Ten Years of Single-Molecule Spectroscopy

The laser pump X-ray probe system at LISA P08 PETRA III

Understanding and controlling the structure and function of liquid interfaces is a constant challenge in biology, nanoscience and nanotechnology, with applications ranging from molecular electronics to controlled drug release. X-ray reflectivity and grazing incidence diffraction provide invaluable probes for studying the atomic scale structure at liquid-air interfaces. The new time-resolved laser system at the LISA liquid diffractometer situated at beamline P08 at the PETRA III synchrotron radiation source in Hamburg provides a laser pump with X-ray probe. The femtosecond laser combined with the LISA diffractometer allows unique opportunities to investigate photo-induced structural changes at liquid interfaces on the pico- and nanosecond time scales with pump-probe techniques. A time resolution of 38 ps has been achieved and verified with Bi. First experiments include laser-induced effects on salt solutions and liquid mercury surfaces with static and varied time scales measurements showing the proof of concept for investigations at liquid surfaces.

Future Paths in Cryogenic Single-Molecule Fluorescence Spectroscopy

In the last three decades, cryogenic single-molecule fluorescence spectroscopy has provided average-free understanding of the photophysics and of fundamental interactions at molecular scales. Furthermore, they propose original pathways and applications in the treatment and storage of quantum information. The ultranarrow lifetime-limited zero-phonon line acts as an excellent sensor to local perturbations caused either by intrinsic dynamical degrees of freedom, or by external perturbations, such as those caused by electric fields, elastic and acoustic deformations, or light-induced dynamics. Single aromatic hydrocarbon molecules, being sensitive to nanoscale probing at nanometer scales, are potential miniaturized platforms for integrated quantum photonics. In this Perspective, we look back at some of the past advances in cryogenic optical microscopy and propose some perspectives for future development.

Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA

The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.

Dynamic Heterogeneity in the Optical Signals from Single Nano-Objects

In contrast to ensemble-averaged measurements, single-molecule experiments directly display the heterogeneity of molecular properties in space and time. In many complex systems, spatial heterogeneity is regularly accompanied by temporal or dynamic heterogeneity; if a property differs from molecule to molecule, it will often vary in time for one and the same molecule. In this short paper, we discuss a few examples of complex systems where dynamical heterogeneity was observed in single-molecule or single-particle optical signals. For single biomolecules, the first demonstration of dynamic heterogeneity in a single enzyme was provided by Xie and colleagues. Other examples are found in glassy systems, and very recently in the magnetic relaxation of single superparamagnetic nanoparticles. The ubiquity of this phenomenon suggests that, rather than an exception, dynamic heterogeneity is the rule in complex systems with multiple degrees of freedom.

Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles

Single-molecule microscopic techniques allow the counting of successive turnover events and the study of the time-dependent fluctuations of the catalytic activities of individual enzymes and different sites on a single heterogeneous nanocatalyst. It is important to establish theoretical methods to obtain the statistical measurements of such stochastic fluctuations that provide insight into the catalytic mechanism. In this review, we discuss a few theoretical frameworks for evaluating the first passage time distribution functions using a self-consistent pathway approach and chemical master equations, to establish a connection with experimental observables. The measurable probability distribution functions and their moments depend on the molecular details of the reaction and provide a way to quantify the molecular mechanisms of the reaction process. The statistical measurements of these fluctuations should provide insight into the enzymatic mechanism.

Progress and perspectives in single-molecule optical spectroscopy

We review some of the progress of single-molecule optical experiments in the past 20 years and propose some perspectives for the coming years. We particularly focus on methodological advances in fluorescence, super-resolution, photothermal contrast, and interferometric scattering and briefly discuss a few of the applications. These advances have enabled the exploration of new emitters and quantum optics; the chemistry and biology of complex heterogeneous systems, nanoparticles, and plasmonics; and the detection and study of non-fluorescing and non-absorbing nano-objects. We conclude by proposing some ideas for future experiments. The field will move toward more and better signals of a broader variety of objects and toward a sharper view of the surprising complexity of the nanoscale world of single (bio-)molecules, nanoparticles, and their nano-environments.

