Probing Photophysical Processes in Individual Multichromophoric Dendrimers by Single-Molecule Spectroscopy

Ultrafast Super-Resolution Imaging Exploiting Spontaneous Blinking of Static Excimer Aggregates

Single-molecule localization methods have been popularly exploited to obtain super-resolved images of biological structures. However, the low blinking frequency of randomly switching emission states of individual fluorophores greatly limits the imaging speed of single-molecule localization microscopy (SMLM). Here we present an ultrafast SMLM technique exploiting spontaneous fluorescence blinking of cyanine dye aggregates confined to DNA framework nanostructures. The DNA template guides the formation of static excimer aggregates as a "light-harvesting nanoantenna", whereas intermolecular excitation energy transfer (EET) between static excimers causes collective ultrafast fluorescence blinking of fluorophore aggregates. This DNA framework-based strategy enables the imaging of DNA nanostructures with 12.5-fold improvement in speed compared to conventional SMLM. Further, we demonstrate the use of this strategy to track the movement of super-resolved DNA nanostructures for over 20 min in a microfluidic system. Thus, this ultrafast SMLM holds great potential for revealing the dynamic processes of biomacromolecules in living cells.

Excited-State Symmetry Breaking in a Multiple Multipolar Chromophore Probed by Single-Molecule Fluorescence Imaging and Spectroscopy

Excited-state symmetry breaking (ESB) has attracted much attention because it is often observed in symmetric multipolar chromophores designed as two-photon absorption/emission materials. Herein, we report an ensemble and single-molecule fluorescence imaging and spectroscopy investigation of ESB in hexakis[4-(p-dioctylaminostyryl)phenylethynyl]benzene(DB6), a two-photon absorber possessing a C₆-symmetric π-D₆ structure (π = hexaethynylbenzene, D = (p-dioctylaminostyryl)phenyl group) consisting of three equivalent D-π-D moieties. Ensemble and single-molecule measurements and theoretical calculations revealed that DB6 undergoes a photoabsorption process with two orthogonal transition dipole moments, whereas it fluoresces with a single transition dipole moment after one- or two-step ESB upon photoexcitation, depending on the environmental polarity. In nonpolar solvents and polymer films, one of the three D-π-D sites becomes planar, and the excited state is localized on this moiety: a [D^δ+-π^δ--D^δ+]* quadrupolar state is formed. In polar solvents, the symmetry is further broken within the planarized D-π-D moiety, and the excited state is localized on one of the two D-π sites; i.e., a D-[π^δ--D^δ+]* dipolar state is generated. Hence, DB6 can behave like a multichromophore with multiple emission sites in the molecule, which was demonstrated by stepwise photobleaching under photon antibunching conditions.

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

Fluorescence polarization is widely used to assess the orientation/rotation of molecules, and the excitation energy transfer between closely located chromophores. Emerging since the 1990s, single molecule fluorescence spectroscopy and imaging stimulate the application of light polarization for studying molecular organization and energy transfer beyond ensemble averaging. Here, traditional fluorescence polarization and linear dichroism methods used for bulk samples are compared with techniques specially developed for, or inspired by, single molecule fluorescence spectroscopy. Techniques for assessing energy transfer in anisotropic samples, where the traditional fluorescence anisotropy framework is not readily applicable, are discussed in depth. It is shown that the concept of a polarization portrait and the single funnel approximation can lay the foundation for alternative energy transfer metrics. Examples ranging from fundamental studies of photoactive materials (conjugated polymers, light-harvesting aggregates, and perovskite semiconductors) to Förster resonant energy transfer (FRET)-based biomedical imaging are presented. Furthermore, novel uses of light polarization for super-resolution optical imaging are mentioned as well as strategies for avoiding artifacts in polarization microscopy.

