomers and they convert, through unclear mechanisms, to toxic oligomers. The distinction is important, because it clarifies the biological origin of synucleinopathy. We suggest that a monomer-only, lipid-centric view of endogenous alpha-synuclein aggregation can explain how alpha-synuclein pathology is triggered, and that the interactions between alpha-synuclein and lipids can represent a target for therapeutic intervention. This discussion is well-timed due to recent studies that show lipids are a significant component of Lewy pathology.

Homo-FRET in π-Conjugated Polygons: Intermediate-Strength Dipole-Dipole Coupling Makes Energy Transfer Reversible

The concept of homo-FRET is often used to describe energy transfer between like chromophores of molecular aggregates such as in π-conjugated polymers. Homo-FRET is revealed by a dynamic depolarization in fluorescence but strictly only applies to the limit of weak dipole-dipole coupling, where energy transfer occurs on time scales much longer than those of nuclear relaxation. By considering the polarization anisotropy of photoluminescence emission and excitation of model multichromophoric aggregates on the single-molecule level, we demonstrate the transition of energy-transfer dynamics from the case of weak coupling to that of strong coupling, revealing the elusive regime of intermediate-strength coupling where energy transfer between degenerate donor and acceptor chromophores becomes reversible so that information on the excitation route of the emitting chromophore is lost.