Unraveling multi-state molecular dynamics in single-molecule FRET experiments. I. Theory of FRET-lines

Conformational dynamics of biomolecules are of fundamental importance for their function. Single-molecule studies of Förster Resonance Energy Transfer (smFRET) between a tethered donor and acceptor dye pair are a powerful tool to investigate the structure and dynamics of labeled molecules. However, capturing and quantifying conformational dynamics in intensity-based smFRET experiments remains challenging when the dynamics occur on the sub-millisecond timescale. The method of multiparameter fluorescence detection addresses this challenge by simultaneously registering fluorescence intensities and lifetimes of the donor and acceptor. Together, two FRET observables, the donor fluorescence lifetime τD and the intensity-based FRET efficiency E, inform on the width of the FRET efficiency distribution as a characteristic fingerprint for conformational dynamics. We present a general framework for analyzing dynamics that relates average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms. We present parametric relations of these observables for interpreting the location of FRET populations in E-τD diagrams, called FRET-lines. To facilitate the analysis of complex exchange equilibria, FRET-lines serve as reference curves for a graphical interpretation of experimental data to (i) identify conformational states, (ii) resolve their dynamic connectivity, (iii) compare different kinetic models, and (iv) infer polymer properties of unfolded or intrinsically disordered proteins. For a simplified graphical analysis of complex kinetic networks, we derive a moment-based representation of the experimental data that decouples the motion of the fluorescence labels from the conformational dynamics of the biomolecule. Importantly, FRET-lines facilitate exploring complex dynamic models via easily computed experimental observables. We provide extensive computational tools to facilitate applying FRET-lines.

Trajectory Ensemble Methods Provide Single-Molecule Statistics for Quantum Dynamical Systems

The emergence of experiments capable of probing quantum dynamics at the single-molecule level requires the development of new theoretical tools capable of simulating and analyzing these dynamics beyond an ensemble-averaged description. In this article, we present an efficient method for sampling and simulating the dynamics of the individual quantum systems that make up an ensemble and apply it to study the nonequilibrium dynamics of the ubiquitous spin-boson model. We generate an ensemble of single-system trajectories, and we analyze this trajectory ensemble using tools from classical statistical mechanics. Our results demonstrate that the dynamics of quantum coherence is highly heterogeneous at the single-system level due to variations in the initial bath configuration, which significantly affects the transient exchange of coherence between the system and its bath. We observe that single systems tend to retain coherence over time scales longer than that of the ensemble. We also compute a novel thermodynamic entanglement entropy that quantifies a thermodynamic driving force favoring system-bath entanglement.

Narrow and Stable Single Photon Emission from Dibenzoterrylene in para-Terphenyl Nanocrystals

Single organic molecules are promising photon sources for quantum technologies. In this work we show photon emission from dibenzoterrylene, a widely used organic emitter, in a new host matrix, para-terphenyl. We present a reprecipitation growth method that produces para-terphenyl nanocrystals which are ideal for integration into nanophotonic devices due to their small size. We characterise the optical properties of dibenzoterrylene in nanocrystals at room and cryogenic temperatures, showing bright, narrow emission from a single molecule. Spectral data on the vibrational energies is presented and a further 25 additional molecules are characterised. This emitter-host combination has potential for quantum technology purposes with wavelengths suitable for interfacing with quantum memories.

Excitonic Fine Structure in Emission of Linear Carbon Chains

We studied monatomic linear carbon chains stabilized by gold nanoparticles attached to their ends and deposited on a solid substrate. We observe spectral features of straight chains containing from 8 to 24 atoms. Low-temperature PL spectra reveal characteristic triplet fine structures that repeat themselves for carbon chains of different lengths. The triplet is invariably composed of a sharp intense peak accompanied by two broader satellites situated 15 and 40 meV below the main peak. We interpret these resonances as an edge-state neutral exciton and positively and negatively charged trions, respectively. The time-resolved PL shows that the radiative lifetime of the observed quasiparticles is about 1 ns, and it increases with the increase of the length of the chain. At high temperatures a nonradiative exciton decay channel appears due to the thermal hopping of carriers between parallel carbon chains. Excitons in carbon chains possess large oscillator strengths and extremely low inhomogeneous broadenings.