Tailoring Fluorescence Brightness and Switching of Nanoparticles through Dye Organization in the Polymer Matrix

Fluorescent nanoparticles (NPs) help to increase spatial and temporal resolution in bioimaging. Advanced microscopy techniques require very bright NPs that exhibit either stable emission for single-particle tracking or complete on/off switching (blinking) for super-resolution imaging. Here, ultrabright dye-loaded polymer NPs with controlled switching properties are developed. To this aim, the salt of a dye (rhodamine B octadecyl ester) with a hydrophobic counterion (fluorinated tetraphenylborate) is encapsulated at very high concentrations up to 30 wt % in NPs made of poly(lactic-co-glycolic acid) (PLGA), poly(methyl methacrylate) (PMMA), and polycaprolactone (PCL) through nanoprecipitation. The obtained 35 nm NPs are nearly 100 times brighter than quantum dots. The nature of the polymer is found to define the collective behavior of the encapsulated dyes so that NPs containing thousands of dyes exhibit either whole particle blinking, for PLGA, or stable emission, for PMMA and PCL. Fluorescence anisotropy measurements together with small-angle X-ray scattering experiments suggest that in less hydrophobic PLGA, dyes tend to cluster, whereas in more hydrophobic PMMA and PCL, dyes are dispersed within the matrix, thus altering the switching behavior of NPs. Experiments using a perylene diimide derivative show a similar effect of the polymer nature. The resulting fluorescent NPs are suitable for a wide range of imaging applications from tracking to super-resolution imaging. The findings on the organization of the load innside NPs will have impact on the development of materials for applications ranging from photovoltaics to drug delivery.

"Supertrap" at Work: Extremely Efficient Nonradiative Recombination Channels in MAPbI3 Perovskites Revealed by Luminescence Super-Resolution Imaging and Spectroscopy

Organo-metal halide perovskites are some of the most promising materials for the new generation of low-cost photovoltaic and light-emitting devices. Their solution processability is a beneficial trait, although it leads to a spatial inhomogeneity of perovskite films with a variation of the trap state density at the nanoscale. Comprehending their properties using traditional spectroscopy therefore becomes difficult, calling for a combination with microscopy in order to see beyond the ensemble-averaged response. We studied photoluminescence (PL) blinking of micrometer-sized individual methylammonium lead iodide (MAPbI₃) perovskite polycrystals, as well as monocrystalline microrods up to 10 μm long. We correlated their PL dynamics with structure employing scanning electron and optical super-resolution microscopy. Combining super-resolution localization imaging and super-resolution optical fluctuation imaging (SOFI), we could detect and quantify preferential emitting regions in polycrystals exhibiting different types of blinking. We propose that blinking in MAPbI₃ occurs by the activation/passivation of a "supertrap" which presumably is a donor-acceptor pair able to trap both electrons and holes. As such, nonradiative recombination via supertraps, in spite being present at a rather low concentrations (10¹²-10¹⁵ cm^-3), is much more efficient than via all other defect states present in the material at higher concentrations (10¹⁶-10¹⁸ cm^-3). We speculate that activation/deactivation of a supertrap occurs by its temporary dissociation into free donor and acceptor impurities. We found that supertraps are most efficient in structurally homogeneous and large MAPbI₃ crystals where carrier diffusion is efficient, which may therefore pose limitations on the efficiency of perovskite-based devices.

Interactions between π-conjugated chromophores in a giant molecular spoked wheel

We discuss the intriguing photophysics of a giant molecular spoked wheel of π-conjugated arylene-alkynylene chromophores on the single-molecule level. This "molecular mesoscopic" structure, C₁₈₇₈H₂₆₈₂, shows fast switching between the 12 identical chromophores since the fluorescence is unpolarised but only one chromophore emits at a time.

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.

A solution-based single-molecule study of surface-bound PBIs: solvent-mediated environmental effects on molecular flexibility

We have investigated the fundamental photophysical properties of surface-bound perylene bisimide (PBI) molecules in solution at the single-molecule level.

Structure-Dependent Electronic Interactions in Ethyne-Bridged Porphyrin Arrays Investigated by Single-Molecule Fluorescence Spectroscopy

By using single-molecule fluorescence spectroscopy, we have investigated the electronic interaction of ethyne-bridged porphyrin arrays (ZNE) depending on their structure. The fluorescence dynamics of ZNE show a large amount of one-step photobleaching behaviors, indicating the high degree of π-conjugation. The ratio of one-step photobleaching behavior decreased as the number of porphyrin units increased. This behavior indicates that the linear and shortest Z2E shows a strong electronic coupling between constituent porphyrin moieties. Structural properties and orientation of ZNE were also measured by wide-field excitation fluorescence spectroscopy (ExPFS) and defocused wide-field imaging (DWFI). The ExPFS and DWFI show that the structure of absorbing and emitting units of Z2E and Z3E are linear. On the other hand, star-shaped pentamer with five porphyrins acts as an absorbing unit, but unidirectional trimer moiety acts as an emitting unit in the Z5E molecule. Collectively, these studies provide further information on the electronic interaction depending on their structure and length.

