Fluorophore−Quencher Distance Correlation Functions from Single-Molecule Photon Arrival Trajectories†

Engineering nanolayered particles for modular drug delivery

Layer-by-layer (LbL) based self-assembly of nanoparticles is an emerging and powerful method to develop multifunctional and tissue responsive nanomedicines for a broad range of diseases. This unique assembly technique is able to confer a high degree of modularity, versatility, and compositional heterogeneity to nanoparticles via the sequential deposition of alternately charged polyelectrolytes onto a colloidal template. LbL assembly can provide added functionality by directly incorporating a range of functional materials within the multilayers including nucleic acids, synthetic polymers, polypeptides, polysaccharides, and functional proteins. These materials can be used to generate hierarchically complex, heterogeneous thin films on an extensive range of both traditional and novel nanoscale colloidal templates, providing the opportunity to engineer highly precise systems capable of performing the numerous tasks required for systemic drug delivery. In this review, we will discuss the recent advancements towards the development of LbL nanoparticles for drug delivery and diagnostic applications, with a special emphasis on the incorporation of biostability, active targeting, desirable drug release kinetics, and combination therapies into LbL nanomaterials. In addition to these topics, we will touch upon the next steps for the translation of these systems towards the clinic.

Single molecule counting statistics for systems with periodic driving

We extend the generating function approach for calculation of event statistics observed in single molecule spectroscopy to cases where the single molecule evolves under explicitly time-dependent and periodic perturbation. Floquet theory is used to recast the generating function equations for the periodically driven system into effective equations devoid of explicit time-dependence. Two examples are considered, one employing simple stochastic dynamics and the other quantum dynamics, to demonstrate the versatility and numerical accuracy of the methodology.

Application of confocal single-molecule FRET to intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are characterized by a large degree of conformational heterogeneity. In such cases, classical experimental methods often yield only mean values, averaged over the entire ensemble of molecules. The microscopic distributions of conformations, trajectories, or sequences of events often remain unknown, and with them the underlying molecular mechanisms. Signal averaging can be avoided by observing individual molecules. A particularly versatile method is highly sensitive fluorescence detection. In combination with Förster resonance energy transfer (FRET), distances and conformational dynamics can be investigated in single molecules. This chapter introduces the practical aspects of applying confocal single-molecule FRET experiments to the study of IDPs.

Resolving inhomogeneity using lifetime-weighted fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) was extended by incorporating information of the fluorescence lifetime. This new experimental approach, called lifetime-weighted FCS, enables us to observe fluorescence lifetime fluctuations in the nano- to millisecond time region. The potential of this method for resolving inhomogeneity in complex systems was demonstrated. First, by measuring a mixture of two dye molecules having different fluorescence lifetimes, it was shown that the lifetime-weighted correlation deviates from the ordinary intensity correlation only when the system is inhomogeneous. This demonstrated that lifetime-weighted FCS is capable of detecting inhomogeneity in an ensemble-averaged fluorescence decay profile without any a priori knowledge about the system. Second, we applied this method to a dye-labeled polypeptide, a prototypical model of complex biopolymers. It was found that the ratio between the lifetime-weighted and ordinary intensity correlation changes with change of the environment around the polypeptide. This result was interpreted in terms of environment-dependent conformational inhomogeneity of the polypeptide. Delay time dependence of the ratio was found to be constant from ∼1 μs to several milliseconds, indicating that the observed inhomogeneity is persistent in the measured time scale. In combination with fluorescence intensity correlation, lifetime-weighted FCS allows us to examine conformational fluctuations of complex systems in the time region from nano- to milliseconds, being free from the translational diffusion signal.

Fluctuations as a source of information in fluorescence microscopy

Fluctuations in fluorescence spectroscopy and microscopy have traditionally been regarded as noise—they lower the resolution and contrast and do not permit high acquisition rates. However, fluctuations can also be used to gain additional information about a system. This fact has been exploited in single-point microscopic techniques, such as fluorescence correlation spectroscopy and analysis of single molecule trajectories, and also in the imaging field, e.g. in spatio-temporal image correlation spectroscopy. Here, we discuss how fluctuations are used to obtain more quantitative information from the data than that given by average values, while minimizing the effects of noise due to stochastic photon detection.

Fluorescence correlation spectroscopy: novel variations of an established technique

Fluorescence correlation spectroscopy (FCS) is one of the major biophysical techniques used for unraveling molecular interactions in vitro and in vivo. It allows minimally invasive study of dynamic processes in biological specimens with extremely high temporal and spatial resolution. By recording and correlating the fluorescence fluctuations of single labeled molecules through the exciting laser beam, FCS gives information on molecular mobility and photophysical and photochemical reactions. By using dual-color fluorescence cross-correlation, highly specific binding studies can be performed. These have been extended to four reaction partners accessible by multicolor applications. Alternative detection schemes shift accessible time frames to slower processes (e.g., scanning FCS) or higher concentrations (e.g., TIR-FCS). Despite its long tradition, FCS is by no means dated. Rather, it has proven to be a highly versatile technique that can easily be adapted to solve specific biological questions, and it continues to find exciting applications in biology and medicine.

New directions in single-molecule imaging and analysis

Optical imaging and analysis of single molecules continue to unfold as powerful ways to study the individual behavior of biological systems, unobscured by ensemble averaging. Current expansion of interest in this field is great, as evidenced by new meetings, journal special issues, and the large number of new investigators. Selected recent advances in biomolecular analysis are described, and two new research directions are summarized: superresolution imaging using single-molecule fluorescence and trapping of single molecules in solution by direct suppression of Brownian motion.

Theory of the statistics of kinetic transitions with application to single-molecule enzyme catalysis

Single-molecule spectroscopy can monitor transitions between two microscopic states when these transitions are associated with the emission of photons. A general formalism is developed for obtaining the statistics of such transitions from a microscopic model when the dynamics is described by master or rate equations or their continuum analog, multidimensional reaction-diffusion equations. The focus is on the distribution of the number of transitions during a fixed observation time, the distribution of times between transitions, and the corresponding correlation functions. It is shown how these quantities are related to each other and how they can be explicitly calculated in a straightforward way for both immobile and diffusing molecules. Our formalism reduces to renewal theory when the monitored transitions either go to or originate from a single state. The influence of dynamics slow compared with the time between monitored transitions is treated in a simple way, and the probability distributions are expressed in terms of Mandel-type formulas. The formalism is illustrated by a detailed analysis of the statistics of catalytic turnovers of enzymes. When the rates of conformational changes are slower than the catalytic rates which are in turn slower than the binding relaxation rate, (1) the mean number of turnovers is shown to have the classical Michaelis-Menten form, (2) the correlation function of the number of turnovers is a direct measure of the time scale of catalytic rate fluctuations, and (3) the distribution of the time between consecutive turnovers is determined by the steady-state distribution.