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.

Single Semiconductor Nanocrystals under Compressive Stress: Reversible Tuning of the Emission Energy.

The photoluminescence of individual CdSe/CdS/ZnS core/shell nanocrystals has been investigated under external forces. After mutual alignment of a correlative atomic force and confocal microscope, individual particles were colocalized and exposed to a series of force cycles by using the tip of the AFM cantilever as a nanoscale piston. Thus, force-dependent changes of photophysical properties could be tracked on a single particle level. Remarkably, individual nanocrystals either shifted to higher or to lower emission energies with no indications of multiple emission lines under applied force. The direction and magnitude of these reversible spectral shifts depend on the orientation of nanocrystal axes relative to the external anisotropic force. Maximum pressures derived from the applied forces within a simple contact-mechanical model lie in the GPa range, comparable to values typically emerging in diamond anvil cells. Average spectral shift parameters of -3.5 meV/GPa and 3.0 meV/GPa are found for red- and blue-shifting species, respectively. Our results clearly demonstrate that the emission energy of single nanocrystals can be reversibly tuned over an appreciable wavelength range without degradation of their performance which appears as a promising feature with respect to tunable single photon sources or the creation of coherently coupled particle dimers.

Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor.

The interest in RNA modification enzymes surges due to their involvement in epigenetic phenomena. Here we present a particularly informative approach to investigate the interaction of dye-labeled RNA with modification enzymes. We investigated pseudouridine (Ψ) synthase TruB interacting with an alleged suicide substrate RNA containing 5-fluorouridine (5FU). A longstanding dogma, stipulating formation of a stable covalent complex was challenged by discrepancies between the time scale of complex formation and enzymatic turnover. Instead of classic mutagenesis, we used differentially positioned fluorescent labels to modulate substrate properties in a range of enzymatic conversion between 6% and 99%. Despite this variegation, formation of SDS-stable complexes occurred instantaneously for all 5FU-substrates. Protein binding was investigated by advanced fluorescence spectroscopy allowing unprecedented simultaneous detection of change in fluorescence lifetime, anisotropy decay, as well as emission and excitation maxima. Determination of Kd values showed that introduction of 5FU into the RNA substrate increased protein affinity by 14× at most. Finally, competition experiments demonstrated reversibility of complex formation for 5FU-RNA. Our results lead us to conclude that the hitherto postulated long-term covalent interaction of TruB with 5FU tRNA is based on the interpretation of artifacts. This is likely true for the entire class of pseudouridine synthases.

A competition smFRET assay to study ligand-induced conformational changes of the dengue virus protease.

Ligand binding to proteins often is accompanied by conformational transitions. Here, we describe a competition assay based on single molecule Förster resonance energy transfer (smFRET) to investigate the ligand-induced conformational changes of the dengue virus (DENV) NS2B-NS3 protease, which can adopt at least two different conformations. First, a competitive ligand was used to stabilize the closed conformation of the protease. Subsequent addition of the allosteric inhibitor reduced the fraction of the closed conformation and simultaneously increased the fraction of the open conformation, demonstrating that the allosteric inhibitor stabilizes the open conformation. In addition, the proportions of open and closed conformations at different concentrations of the allosteric inhibitor were used to determine its binding affinity to the protease. The KD value observed is in accordance with the IC50 determined in the fluorometric assay. Our novel approach appears to be a valuable tool to study conformational transitions of other proteases and enzymes.

The effects of allosteric and competitive inhibitors on ZIKV protease conformational dynamics explored through smFRET, nanoDSF, DSF, and 19F NMR.

Zika and dengue viruses cause mosquito-borne diseases of high epidemic relevance. The viral NS2B-NS3 proteases play crucial roles in the pathogen replication cycle and are validated drug targets. They can adopt at least two conformations depending on the position of the NS2B cofactor. Recently, we reported ligand-induced conformational changes of dengue virus NS2B-NS3 protease by single-molecule Förster resonance energy transfer (smFRET). Here, we investigated the conformational dynamics of the homologous Zika virus protease through an integrated methodological approach combining smFRET, thermal shift assays (DSF and nanoDSF) and 19F NMR spectroscopy. Our results show that allosteric inhibitors favor the open conformation and competitive inhibitors stabilize the closed conformation of the Zika virus protease.

Probing the electronic state of a single coronene molecule by the emission from proximate fluorophores.