The origin of emissive states of carbon nanoparticles derived from ensemble-averaged and single-molecular studies

At present, there is no consensus understanding on the origin of photoluminescence of carbon nanoparticles, particularly the so-called carbon dots. Providing comparative analysis of spectroscopic studies in solution and on a single-molecular level, we demonstrate that these particles behave collectively as fixed single dipoles and probably are the quantum emitter entities. Their spectral and lifetime heterogeneity in solutions is explained by variation of the local chemical environment within and around luminescence centers. Hence, the carbon dots possess a unique hybrid combination of fluorescence properties peculiar to dye molecules, their conjugates and semiconductor nanocrystals. It is proposed that their optical properties are due to generation of H-aggregate-type excitonic states with their coherence spreading over the whole nanoparticles.

Synthesis of Polyamide Dendrimers bearing Multiple Hydrogen Bonding Parts on the Periphery

A series of polyamide dendrimers (GO-G2) having carboxy1 groups on the periphery were prepared by the divergent method. The reaction of G 18NH2 dendrimer with glutaric acid anhydride gave polyamide dendrimer (Gi-8COOH). The structure of polyamide dendrimers were confirmed by IR, 1H, 13C NMR, MALDI-TOF mass, and elemental analysis. Poly(4-vinylpyridine) (P4VP) was prepared by atom transfer radical polymerization of 4-vinylpyridine. A hydrogen bonded GI-8COOH/P4VP 1/8 (molar ratio) complex was prepared by mixing GIA8COOH with P4VP in methanol, followed by removing the solvent. IR spectrum of Gl-8COOH/P4VP 1/8 complex showed the characteristic absorptions at 2550 and 1950 cm-1 due to the hydrogen bonding. A glass transition temperature (Tg) of GI-8COOH/P4VP 1/8 complex was observed at 177°C by DSC measurement, whereas the Tg values of G 1-8COOH and P4VP were at 147 and 138°C, respectively.

Structure-property relationships in two-dimensionally extended benzoporphyrin molecules probed using single-molecule fluorescence spectroscopy

The photophysical properties of a series of highly π-conjugated benzoporphyrin molecules (s) with different shapes were investigated in the condensed phase using single-molecule fluorescence spectroscopy. The fluorescence properties of single s were found to be affected by the number of porphyrin units and their molecular shapes. Notably, the single-molecule fluorescence dynamics of the s revealed an increase in the fluorescence lifetimes and blue shifts of the fluorescence spectra indicative of decreasing π-conjugation pathways in the molecules. The distributions of the spectroscopic parameters and the photostability for the molecules also suggest conformational complexities and heterogeneities. Specifically, as the number of constituent porphyrin units increased, the one-step photobleaching behavior ratio and photostability decreased, and the spectroscopic parameter distributions broadened. The structural properties of the s were also directly determined using defocused wide-field imaging and linear dichroism analyses. In particular, molecules with the same number of constituent porphyrins but different molecular shapes exhibited distinct photophysical properties. In summary, these observations provide guidance for the design of molecular systems that can enhance the performance of molecular electronic devices.

Direct observation of structural properties and fluorescent trapping sites in macrocyclic porphyrin arrays at the single-molecule level

By utilizing single-molecule defocused wide-field fluorescence microscopy, we have investigated the molecular structural properties such as transition dipole moment orientations and the angular relationship among chromophores, as well as structural distortions and flexibilities depending on the ring size, in a series of cyclic porphyrin arrays bearing close likeness in overall architectures to the LH2 complexes in purple bacterial photosynthetic systems. Furthermore, comparing the experimental results with molecular dynamics simulations, we ascertained site selection for fluorescent trapping sites. Collectively, these experimental and computational results provide the basis for structure-property relationships and energy hopping/emitting processes in an important class of artificial light-harvesting molecular systems widely used in molecular electronics technology.