Phonon-Induced Optical Dephasing in Single Organic Molecules

We present a joint experiment-theory analysis of the temperature-dependent emission spectra, zero-phonon linewidth, and second-order correlation function of light emitted from a single organic molecule. We observe spectra with a zero-phonon line together with several additional sharp peaks, broad phonon sidebands, and a strongly temperature dependent homogeneous broadening. Our model includes both localized vibrational modes of the molecule and a thermal phonon bath, which we include nonperturbatively, and is able to capture all observed features. For resonant driving we measure Rabi oscillations that become increasingly damped with temperature, which our model naturally reproduces. Our results constitute an essential characterization of the photon coherence of molecules, paving the way to their use in future quantum information applications.

3D optical nanoscopy with excited state saturation at liquid helium temperatures

We present a 3D fluorescence nanoscopy method operating at cryogenic temperatures, based on optical saturation of the excited state of individual molecules. Using a focused laser beam structured with a zero-intensity central region surrounded by intensity gradients in the three space directions, we achieve a sub-30 nm 3D optical resolution. Moreover, the analysis of the fluorescence scanning images of single molecules reveals the 3D orientation of their transition dipole with an accuracy of a few degrees. This method provides a valuable tool for locating neighboring molecules with overlapping optical transitions in order to study their interactions.

Quantum electrodynamics at room temperature coupling a single vibrating molecule with a plasmonic nanocavity

Interactions between a single emitter and cavity provide the archetypical system for fundamental quantum electrodynamics. Here we show that a single molecule of Atto647 aligned using DNA origami interacts coherently with a sub-wavelength plasmonic nanocavity, approaching the cooperative regime even at room temperature. Power-dependent pulsed excitation reveals Rabi oscillations, arising from the coupling of the oscillating electric field between the ground and excited states. The observed single-molecule fluorescent emission is split into two modes resulting from anti-crossing with the plasmonic mode, indicating the molecule is strongly coupled to the cavity. The second-order correlation function of the photon emission statistics is found to be pump wavelength dependent, varying from g(2)(0) = 0.4 to 1.45, highlighting the influence of vibrational relaxation on the Jaynes-Cummings ladder. Our results show that cavity quantum electrodynamic effects can be observed in molecular systems at ambient conditions, opening significant potential for device applications.

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.

Fano Description of Single-Hydrocarbon Fluorescence Excited by a Scanning Tunneling Microscope

The detection of fluorescence with submolecular resolution enables the exploration of spatially varying photon yields and vibronic properties at the single-molecule level. By placing individual polycyclic aromatic hydrocarbon molecules into the plasmon cavity formed by the tip of a scanning tunneling microscope and a NaCl-covered Ag(111) surface, molecular light emission spectra are obtained that unravel vibrational progression. In addition, light spectra unveil a signature of the molecule even when the tunneling current is injected well separated from the molecular emitter. This signature exhibits a distance-dependent Fano profile that reflects the subtle interplay between inelastic tunneling electrons, the molecular exciton and localized plasmons in at-distance as well as on-molecule fluorescence. The presented findings open the path to luminescence of a different class of molecules than investigated before and contribute to the understanding of single-molecule luminescence at surfaces in a unified picture.

Correlating Transcription Initiation and Conformational Changes by a Single-Subunit RNA Polymerase with Near Base-Pair Resolution

We provide a comprehensive analysis of transcription in real time by T7 RNA Polymerase (RNAP) using single-molecule fluorescence resonance energy transfer by monitoring the entire life history of transcription initiation, including stepwise RNA synthesis with near base-pair resolution, abortive cycling, and transition into elongation. Kinetically branching pathways were observed for abortive initiation with an RNAP either recycling on the same promoter or exchanging with another RNAP from solution. We detected fast and slow populations of RNAP in their transition into elongation, consistent with the efficient and delayed promoter release, respectively, observed in ensemble studies. Real-time monitoring of abortive cycling using three-probe analysis showed that the initiation events are stochastically branched into productive and failed transcription. The abortive products are generated primarily from initiation events that fail to progress to elongation, and a majority of the productive events transit to elongation without making abortive products.

