A microscopic model for the fluctuations of local field and spontaneous emission of single molecules in disordered media.

We develop a microscopic model to describe the observed temporal fluctuations of the fluorescence lifetime of single molecules embedded in a polymer at room temperature. The model represents the fluorescent probe and the macromolecular matrix on the sites of a cubic lattice and introduces voids in the matrix to account for its mobility. We generalize Lorentz's approach to dielectrics by considering three domains of electrostatic interaction of the probe molecule with its nanoenvironment: (1) the probe molecule with its elongated shape and its specific polarizability, (2) the first few solvent shells with their discrete structure and their inhomogeneity, (3) the remainder of the solvent at larger distances, treated as a continuous dielectric. The model is validated by comparing its outcome for homogeneous systems with those of existing theories. When realistic inhomogeneities are introduced, the model correctly explains the observed fluctuations of the lifetimes of single molecules. Such a comparison is only possible with single-molecule observations, which provide a new access to local field effects.     

Fluorescent perylene diimide rotaxanes: spectroscopic signatures of wheel-chromophore interactions

[2]- and [3]-rotaxanes with a tetraphenoxy perylene diimide core were synthesized. Hydrogen bonding between the wheel and the imide changes the optical properties of the perylene chromophore: the absorption and fluorescence spectra are red-shifted. The decay times of the rotaxanes are shorter in comparison with that of the axle. Single molecule fluorescence measurements reveal relatively narrow distributions of emission maxima and decay times. The averages are in agreement with ensemble measurements. The observed red shifts make the perylene diimide a suitable chromophore for sensing the position of the wheel on the axle.     

Direct measurement of the end-to-end distance of individual polyfluorene polymer chains.

Wide-field imaging of individual multichromophoric molecules and successive photobleaching were used to determine, accurately, the relative position of the chromophores in such systems. First, a polyphenylene dendrimer with well-defined geometry was used to establish the accuracy in localization that can be obtained by this methodology. For a signal-to-noise ratio of 20, interchromophoric distances could be measured with 4 nm accuracy. Next, the method was used to determine the end-to-end distribution of an end-capped polyfluorene polymer. From comparison between the experimental and simulated distributions, information on the conformation of the polymer could be deduced. It was found that the polymer has a nonlinear conformation. A conjugation length of six monomer units gave the best fit of the experimental data to the proposed model.     

Design of molecular photonic wires based on multistep electronic excitation transfer.

Light-harvesting complexes, one of nature's supreme examples of nanoscale engineering, have inspired researchers to construct molecular optical devices, such as photonic wires, which are optimised for efficient transfer of excited-state energy over large distances. The control parameters for the design and the advantages of single-molecule fluorescence spectroscopy for the study of such complex systems are discussed with respect to energy-transfer mechanisms, chromophore selection and arrangement as well as static and dynamic heterogeneity.     

Fluorescence Spectroscopy of Single Molecules under Ambient Conditions: Methodology and Technology

This review presents an overview of the fluorescence detection and spectroscopy of single molecules (SMS) in liquids and on surfaces under ambient conditions. The various techniques of SMS, such as confocal epifluorescence detection and wide‐field imaging are presented and discussed, together with the different methods of data analysis such as fluorescence correlation spectroscopy and burst‐by‐burst analysis. Selected applications of the various techniques in physics, chemistry, and biology are described.     