We measured electronic transitions of the 2D graphene-type molecule hexa-peri-hexabenzocoronene (HBC) at the single-molecule level. The large intersystem crossing rate and long triplet state lifetime in the range of seconds are prohibitive for direct single-molecule observation. By covalently coupling fluorescent acceptor molecules (perylenecarboximide, PMI) to HBC, efficient singlet energy transfer gives rise to strong PMI fluorescence. Confocal single-molecule fluorescence microscopy with two excitation colours matching the HBC and PMI transition frequencies, respectively, was conducted. Single HBC-6PMI molecules were readily observed via the PMI emission. It was found that after selective excitation of the HBC the PMI emission is interrupted by dark intervals whose length of several seconds is in agreement with the triplet state lifetime of HBC. Accordingly, the presence/absence of PMI emission permits to read out the spin state of a single HBC molecule. Moreover, due to spectral overlap, the HBC triplet state acts as an energy acceptor for PMI in the excited singlet state, thus leading to efficient singlet-triplet annihilation (STA) during its lifetime. Hence, intersystem crossing into the HBC triplet state serves as a collective fluorescence switch for individual multichromophores.

Assembly and separation of semiconductor quantum dot dimers and trimers.

Repeated precipitation of colloidal semiconductor quantum dots (QD) from a good solvent by adding a poor solvent leads to an increasing number of QD oligomers after redispersion in the good solvent. By using density gradient ultracentrifugation we have been able to separate QD monomer, dimer, and trimer fractions from higher oligomers in such solutions. In the corresponding fractions QD dimers and trimers have been enriched up to 90% and 64%, respectively. Besides directly coupled oligomers, QD dimers and trimers were also assembled by linkage with a rigid terrylene diimide dye (TDI) and separated again by ultracentrifugation. High-resolution transmission electron micrographs show that the interparticle distances are clearly larger than those for directly coupled dots proving that the QDs indeed are cross-linked by the dye. Moreover, energy transfer from the QDs to the TDI "bridge" has been observed. Individual oligomers (directly coupled or dye-linked) can be readily deposited on a substrate and studied simultaneously by scanning force and optical microscopy. Our simple and effective scheme is applicable to a wide range of ligand stabilized colloidal nanoparticles and opens the way to a detailed study of electronic coupling in, e.g., QD molecules.

Conformational Dynamics of the Dengue Virus Protease Revealed by Fluorescence Correlation and Single-Molecule FRET Studies.

The dengue virus protease (DENV-PR) represents an attractive target for counteracting DENV infections. It is generally assumed that DENV-PR can exist in an open and a closed conformation and that active site directed ligands stabilize the closed state. While crystal structures of both the open and the closed conformation were successfully resolved, information about the prevalence of these conformations in solution remains elusive. Herein, we address the question of whether there is an equilibrium between different conformations in solution which can be influenced by addition of a competitive inhibitor. To this end, DENV-PR was statistically labeled by two dye molecules constituting a FRET (fluorescence resonance energy transfer) couple. Fluorescence correlation spectroscopy and photon-burst detection were employed to examine FRET pair labeled DENV-PRs freely diffusing in solution. The measurements were performed with two double mutants and with two dye couples. The data provide strong evidence that an equilibrium of at least two conformations of DENV-PR exists in solution. The competitive inhibitor stabilizes the closed state. Because the open and closed conformations appear to coexist in solution, our results support the picture of a conformational selection rather than that of an induced fit mechanism with respect to the inhibitor-induced formation of the closed state.

Quantification of the singlet-singlet annihilation times of individual bichromophoric molecules by photon coincidence measurements.

Singlet-singlet annihilation (SSA) times in individual bichromophoric molecules have been quantified by time-resolved photon coincidence measurements. An analytical expression has been derived to obtain the SSA times from the coincidence histograms. The results have been confirmed by Monte Carlo simulations. SSA was found to be about three times faster than the fluorescence lifetime of the chromophores. Considering the spectral overlap for SSA and for energy transfer from an excited to a ground state chromophore, we conclude that in the weak coupling limit for any arrangement of the two chromophores both processes occur on similar time scales.

Impact of local compressive stress on the optical transitions of single organic dye molecules.