Role of missing carotenoid in reducing the fluorescence of single monomeric photosystem II core complexes

The fluorescence of monomeric photosystem II core complexes (mPSIIcc) of the cyanobacterium Thermosynechococcus elongatus, originating from redissolved crystals, is investigated by using single-molecule spectroscopy (SMS) at 1.6 K. The emission spectra of individual mPSIIcc are dominated by sharp zero-phonon lines, showing the existence of different emitters compatible with the F685, F689, and F695 bands reported formerly. The intensity of F695 is reduced in single mPSIIcc as compared to single PSIIcc-dimers (dPSIIcc). Crystal structures show that one of the β-carotene (β-Car) cofactors located at the monomer-monomer interface in dPSIIcc is missing in mPSIIcc. This β-Car in dPSIIcc is in van der Waals distance to chlorophyll (Chl) 17 in the CP47 subunit. We suggest that this Chl contributes to the F695 emitter. A loss of β-Car cofactors in mPSIIcc preparations will lead to an increased lifetime of the triplet state of Chl 17, which can explain the reduced singlet emission of F695 as observed in SMS.

Temperature dependence of metal-enhanced fluorescence of photosystem I from Thermosynechococcus elongatus

We report the temperature dependence of metal-enhanced fluorescence (MEF) of individual photosystem I (PSI) complexes from Thermosynechococcus elongatus (T. elongatus) coupled to gold nanoparticles (AuNPs). A strong temperature dependence of shape and intensity of the emission spectra is observed when PSI is coupled to AuNPs. For each temperature, the enhancement factor (EF) is calculated by comparing the intensity of individual AuNP-coupled PSI to the mean intensity of 'uncoupled' PSI. At cryogenic temperature (1.6 K) the average EF was 4.3-fold. Upon increasing the temperature to 250 K the EF increases to 84-fold. Single complexes show even higher EFs up to 441.0-fold. At increasing temperatures the different spectral pools of PSI from T. elongatus become distinguishable. These pools are affected differently by the plasmonic interactions and show different enhancements. The remarkable increase of the EFs is explained by a rate model including the temperature dependence of the fluorescence yield of PSI and the spectral overlap between absorption and emission spectra of AuNPs and PSI, respectively.

Quantitative deconvolution of autocorrelations and cross correlations from two-dimensional lifetime decay maps in fluorescence lifetime correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is a widely used method for measuring molecular diffusion and chemical kinetics. However, when a mixture of fluorescent species is taken into account, the conventional FCS method has limitations in extracting autocorrelations for different species and cross correlations between different species. Recently developed fluorescence lifetime correlation spectroscopy (FLCS) based on time-tagged time-resolved (TTTR) photon recording, which can record the global and micro arrival time for each individual photon, has been used to discriminate different species according to fluorescence lifetime. Here, based on two-dimensional lifetime decay maps constructed from TTTR photon stream, we have developed a quantitative lifetime-deconvolution FCS model (LDFCS) to extract precise chemical rates for chemical conversions in multi-species systems. The key point of LDFCS model is separation of different species according to the global distribution of fluorescence lifetime and then deconvolution of autocorrelations and cross-correlations from the two-dimensional lifetime decay maps constructed by the micro arrival times of photon pairs at each delay time.

Theoretical aspects of femtosecond double-pump single-molecule spectroscopy. I. Weak-field regime

We present a theoretical description of double-pump femtosecond single-molecule signals with fluorescence detection.

Analyzing Single-Molecule Protein Transportation Experiments via Hierarchical Hidden Markov Models

To maintain proper cellular functions, over 50% of proteins encoded in the genome need to be transported to cellular membranes. The molecular mechanism behind such a process, often referred to as protein targeting, is not well understood. Single-molecule experiments are designed to unveil the detailed mechanisms and reveal the functions of different molecular machineries involved in the process. The experimental data consist of hundreds of stochastic time traces from the fluorescence recordings of the experimental system. We introduce a Bayesian hierarchical model on top of hidden Markov models (HMMs) to analyze these data and use the statistical results to answer the biological questions. In addition to resolving the biological puzzles and delineating the regulating roles of different molecular complexes, our statistical results enable us to propose a more detailed mechanism for the late stages of the protein targeting process.