Fluorinated counterion-enhanced emission of rhodamine aggregates: ultrabright nanoparticles for bioimaging and light-harvesting

The key to ultrabright fluorescent nanomaterials is the control of dye emission in the aggregated state. Here, lipophilic rhodamine B derivatives are assembled into nanoparticles (NPs) using tetraphenylborate counterions with varied fluorination levels that should tune the short-range dye ordering. Counterion fluorination is found to drastically enhance the emission characteristics of these NPs. Highly fluorinated counterions produce 10-20 nm NPs containing >300 rhodamine dyes with a fluorescence quantum yield of 40-60% and a remarkably narrow emission band (34 nm), whereas, for other counterions, aggregation caused quenching with a weak broad-band emission is observed. NPs with the most fluorinated counterion (48 fluorines) are ∼40-fold brighter than quantum dots (QD585 at 532 nm excitation) in single-molecule microscopy, showing improved photostability and suppressed blinking. Due to exciton diffusion, revealed by fluorescence anisotropy, these NPs are efficient FRET donors to single cyanine-5 acceptors with a light-harvesting antenna effect reaching 200. Finally, NPs with the most fluorinated counterion are rather stable after entry into living cells, in contrast to their less fluorinated analogue. Thus, the present work shows the crucial role of counterion fluorination in achieving high fluorescence brightness and photostability, narrow-band emission, efficient energy transfer and high intracellular stability of nanomaterials for light harvesting and bioimaging applications.

Spontaneous Fluctuations of Transition Dipole Moment Orientation in OLED Triplet Emitters

The efficiency of an organic light-emitting diode (OLED) depends on the microscopic orientation of transition dipole moments of the molecular emitters. The most effective materials used for light generation have 3-fold symmetry, which prohibits a priori determination of dipole orientation due to the degeneracy of the fundamental transition. Single-molecule spectroscopy reveals that the model triplet emitter tris(1-phenylisoquinoline)iridium(III) (Ir(piq)3) does not behave as a linear dipole, radiating with lower polarization anisotropy than expected. Spontaneous symmetry breaking occurs in the excited state, leading to a random selection of one of the three ligands to form a charge-transfer state with the metal. This nondeterministic localization is revealed in switching of the degree of linear polarization of phosphorescence. Polarization scrambling likely raises out-coupling efficiency and should be taken into account when deriving molecular orientation of the guest emitter within the OLED host from ensemble angular emission profiles.

Inhomogeneity in the excited-state torsional disorder of a conjugated macrocycle

The photophysics of conjugated polymers has generally been explained based on the interactions between the component conjugated chromophores in a tangled chain. However, conjugated chromophores are entities with static and dynamic structural disorder, which directly affects the conjugated polymer photophysics. Here we demonstrate the impact of chain structure torsional disorder on the spectral characteristics for a macrocyclic oligothiophene 1, which is obscured in conventional linear conjugated chromophores by diverse structural disorders such as those in chromophore size and shape. We used simultaneous multiple fluorescence parameter measurement for a single molecule and quantum-mechanical calculations to show that within the fixed conjugation length across the entire ring an inhomogeneity from torsional disorder in the structure of 1 plays a crucial role in causing its energetic disorder, which affords the spectral broadening of ∼220 meV. The torsional disorder in 1 fluctuated on the time scale of hundreds of milliseconds, typically accompanied by spectral drifts on the order of ∼10 meV. The fluctuations could generate torsional defects and change the electronic structure of 1 associated with the ring symmetry. These findings disclose the fundamental nature of conjugated chromophore that is the most elementary spectroscopic unit in conjugated polymers and suggest the importance of engineering structural disorder to optimize polymer-based device photophysics. Additionally, we combined defocused wide-field fluorescence microscopy and linear dichroism obtained from the simultaneous measurements to show that 1 emits polarized light with a changing polarization direction based on the torsional disorder fluctuations.