The ability to mechanically control the optical properties of individual molecules is a grand challenge in nanoscience and could enable the manipulation of chemical reactivity at the single-molecule level. In the past, light has been used to alter the emission wavelength of individual molecules or modulate the energy transfer quantum yield between them. Furthermore, tensile stress has been applied to study the force dependence of protein folding/unfolding and of the chemistry and photochemistry of single molecules, although in these mechanical experiments the strength of the weakest bond limits the amount of applicable force. Here, we show that compressive stress modifies the photophysical properties of individual dye molecules. We use an atomic force microscope tip to prod individual molecules adsorbed on a surface and follow the effect of the applied force on the electronic states of the molecule by fluorescence spectroscopy. Applying a localized compressive force on an isolated molecule induces a stress that is redistributed throughout the structure. Accordingly, we observe reversible spectral shifts and even shifts that persist after retracting the microscope tip, which we attribute to transitions to metastable states. Using quantum-mechanical calculations, we show that these photophysical changes can be associated with transitions among the different possible conformers of the adsorbed molecule.

Control of the electronic energy transfer pathway between two single fluorophores by dual pulse excitation.

We report on the control of the energy transfer pathway in individual donor-acceptor dyads by proper timing of light pulses matching the donor and acceptor transition frequencies, respectively. Excitation of both chromophores at virtually the same time induces efficient singlet-singlet annihilation, whereby excitation energy effectively flows from the acceptor to the donor. The dual pulse excitation scheme implemented here allows for all-optical switching of the fluorescence intensity at the single-molecule level. The population of higher excited states at the donor site was found to significantly increase the photobleaching probability.

Theoretical investigation of electronic excitation energy transfer in bichromophoric assemblies.

Electronic excitation energy transfer (EET) rates in rylene diimide dyads are calculated using second-order approximate coupled-cluster theory and time-dependent density functional theory. We investigate the dependence of the EET rates on the interchromophoric distance and the relative orientation and show that Forster theory works quantitatively only for donor-acceptor separations larger than roughly 5 nm. For smaller distances the EET rates are over- or underestimated by Forster theory depending on the respective orientation of the transition dipole moments of the chromophores. In addition to the direct transfer rates we consider bridge-mediated transfer originating from oligophenylene units placed between the chromophores. We find that the polarizability of the bridge significantly enhances the effective interaction. We compare our calculations to single molecule experiments on two types of dyads and find reasonable agreement between theory and experiment.

Flexibility of phenylene oligomers revealed by single molecule spectroscopy.

The rigidity of a p-phenylene oligomer (p-terphenyl) has been investigated by single molecule confocal fluorescence microscopy. Two different rylene diimide dyes attached to the terminal positions of the oligomer allowed for wavelength selective excitation of the two chromophores. In combination with polarization modulation the spatial orientation of the transition dipoles of both end groups could be determined independently. We have analyzed 597 single molecules in two different polymer hosts, polymethylmethacrylate and Zeonex. On average we find a 22 degrees deviation from the linear gas phase geometry (T = 0 K), indicating a rather high flexibility of the p-phenylene oligomer independent of the matrix. To substantiate our experimental results, we have performed quantum chemical calculations at the density functional theory level for the molecular geometry and the electronic excitations. Our findings are in agreement with former experiments on the persistence length of poly(p-phenylenes).

Formation of self-supporting reversible cellular networks in suspensions of colloids and liquid crystals.

In mixtures of thermotropic liquid crystals with spherical poly (methyl methacrylate) particles, self-supporting networklike structures are formed during slow cooling past the isotropic-to-nematic phase transformation. To characterize the process of network formation in terms of morphology, phase transformation kinetics, and mechanical properties, we have combined data from polarization and laser scanning confocal microscopy with calorimetric, NMR, and rheological results. Our data suggest that the mechanism of network formation is dominated by a broadened temperature and time interval of phase transformation rather than by particle size or concentration. The observation that the width of the transformation interval strongly depends on sample preparation supports the hypothesis that a third component, most likely alkane remnants slowly liberated from the particles, plays a crucial role. In addition, calorimetric findings for liquid crystal/colloid mixtures, heated and cooled up to 13 times, point to separation of the liquid crystal into two compartments with different phase transformation kinetics. This could be explained by redistribution and enrichment of alkane in the particle-composed network walls. A further increase of the storage modulus, G', and incomplete dissolution of the networks in the isotropic state indicate that the formation of two compartments during repeated temperature cycles stabilizes the network and confers strong memory effects.