Stable, single-photon emitter in a thin organic crystal for application to quantum-photonic devices

Single dibenzoterrylene (DBT) molecules offer great promise as bright, reliable sources of single photons on demand, capable of integration into solid-state devices. It has been proposed that DBT in anthracene might be placed close to an optical waveguide for this purpose, but so far there have been no demonstrations of sufficiently thin crystals, with a controlled concentration of the dopant molecules. Here we present a method for growing very thin anthracene crystals from super-saturated vapour, which produces crystals of extreme flatness and controlled thickness. We show how this crystal can be doped with an adjustable concentration of dibenzoterrylene (DBT) molecules and we examine the optical properties of these molecules to demonstrate their suitability as quantum emitters in nanophotonic devices. Our measurements show that the molecules are available in the crystal as single quantum emitters, with a well-defined polarisation relative to the crystal axes, making them amenable to alignment with optical nanostructures. We find that the radiative lifetime and saturation intensity vary little within the crystal and are not in any way compromised by the unusual matrix environment. We show that a large fraction of these emitters can be excited more than 10¹² times without photo-bleaching, making them suitable for real applications.

Observing Single Molecules Complexing with Cucurbit[7]uril through Nanogap Surface-Enhanced Raman Spectroscopy

In recent years, single-molecule sensitivity achievable by surface-enhanced Raman spectroscopy (SERS) has been widely reported. We use this to investigate supramolecular host-guest chemistry with the macrocyclic host cucurbit[7]uril, on a few-to-single-molecule level. A nanogap geometry, comprising individual gold nanoparticles on a planar gold surface spaced by a single layer of molecules, gives intense SERS signals. Plasmonic coupling between the particle and the surface leads to strongly enhanced optical fields in the gap between them, with single-molecule sensitivity established using a modification of the well-known bianalyte method. Changes in the Raman modes of the host molecule are observed when single guests included inside its cavity internally stretch it. Anisotropic intermolecular interactions with the guest are found which show additional distinct features in the Raman modes of the host molecule.

Influence of the Conjugation Length on the Optical Spectra of Single Ladder-Type (p-Phenylene) Dimers and Polymers

We employ low-temperature single-molecule photoluminescence spectroscopy on a π-conjugated ladder-type (p-phenylene) dimer and the corresponding polymer methyl-substituted ladder-type poly(p-phenylene), MeLPPP, to study the impact of the conjugation length (π-electron delocalization) on their optical properties on a molecular scale. Our data show that the linear electron-phonon coupling to intramolecular vibrational modes is very sensitive to the conjugation length, a well-known behavior of organic (macro-) molecules. In particular, the photoluminescence spectra of single dimers feature a rather strong low-energy (150 cm(-1)) skeletal mode of the backbone, which does not appear in the spectra of individual chromophores on single MeLPPP chains. We attribute this finding to a strongly reduced electron-phonon coupling strength and/or vibrational energy of this mode for MeLPPP with its more delocalized π-electron system as compared to the dimer. In contrast, the line widths of the purely electronic zero-phonon lines (ZPL) in single-molecule spectra do not show differences between the dimer and MeLPPP; for both systems the ZPLs are apparently broadened by fast unresolved spectral diffusion. Finally, we demonstrate that the low-temperature ensemble photoluminescence spectrum of the dimer cannot be reproduced by the distribution of spectral positions of the ZPLs. The dimer's bulk spectrum is rather apparently broadened by electron-phonon coupling to the low-energy skeletal mode, whereas for MeLPPP the inhomogeneous bulk line shape resembles the distribution of spectral positions of the ZPLs of single chromophores.

Design and synthesis of aromatic molecules for probing electric fields at the nanoscale

We propose using halogenated organic dyes as nanoprobes for electric fields and show their greatly enhanced Stark coefficients using density functional theory (DFT) calculations. We analyse halogenated variants of three molecules that have been of interest for cryogenic single molecule spectroscopy: perylene, terrylene, and dibenzoterrylene, with the zero-phonon optical transitions at blue, red, and near-infrared. Out of all the combinations of halides and binding sites that are calculated, we have found that fluorination of the optimum binding site induces a dipole difference between the ground and excited states larger than 0.5 D for all three molecules with the highest value of 0.69 D for fluoroperylene. We also report on the synthesis of 3-fluoroterrylene and the bulk spectroscopy of this compound in liquid and solid organic environments.