Single molecule laser spectroscopy

In this article, we discussed some single molecule spectroscopy techniques and methods. We have chosen the simplicity in this survey based on our laboratory experience in this field. We concentrated on the imaging by both techniques the wide field and the scanning microscopes. Other imaging enhancements on the technique like extended resolution wide field, the total internal reflection imaging, and its derivatives are also reviewed. In addition to the imaging techniques, some diffusion techniques also are discussed like fluorescence correlation spectroscopy. The related methods like Forester resonance transfer, photo-induced electron transfer and anisotropy (steady state and time decay) are also discussed. In addition, we elucidated some simple details about the theory behind the FCS and its resulting curve fitting. This review is preceded by general introduction and ended with the conclusion.

Single Lévy states-disorder induced energy funnels in molecular aggregates

Using fluorescence super-resolution microscopy we studied simultaneous spectral, spatial localization, and blinking behavior of individual 1D J-aggregates. Excitons migrating 100 nm are funneled to a trap appearing as an additional red-shifted blinking fluorescence band. We propose that the trap is a Frenkel exciton state formed much below the main exciton band edge due to an environmentally induced heavy-tailed Lévy disorder. This points to disorder engineering as a new avenue in controlling light-harvesting in molecular ensembles.

A multi-property fluorescent probe for the investigation of polymer dynamics near the glass transition

In addition to the commonly observed single molecule fluorescence intensity fluctuations due to molecular reorientation dynamics, a perylene bisimide-calixarene compound (1) shows additional on-off fluctuations due to its ability to undergo intramolecular excited state electron transfer (PET). This quenching process is turned on rather sharply when a film of poly(vinylacetate) containing 1 is heated above its glass transition temperature (T g), which indicates that the electron transfer process depends on the availability of sufficient free volume. Spatial heterogeneities cause different individual molecules to reach the electron transfer regime at different temperatures, but these heterogeneities also fluctuate in time: in the matrix above T g molecules that are mostly nonfluorescent due to PET can become fluorescent again on timescales of seconds to minutes.

The two different mechanisms for intensity fluctuation, rotation and PET, thus far only observed in compound 1, make it a unique probe for the dynamics of supercooled liquids.

Reconstruction of the Molecular Structure of a Multichromophoric System Using Single-Molecule Defocused Wide-Field Imaging

Single-molecule defocused wide-field imaging (DWFI) has been demonstrated to be useful to determine molecular structure parameters, such as the orientations of transition dipole moments and the angular relationships between chromophores in multichromophoric molecular systems. For a series of acetylene-linked perylene bisimide (PBI) macrocycles with different ring size comprising three to six PBI dyes, we reconstructed the molecular structure of the multichromophoric system using DWFI method. Furthermore, we revealed that the structural heterogeneities and distortions depend on the ring size. Our findings illustrate the use of DWFI to gain deeper insight into the structure-property relationships of artificial light-harvesting molecular systems.

Pulsed interleaved excitation fluctuation imaging

Fluorescence fluctuation imaging is a powerful means to investigate dynamics, interactions, and stoichiometry of proteins inside living cells. Pulsed interleaved excitation (PIE) is the method of nanosecond alternating excitation with time-resolved detection and allows accurate, independent, and quasi-simultaneous determination of fluorescence intensities and lifetimes of different fluorophores. In this work, we combine pulsed interleaved excitation with fluctuation imaging methods (PIE-FI) such as raster image correlation spectroscopy (RICS) or number and brightness analysis (N&B). More specifically, we show that quantitative measurements of diffusion and molecular brightness of Venus fluorescent protein (FP) can be performed in solution with PIE-RICS and compare PIE-RICS with single-point PIE-FCS measurements. We discuss the advantages of cross-talk free dual-color PIE-RICS and illustrate its proficiency by quantitatively comparing two commonly used FP pairs for dual-color microscopy, eGFP/mCherry and mVenus/mCherry. For N&B analysis, we implement dead-time correction to the PIE-FI data analysis to allow accurate molecular brightness determination with PIE-NB. We then use PIE-NB to investigate the effect of eGFP tandem oligomerization on the intracellular maturation efficiency of the fluorophore. Finally, we explore the possibilities of using the available fluorescence lifetime information in PIE-FI experiments. We perform lifetime-based weighting of confocal images, allowing us to quantitatively determine molecular concentrations from 100 nM down to <30 pM with PIE-raster lifetime image correlation spectroscopy (RLICS). We use the fluorescence lifetime information to perform a robust dual-color lifetime-based FRET analysis of tandem fluorescent protein dimers. Lastly, we investigate the use of dual-color RLICS to resolve codiffusing FRET species from non-FRET species in cells. The enhanced capabilities and quantitative results provided by PIE-FI make it a powerful method that is broadly applicable to a large number of interesting biophysical studies.

