Spectral Diffusion of Single Molecules in a Hierarchical Energy Landscape

Single-molecule excitation-emission spectroscopy

Single-molecule spectroscopy (SMS) provides a detailed view of individual emitter properties and local environments without having to resort to ensemble averaging. While the last several decades have seen substantial refinement of SMS techniques, recording excitation spectra of single emitters still poses a significant challenge. Here we address this problem by demonstrating simultaneous collection of fluorescence emission and excitation spectra using a compact common-path interferometer and broadband excitation, which is implemented as an extension of a standard SMS microscope. We demonstrate the technique by simultaneously collecting room-temperature excitation and emission spectra of individual terrylene diimide molecules and donor-acceptor dyads embedded in polystyrene. We analyze the resulting spectral parameters in terms of optical lineshape theory to obtain detailed information on the interactions of the emitters with their nanoscopic environment. This analysis finally reveals that environmental fluctuations between the donor and acceptor in the dyads are not correlated.

State transition identification in multivariate time series (STIMTS) applied to rotational jump trajectories from single molecules

Time resolved data from single molecule experiments often suffer from contamination with noise due to a low signal level. Identifying a proper model to describe the data thus requires an approach with sufficient model parameters without misinterpreting the noise as relevant data. Here, we report on a generalized data evaluation process to extract states with piecewise constant signal level from simultaneously recorded multivariate data, typical for multichannel single molecule experiments. The method employs the minimum description length principle to avoid overfitting the data by using an objective function, which is based on a tradeoff between fitting accuracy and model complexity. We validate our method with synthetic data from Monte Carlo simulations modeling fluorescence resonance energy transfer and rotational jumps, respectively. The method is applied to quantify rotational jump dynamics of single terrylene diimide (TDI) molecules deposited on a solid substrate. Depending on the substitution pattern of the TDI molecules and the chosen substrate materials, we find significant differences in time scale and geometry of molecular reorientation. From an additional application of our state transition identification in multivariate time series approach, a significant correlation between shifts of emission spectra and the occurrence of rotational jumps was found.

Dynamics of Single-Molecule Stokes Shifts: Influence of Conformation and Environment

We report on time-dependent Stokes shift measurements of single molecules. Excitation and emission spectroscopy were applied to study the temporal Stokes shift evolution of single perylene diimide molecules embedded in a polymer matrix on the time scale of seconds. The Stokes shift varied between individual molecules as well as for single molecules undergoing different conformations and geometries. From the distribution and temporal evolution of Stokes shifts, we unravel the interplay of nanoenvironment and molecular conformation. We found that Stokes shift fluctuations are related to simultaneous and unidirectional shifts of both emission and excitation spectra.

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.

Excitation Spectra and Stokes Shift Measurements of Single Organic Dyes at Room Temperature

We report measurements of excitation and emission spectra of single, polymer-embedded, perylene dye molecules at room temperature. From these measurements, we can derive the Stokes shift for each single molecule. We determined the distribution of excitation and emission peak energies and, thus, the distribution of single molecule Stokes shifts. Single molecule Stokes shifts have not been recorded to date, and the Stokes shift has often been assumed to be constant in single molecule studies. Our data show that the observed spectral heterogeneity in single molecule emission originates not only from synchronous energetic shifts of the excitation and the emission spectra but also from variations in the Stokes shift, speaking against the assumption of constant Stokes shift.

BOBA FRET: bootstrap-based analysis of single-molecule FRET data

Time-binned single-molecule Förster resonance energy transfer (smFRET) experiments with surface-tethered nucleic acids or proteins permit to follow folding and catalysis of single molecules in real-time. Due to the intrinsically low signal-to-noise ratio (SNR) in smFRET time traces, research over the past years has focused on the development of new methods to extract discrete states (conformations) from noisy data. However, limited observation time typically leads to pronounced cross-sample variability, i.e., single molecules display differences in the relative population of states and the corresponding conversion rates. Quantification of cross-sample variability is necessary to perform statistical testing in order to assess whether changes observed in response to an experimental parameter (metal ion concentration, the presence of a ligand, etc.) are significant. However, such hypothesis testing has been disregarded to date, precluding robust biological interpretation. Here, we address this problem by a bootstrap-based approach to estimate the experimental variability. Simulated time traces are presented to assess the robustness of the algorithm in conjunction with approaches commonly used in thermodynamic and kinetic analysis of time-binned smFRET data. Furthermore, a pair of functionally important sequences derived from the self-cleaving group II intron Sc.ai5γ (d3'EBS1*/IBS1*) is used as a model system. Through statistical hypothesis testing, divalent metal ions are shown to have a statistically significant effect on both thermodynamic and kinetic aspects of their interaction. The Matlab source code used for analysis (bootstrap-based analysis of smFRET data, BOBA FRET), as well as a graphical user interface, is available via http://www.aci.uzh.ch/rna/.

Efficient simultaneous fluorescence orientation, spectrum, and lifetime detection for single molecule dynamics

We report on the simultaneous detection of the fluorescence lifetime, spectrum, and three-dimensional dipole orientation determination of single perylene diimide molecules deposited on a silica surface as a model system for studying fluorophore internal and orientational dynamics. We employ a multi-parameter detection scheme to demonstrate how jumps in the orientation of the molecule can be disentangled from spectral jumps, both leading to changes of the detected total fluorescence intensity. The fluorescence lifetime determined simultaneously from the same photons is also sensitive to the orientation of the dipole with respect to the interface between media with different refractive indices. The correlated changes of the lifetime and orientation we observe are in good agreement with theory.

Photoluminescence intermittency from single quantum dots to organic molecules: emerging themes

Recent experimental and theoretical studies of photoluminescence intermittency (PI) or “blinking” exhibited by single core/shell quantum dots and single organic luminophores are reviewed. For quantum dots, a discussion of early models describing the origin of PI in these materials and recent challenges to these models are presented. For organic luminophores the role of electron transfer, proton transfer and other photophysical processes in PI are discussed. Finally, new experimental and data analysis methods are outlined that promise to be instrumental in future discoveries regarding the origin(s) of PI exhibited by single emitters.