Variation of exciton-vibrational coupling in photosystem II core complexes from Thermosynechococcus elongatus as revealed by single-molecule spectroscopy

The spectral properties and dynamics of the fluorescence emission of photosystem II core complexes are investigated by single-molecule spectroscopy at 1.6 K. The emission spectra are dominated by sharp zero-phonon lines (ZPLs). The sharp ZPLs are the result of weak to intermediate exciton-vibrational coupling and slow spectral diffusion. For several data sets, it is possible to surpass the effect of spectral diffusion by applying a shifting algorithm. The increased signal-to-noise ratio enables us to determine the exciton-vibrational coupling strength (Huang-Rhys factor) with high precision. The Huang-Rhys factors vary between 0.03 and 0.8. The values of the Huang-Rhys factors show no obvious correlation between coupling strength and wavelength position. From this result, we conclude that electrostatic rather than exchange or dispersive interactions are the main contributors to the exciton-vibrational coupling in this system.

Stepwise Signal Extraction via Marginal Likelihood

This paper studies the estimation of stepwise signal. To determine the number and locations of change-points of the stepwise signal, we formulate a maximum marginal likelihood estimator, which can be computed with a quadratic cost using dynamic programming. We carry out extensive investigation on the choice of the prior distribution and study the asymptotic properties of the maximum marginal likelihood estimator. We propose to treat each possible set of change-points equally and adopt an empirical Bayes approach to specify the prior distribution of segment parameters. Detailed simulation study is performed to compare the effectiveness of this method with other existing methods. We demonstrate our method on single-molecule enzyme reaction data and on DNA array CGH data. Our study shows that this method is applicable to a wide range of models and offers appealing results in practice.

Single-molecule spectromicroscopy: a route towards sub-wavelength refractometry

We suggest a novel approach for spatially resolved probing of local fluctuations of the refractive index n in solids by means of single-molecule (SM) spectroscopy. It is based on the dependence T₁(n) of the effective radiative lifetime T₁ of dye centres in solids on n due to the local-field effects. Detection of SM zero-phonon lines at low temperatures gives the values of the SM natural spectral linewidth (which is inversely proportional to T₁) and makes it possible to reveal the distribution of the local n values in solids. Here we demonstrate this possibility on the example of amorphous polyethylene and polycrystalline naphthalene doped with terrylene. In particular, we show that the obtained distributions of lifetime limited spectral linewidths of terrylene molecules embedded into these matrices are due to the spatial fluctuations of the refractive index local values.

Single-molecule enzymatic conformational dynamics: spilling out the product molecules

Product releasing is an essential step of an enzymatic reaction, and a mechanistic understanding primarily depends on the active-site conformational changes and molecular interactions that are involved in this step of the enzymatic reaction. Here we report our work on the enzymatic product releasing dynamics and mechanism of an enzyme, horseradish peroxidase (HRP), using combined single-molecule time-resolved fluorescence intensity, anisotropy, and lifetime measurements. Our results have shown a wide distribution of the multiple conformational states involved in active-site interacting with the product molecules during the product releasing. We have identified that there is a significant pathway in which the product molecules are spilled out from the enzymatic active site, driven by a squeezing effect from a tight active-site conformational state, although the conventional pathway of releasing a product molecule from an open active-site conformational state is still a primary pathway. Our study provides new insight into the enzymatic reaction dynamics and mechanism, and the information is uniquely obtainable from our combined time-resolved single-molecule spectroscopic measurements and analyses.

Development of a novel cryogenic microscope with numerical aperture of 0.9 and its application to photosynthesis research

A novel cryogenic optical-microscope system was developed in which the objective lens is set inside of the cryostat adiabatic vacuum space. Being isolated from the sample when it was cooled, the objective lens was maintained at room temperature during the cryogenic measurement. Therefore, the authors were able to use a color-aberration corrected objective lens with a numerical aperture of 0.9. The lens is equipped with an air vent for compatibility to the vacuum. The theoretically expected spatial resolutions of 0.39μm along the lateral direction and 1.3μm along the axial direction were achieved by the developed system. The system was applied to the observations of non-uniform distributions of the photosystems in the cells of a green alga, Chlamydomonas reinhardtii, at 94K. Gaussian decomposition analysis of the fluorescence spectra at all the pixels clearly demonstrated a non-uniform distribution of the two photosystems, as reflected in the variable ratios of the fluorescence intensities assigned to photosystem II and to those assigned to photosystem I. The system was also applied to the fluorescence spectroscopy of single isolated photosystem I complexes at 90K. The fluorescence, assigned to be emitted from a single photosystem I trimer, showed an intermittent fluctuation called blinking, which is typical for a fluorescence signal from a single molecule. The vibronic fluorescence bands at around 790nm were observed for single photosystem I trimers, suggesting that the color aberration is not serious up to the 800nm spectral region.