Stepwise decrease of fluorescence versus sequential photobleaching in a single multichromophoric system

For individual molecules from the newly synthesized calix[4]arene tethered perylene bisimide (PBI) trimer, we studied the emitted fluorescence intensity as a function of time. Owing to the zigzag arrangement of PBI dyes in these trimers, the polarization state of the emission provides directly information about the emitting subunit within the trimer. Interestingly, we observed emission from all neutral subunits within a trimer rather than exclusively from the subunit with the lowest site energy. This can be understood in terms of thermally activated uphill energy transfer that repopulates the higher energetic chromophores. Together with the simultaneously recorded polarization-resolved emission spectra, this reveals that the emission from a multichromophoric system is governed by a complex interplay between the temporal variations of the photophysical parameters of the subunits, bidirectional hopping processes within the trimer, and unavoidable photobleaching. Moreover, it is demonstrated that the typically observed stepwise decrease of the signal from a multichromophoric system does not necessarily reflect sequential bleaching of the individual chromophores within the macromolecule.

Optical probing of single fluorescent molecules and proteins

Single-molecule detection and analysis of organic fluorescent molecules and proteins are presented, with emphasis on the underlying principles, methodology and the application of single-molecule analysis at room temperature. This Minireview is mainly focused on the application of confocal and near-field optical microscopy to investigate the photodynamics of individual molecules embedded in ultrathin polymer layers. We discuss rotational mobility of individual probe molecules in polystyrene and poly(methylmethacrylate) thin films, fluorescence lifetime trajectories and their spatial distribution, and real-time singlet-triplet dynamics. As a whole, the single-molecule photodynamics observed is due to the dynamic nature of both polymers at room temperature, where local polymer conformational dynamics modulates the oxygen concentration and diffusion on a molecular scale, influencing the fluorescence lifetime and intersystem crossing parameters. We also discuss the photodynamics of individual autofluorescent proteins, in particular the on/off blinking and the apparent stability of the protein against bleaching. These studies illustrate the unique information obtainable with the single-molecule approach, information that is otherwise hidden in ensemble-averaged measurements.

Dendrimer probes for enhanced photostability and localization in fluorescence imaging

Recent advances in fluorescence microscopy have enabled high-resolution imaging and tracking of single proteins and biomolecules in cells. To achieve high spatial resolutions in the nanometer range, bright and photostable fluorescent probes are critically required. From this view, there is a strong need for development of advanced fluorescent probes with molecular-scale dimensions for fluorescence imaging. Polymer-based dendrimer nanoconjugates hold strong potential to serve as versatile fluorescent probes due to an intrinsic capacity for tailored spectral properties such as brightness and emission wavelength. In this work, we report a new, to our knowledge, class of molecular probes based on dye-conjugated dendrimers for fluorescence imaging and single-molecule fluorescence microscopy. We engineered fluorescent dendritic nanoprobes (FDNs) to contain multiple organic dyes and reactive groups for target-specific biomolecule labeling. The photophysical properties of dye-conjugated FDNs (Cy5-FDNs and Cy3-FDNs) were characterized using single-molecule fluorescence microscopy, which revealed greatly enhanced photostability, increased probe brightness, and improved localization precision in high-resolution fluorescence imaging compared to single organic dyes. As proof-of-principle demonstration, Cy5-FDNs were used to assay single-molecule nucleic acid hybridization and for immunofluorescence imaging of microtubules in cytoskeletal networks. In addition, Cy5-FDNs were used as reporter probes in a single-molecule protein pull-down assay to characterize antibody binding and target protein capture. In all cases, the photophysical properties of FDNs resulted in enhanced fluorescence imaging via improved brightness and/or photostability.