Monitoring molecular beacon DNA probe hybridization at the single-molecule level

We have monitored the reaction dynamics of the DNA hybridization process on a liquid/solid interface at the single-molecule level by using a hairpin-type molecular beacon DNA probe. Fluorescence images of single DNA probes were recorded by using total internal reflection fluorescence microscopy. The fluorescence signal of single DNA probes during the hybridization to individual complementary DNA probes was monitored over time. Among 400 molecular beacon DNA probes that we tracked, 349 molecular beacons (87.5 %) were hybridized quickly and showed an abrupt fluorescence increase, while 51 probes (12.5 %) reacted slowly, resulting in a gradual fluorescence increase. This ratio stayed about the same when varying the concentrations of cDNA in MB hybridization on the liquid/surface interface. Statistical data of the 51 single-molecule hybridization images showed that there was a multistep hybridization process. Our results also showed that photostability for the dye molecules associated with the double-stranded hybrids was better than that for those with the single-stranded molecular beacon DNA probes. Our results demonstrate the ability to obtain a better understanding of DNA hybridization processes using single-molecule techniques, which will improve biosensor and biochip development where surface-immobilized molecular beacon DNA probes provide unique advantages in signal transduction.     

Single dibenzoterrylene molecules in an anthracene crystal: spectroscopy and photophysics.

We study single dibenzoterrylene molecules in an anthracene single crystal at 1.4 K in two insertion sites at 785.1 and 794.3 nm. The single-molecule zero-phonon lines are narrow (about 30 MHz), intense (the detected fluorescence rates at saturation reach 100,000 counts s(-1)), and very photostable. The intersystem-crossing yield is extremely low (10(-7) or lower). All of these features are hallmarks of an excellent system for high-resolution spectroscopy and nanoscale probing at cryogenic temperatures.     

Investigation of an acid-base and redox molecular switch: from bulk to the single-molecule level

In this work we investigate a new fluorescent molecular switch based on the interconversion between the fluorescent zwitterionic form (ZW1) and the non-fluorescent anionic state (MC2) of a spirocyclic Meisenheimer complex of 1,3,5-trinitrobenzene. Density functional theory molecular orbital calculations reveal that photo-induced electron transfer from a guanidine group to the trinitrocyclohexadiene fluorophore of the complex quenches the emission from MC2. Protonation, as well as coordination of other Lewis acids to the guanidine group, suppress the quenching mechanism and allow the complex to fluoresce. In agreement with the calculations, reversible on-off fluorescence switching of the ZW1-MC2 bulk system occurs by protonation-deprotonation of the guanidine moiety upon acid-base addition. Interestingly, spectroelectrochemical ensemble measurements show that switching of the ZW1-MC2 pair can also be attained electrochemically, thus unraveling the versatile functioning of this system. The ultimate limit of monitoring the reversible on-off operation of individual switch molecules is reached by means of single-molecule fluorescence spectroscopy, which demonstrates the potential of the ZW1-MC2 system to be used as a true single-molecule switch on the nanometer scale.     

Mechanism of Intramolecular Photostabilization in Self‐Healing Cyanine Fluorophores

Organic fluorophores, which are popular labels for microscopy applications, intrinsically suffer from transient and irreversible excursions to dark‐states. An alternative to adding photostabilizers at high concentrations to the imaging buffer relies on the direct linkage to the fluorophore. However, the working principles of this approach are not yet fully understood. In this contribution, we investigate the mechanism of intramolecular photostabilization in self‐healing cyanines, in which photodamage is automatically repaired. Experimental evidence is provided to demonstrate that a single photostabilizer, that is, the vitamin E derivative Trolox, efficiently heals the cyanine fluorophore Cy5 in the absence of any photostabilizers in solution. A plausible mechanism is that Trolox interacts with the fluorophore through intramolecular quenching of triplet‐related dark‐states, which is a mechanism that appears to be common for both triplet‐state quenchers (cyclooctatetraene) and redox‐active compounds (Trolox, ascorbic acid, methylviologen). Additionally, the influence of solution‐additives, such as cysteamine and procatechuic acid, on the self‐healing process are studied. The results suggest the potential applicability of self‐healing fluorophores in stochastic optical reconstruction microscopy (STORM) with optical super‐resolution. The presented data contributes to an improved understanding of the mechanism involved in intramolecular photostabilization and has high relevance for the future development of self‐healing fluorophores, including their applications in various research fields.