Signal-pair correlation analysis of single-molecule trajectories

There you go: How to get kinetic information from trajectories of single biomolecules? A method based on correlating signal ranges (here for a three-state DNA hairpin with F = folded, I = intermediate, and U = unfolded state) is reported and shows how to get the kinetic scheme and the corresponding rates, even for states with low occupancy or very short lifetime, states which overlap because of noise, and systems with very similar or very different rates.     

Reaction pathways from single-molecule trajectories

Signal-pair histograms map transitions between different states of a single molecule and open new opportunities for the reconstruction of kinetic pathways.     

Microcavity-controlled single-molecule fluorescence.

We present for the first time cavity-controlled fluorescence spectra and decay curves of single dipole emitters interacting at room temperature with the first longitudinal mode of a Fabry-Perot microcavity offering a lambda/2-spacing between its silver mirrors. The spontaneous emission rate of individual dye molecules was found to be enhanced by the Purcell effect by up to three times compared to the rate in free space, in agreement with theoretical predictions. Moreover, our new microcavity design was found to provide long-term stability and single-molecule sensitivity under ambient conditions for several months without noticeable reduction of the cavity-Q value. We consider this as a significant advance for single-photon sources operating at room temperature.     

Photophysical aspects of single-molecule detection by two-photon excitation with consideration of sequential pulsed illumination.

An important goal in single molecule fluorescence correlation spectroscopy is the theoretical simulation of the fluorescence signal stemming from individual molecules and its autocorrelation function. The simulation approaches developed up to now are based exclusively on continuous-wave (cw) illumination and consequently on cw-excitation. However, this approximation is no longer valid in the case of two-photon excitation, for which pulsed illumination is usually employed. We present a novel theoretical model for the simulation of the fluorescence signal of single molecules and its autocorrelation function with consideration of the time dependence of the excitation flux and thus of all illumination-dependent photoprocesses: two-photon excitation, induced emission and photobleaching. Further important characteristics of our approach are the consideration of the dependence of the photobleaching rate on illumination and the low intersystem-crossing rates of the studied coumarins. Moreover, using our approach, we can predict quantitatively the effect of the laser pulse width on the fluorescence signal of a molecule, that is, the contributions of the photobleaching and saturation effects, and thus we can calculate the optimal laser pulse width. The theoretical autocorrelation functions were fitted to the experimental data, and we could ascertain a good agreement between the resulting and the expected parameters. The most important parameter is the photobleaching constant sigma, the cross section of the transition Sn<--S1, which characterises the photostability of the molecules independent of the experimental conditions. Its value is 1.7 x 10(-23) cm2 for coumarin 153 and 5 x 10(-23) cm2 for coumarin 314.     

Using single-molecule fluorescence spectroscopy to study electron transfer.

Techniques in single-molecule fluorescence spectroscopy now allow sophisticated studies of photophysical processes in single molecules. As interest grows in the possibilities of molecular electronics, researchers have begun to turn these techniques to the study of electron transfer. Electron-transfer reactions have now been detected and measured at the single-molecule level in a variety of systems and on a variety of timescales by adapting techniques from previous single-molecule fluorescence studies.     

Kinetics of the initial steps of G protein-coupled receptor-mediated cellular signaling revealed by single-molecule imaging.

We report on an in vivo single-molecule study of the signaling kinetics of G protein-coupled receptors (GPCR) performed using the neurokinin 1 receptor (NK1R) as a representative member. The NK1R signaling cascade is triggered by the specific binding of a fluorescently labeled agonist, substance P (SP). The diffusion of single receptor-ligand complexes in plasma membrane of living HEK 293 cells is imaged using fast single-molecule wide-field fluorescence microscopy at 100 ms time resolution. Diffusion trajectories are obtained which show intra- and intertrace heterogeneity in the diffusion mode. To investigate universal patterns in the diffusion trajectories we take the ligand-binding event as the common starting point. This synchronization allows us to observe changes in the character of the ligand-receptor-complex diffusion. Specifically, we find that the diffusion of ligand-receptor complexes is slowed down significantly and becomes more constrained as a function of time during the first 1000 ms. The decelerated and more constrained diffusion is attributed to an increasing interaction of the GPCR with cellular structures after the ligand-receptor complex is formed.     

The role of electronic coupling in linear porphyrin arrays probed by single-molecule fluorescence spectroscopy

Single-molecule photophysical properties of two families of linear porphyrin arrays have been investigated by single-molecule fluorescence detection techniques. Butadiyne-linked arrays (Z(N)B) with extensive π-conjugation perform as photostable one-quantum systems. This demonstration has been suggested by the long-lasting initial emissive state and subsequent discrete one-step photobleaching in the fluorescence intensity trajectories (FITs). As in the behavior of a one-quantum system, Z(N)B shows anti-bunching data in the coincidence measurements. On the other hand, in directly-linked arrays (Z(N)) with strong dipole coupling, each porphyrin moiety keeps individual character in photobleaching dynamics. The stepwise photobleachings in the FITs account for this explanation. Most of the FITs of Z(N) do not carry momentary cessation of fluorescence emission, which has been explained by the strongly bound electron-hole pair of Frenkel exciton that suppresses charge transfer between the molecule and surrounding polymers. These results give insight into the influences of interchromophorinc interactions between porphyrin moieties in the multiporphyrin arrays on their fluorescence dynamics at the single-molecule level.     

Single carbon nanotube optical spectroscopy.

This Minireview discusses novel insights into the electronic structure of carbon nanotubes obtained using single-molecule fluorescence spectroscopy. Fluorescence spectra from single nanotubes are well described by a single, Lorentzian lineshape. Nanotubes with identical structures fluoresce with different energies due to local electronic perturbations. Carbon nanotube fluorescence unexpectedly does not-show any intensity or spectral fluctuations at 300 K The lack of intensity blinking or bleaching demonstrates that carbon nanotubes have the potential to provide a stable, single-molecule infrared photon source, allowing for the exciting possibility of applications in quantum optics and biophotonics.     

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.