Cyclodextrin insulation prevents static quenching of conjugated polymer fluorescence at the single molecule level

Conjugated polymers (CPs) are promising materials for fluorescence imaging application. However, a significant problem in this field is the unexplained abnormally low fluorescence brightness (or number of fluorescence photons detected per one excitation photon) exhibited by most of CP single chains in solid polymer hosts. Here it is shown that this detrimental effect can be fully avoided for short chains of polyfluorene-bis-vinylphenylene (PFBV) embedded in a host polymer matrix of PMMA, if the conjugated backbone is insulated by cyclodextrin rings to form a polyrotaxane (PFBV-Rtx). Fluorescence kinetics and quantum yields are measured for the polymers in liquid solutions, pristine films, and solid PMMA blends. The fluorescence brightness of PFBV-Rtx single chains dispersed in a solid PMMA is very close to that expected for a chain with 100% fluorescence quantum yield, while the unprotected PFBV chains of the same length possess 4 times lower brightness. Despite this, the fluorescence decay kinetics are the same for both polymers, suggesting the presence of static or ultrafast fluorescence quenching in the unprotected polymer. About 80% of an unprotected PFBV chain is estimated to be completely quenched. The hypothesis is that the cyclodextrin rings prevent the quenching by working as 'bumpers' reducing the mechanical forces applied by the host polymer to the conjugated backbone and help retaining its conformational freedom. While providing a recipe for making CP fluorescence bright at the single-molecule level, these results identify a lack of fundamental understanding in the community of the influence of the environment on excited states in conjugated materials.

Structure-property relationship of perylene bisimide macrocycles probed by atomic force microscopy and single-molecule fluorescence spectroscopy

Properties of a series of acetylene-linked perylene bisimide (PBI) macrocycles with different ring size composed of three to six PBI dyes were investigated by atomic force microscopy (AFM) and single-molecule fluorescence spectroscopy in a condensed phase. It was demonstrated that the structures of PBI cyclic arrays (CNs, N = 3, 4, 5, and 6) become distorted with increasing the ring size through molecular dynamics (MD) simulations (PM6-DH2 method) and AFM height images of CNs on highly ordered pyrolytic graphite (HOPG) surface. The MD simulations showed that only C5 and C6 rings are highly flexible molecules whose planarization goes along with a significant energetic penalty. Accordingly, both molecules did not show ordered adlayers on a HOPG surface. In contrast, C3 and C4 are far more rigid molecules leading to well-ordered hexagonal (C3) and rectangular (C4) 2D lattices. At the single-molecule level, we showed that the fluorescence properties of single CNs are affected by the structural changes. The fluorescence lifetimes of CNs became shorter and their distributions became broader due to the structural distortions with increasing the ring size. Furthermore, the CNs of smaller ring size exhibit a higher photostability and an efficient excitation energy transfer (EET) due to the more well-defined and planar structures compared to the larger CNs. Consequently, these observations provide evidence that not only PBI macrocycles are promising candidates for artificial light-harvesting systems, but also the photophysical properties of CNs are strongly related to the structural rigidity of CNs.

Watching conformational- and photo-dynamics of single fluorescent proteins in solution

Observing the dynamics of single biomolecules over prolonged time periods is difficult to achieve without significantly altering the molecule through immobilization. It can, however, be accomplished using the Anti-Brownian ELectrokinetic (ABEL) Trap, which allows extended investigation of solution-phase biomolecules - without immobilization -through real-time electrokinetic feedback. Here we apply the ABEL trap to study an important photosynthetic antenna protein, Allophycocyanin (APC). The technique allows the observation of single molecules of solution-phase APC for more than one second. We observe a complex relationship between fluorescence intensity and lifetime that cannot be explained by simple static kinetic models. Light-induced conformational changes are shown to occur and evidence is obtained for fluctuations in the spontaneous emission lifetime, which is typically assumed to be constant. Our methods provide a new window into the dynamics of fluorescent proteins and the observations are relevant for the interpretation of in vivo single-molecule imaging experiments, bacterial photosynthetic regulation, and biomaterials for solar energy harvesting.