Ultrafast dynamics of single molecules

Room-temperature studies of single molecules at femtosecond timescales provide detailed observation and control of ultrafast electronic and vibrational dynamics of organic dyes and photosynthetic complexes, probing quantum dynamics at ambient conditions and elucidating its role in chemistry and biology.

Single-molecule FRET of protein structure and dynamics - a primer

Single-molecule spectroscopy has developed into a widely used method for probing the structure, dynamics, and mechanisms of biomolecular systems, especially in combination with Förster resonance energy transfer (FRET). In this introductory tutorial, essential concepts and methods will be outlined, from the FRET process and the basic considerations for sample preparation and instrumentation to some key elements of data analysis and photon statistics. Different approaches for obtaining dynamic information over a wide range of timescales will be explained and illustrated with examples, including the quantitative analysis of FRET efficiency histograms, correlation spectroscopy, fluorescence trajectories, and microfluidic mixing.

Disorder influenced absorption line shapes of a chromophore coupled to two-level systems

We have carried out a theoretical and numerical study of disorder-induced changes in the absorption line shape of a chromophore embedded in a host matrix. The stochastic sudden jump model is employed wherein the host matrix molecules are treated as noninteracting two-level systems (TLSs) occupying points on a three-dimensional lattice with randomly oriented dipole moments. By systematically controlling the degree of positional disorder (α) attributed to them, a perfectly crystalline (α = 0) or a glassy environment (α = 1) or a combination of the two is obtained. The interaction between the chromophore and the TLSs is assumed to be of the dipole-dipole form. With an increase in α, the broadening of the absorption line shape was found to follow a power-law behavior. More importantly, it is revealed in the long-time limit that the resultant line shape is Gaussian in the absence of disorder but transforms to Lorentzian for a completely disordered environment. For an arbitrarily intermediate value of α, the resultant line shape can be approximately fitted by a linear combination of Gaussian and Lorentzian components. The Lorentzian profile for the disordered medium is attributed to the chomophore-TLS pairs with vanishingly small separation between them.

Single molecule detection of nanomechanical motion

We investigate theoretically how single molecule spectroscopy techniques can be used to perform fast and high resolution displacement detection and manipulation of nanomechanical oscillators, such as singly clamped carbon nanotubes. We analyze the possibility of real time displacement detection by the luminescence signal and of displacement fluctuations by the degree of second order coherence. Estimates of the electromechanical coupling constant indicate that intriguing regimes of strong backaction between the two-level system of a molecule and the oscillator can be realized.

Confocal sample-scanning microscope for single-molecule spectroscopy and microscopy with fast sample exchange at cryogenic temperatures

The construction of a microscope with fast sample transfer system for single-molecule spectroscopy and microscopy at low temperatures using 2D/3D sample-scanning is reported. The presented construction enables the insertion of a sample from the outside (room temperature) into the cooled (4.2 K) cryostat within seconds. We describe the mechanical and optical design and present data from individual Photosystem I complexes. With the described setup numerous samples can be investigated within one cooling cycle. It opens the possibility to investigate biological samples (i) without artifacts introduced by prolonged cooling procedures and (ii) samples that require preparation steps like plunge-freezing or specific illumination procedures prior to the insertion into the cryostat.

Correlation Analysis of Enzymatic Reaction of a Single Protein Molecule

New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme molecules behave fundamentally differently from what classical model predicts. A stochastic network model was previously proposed to explain the experimental discovery. This paper conducts detailed theoretical and data analyses of the stochastic network model, focusing on the correlation structure of the successive reaction times of a single enzyme molecule. We investigate the correlation of experimental fluorescence intensity and the correlation of enzymatic reaction times, and examine the role of substrate concentration in enzymatic reactions. Our study shows that the stochastic network model is capable of explaining the experimental data in depth.