Generalizing HMMs to Continuous Time for Fast Kinetics: Hidden Markov Jump Processes

The hidden Markov model (HMM) is a framework for time series analysis widely applied to single-molecule experiments. Although initially developed for applications outside the natural sciences, the HMM has traditionally been used to interpret signals generated by physical systems, such as single molecules, evolving in a discrete state space observed at discrete time levels dictated by the data acquisition rate. Within the HMM framework, transitions between states are modeled as occurring at the end of each data acquisition period and are described using transition probabilities. Yet, whereas measurements are often performed at discrete time levels in the natural sciences, physical systems evolve in continuous time according to transition rates. It then follows that the modeling assumptions underlying the HMM are justified if the transition rates of a physical process from state to state are small as compared to the data acquisition rate. In other words, HMMs apply to slow kinetics. The problem is, because the transition rates are unknown in principle, it is unclear, a priori, whether the HMM applies to a particular system. For this reason, we must generalize HMMs for physical systems, such as single molecules, because these switch between discrete states in "continuous time". We do so by exploiting recent mathematical tools developed in the context of inferring Markov jump processes and propose the hidden Markov jump process. We explicitly show in what limit the hidden Markov jump process reduces to the HMM. Resolving the discrete time discrepancy of the HMM has clear implications: we no longer need to assume that processes, such as molecular events, must occur on timescales slower than data acquisition and can learn transition rates even if these are on the same timescale or otherwise exceed data acquisition rates.

Dual functional luminescent nanoprobes for monitoring oxygen and chloride concentration changes in cells

A dual functional nanoprobe Pd-Q+@PDMS was proposed to simultaneously monitor Cl- and O2, leading to the determination of an average Cl- concentration of 85.7 ± 5.5 mM in lysosomes of HeLa cells. Mimicking ischemic conditions, the cells exhibited a luminescence change corresponding to a decreasing subcellular Cl- concentration.

Quantitative Imaging of Biochemistry in Situ and at the Nanoscale

Biochemical reactions in eukaryotic cells occur in subcellular, membrane-bound compartments called organelles. Each kind of organelle is characterized by a unique lumenal chemical composition whose stringent regulation is vital to proper organelle function. Disruption of the lumenal ionic content of organelles is inextricably linked to disease. Despite their vital roles in cellular homeostasis, there are large gaps in our knowledge of organellar chemical composition largely from a lack of suitable probes. In this Outlook, we describe how, using organelle-targeted ratiometric probes, one can quantitatively image the lumenal chemical composition and biochemical activity inside organelles. We discuss how excellent fluorescent detection chemistries applied largely to the cytosol may be expanded to study organelles by chemical imaging at subcellular resolution in live cells. DNA-based reporters are a new and versatile platform to enable such approaches because the resultant probes have precise ratiometry and accurate subcellular targeting and are able to map multiple chemicals simultaneously. Quantitatively mapping lumenal ions and biochemical activity can drive the discovery of new biology and biomedical applications.

Single-Molecule FRET Detection of Sub-Nanometer Distance Changes in the Range below a 3-Nanometer Scale

Single-molecule fluorescence energy transfer (FRET) detection has become a key technique to monitor intra- and intermolecular distance changes in biological processes. As the sensitive detection range of conventional FRET pairs is limited to 3-8 nm, complement probes are necessary for extending this typical working range. Here, we realized a single-molecule FRET assay for a short distance range of below 3 nm by using a Cy2-Cy7 pair having extremely small spectral overlap. Using two DNA duplexes with a small difference in the labeling position, we demonstrated that our assay can observe subtle changes at a short distance range. High sensitivity in the range of 1-3 nm and compatibility with the conventional FRET assay make this approach useful for understanding dynamics at a short distance.

Multiple-Labeled Antibodies Behave Like Single Emitters in Photoswitching Buffer

The degree of labeling (DOL) of antibodies has so far been optimized for high brightness and specific and efficient binding. The influence of the DOL on the blinking performance of antibodies used in direct stochastic optical reconstruction microscopy (dSTORM) has so far attained limited attention. Here, we investigated the spectroscopic characteristics of IgG antibodies labeled at DOLs of 1.1-8.3 with Alexa Fluor 647 (Al647) at the ensemble and single-molecule level. Multiple-Al647-labeled antibodies showed weak and strong quenching interactions in aqueous buffer but could all be used for dSTORM imaging with spatial resolutions of ∼20 nm independent of the DOL. Single-molecule fluorescence trajectories and photon antibunching experiments revealed that individual multiple-Al647-labeled antibodies show complex photophysics in aqueous buffer but behave as single emitters in photoswitching buffer independent of the DOL. We developed a model that explains the observed blinking of multiple-labeled antibodies and can be used for the development of improved fluorescent probes for dSTORM experiments.

Faster Uphill Relaxation in Thermodynamically Equidistant Temperature Quenches

We uncover an unforeseen asymmetry in relaxation: for a pair of thermodynamically equidistant temperature quenches, one from a lower and the other from a higher temperature, the relaxation at the ambient temperature is faster in the case of the former. We demonstrate this finding on hand of two exactly solvable many-body systems relevant in the context of single-molecule and tracer-particle dynamics. We prove that near stable minima and for all quadratic energy landscapes it is a general phenomenon that also exists in a class of non-Markovian observables probed in single-molecule and particle-tracking experiments. The asymmetry is a general feature of reversible overdamped diffusive systems with smooth single-well potentials and occurs in multiwell landscapes when quenches disturb predominantly intrawell equilibria. Our findings may be relevant for the optimization of stochastic heat engines.

Tuning the Baird aromatic triplet-state energy of cyclooctatetraene to maximize the self-healing mechanism in organic fluorophores

Bright, photostable, and nontoxic fluorescent contrast agents are critical for biological imaging. "Self-healing" dyes, in which triplet states are intramolecularly quenched, enable fluorescence imaging by increasing fluorophore brightness and longevity, while simultaneously reducing the generation of reactive oxygen species that promote phototoxicity. Here, we systematically examine the self-healing mechanism in cyanine-class organic fluorophores spanning the visible spectrum. We show that the Baird aromatic triplet-state energy of cyclooctatetraene can be physically altered to achieve order of magnitude enhancements in fluorophore brightness and signal-to-noise ratio in both the presence and absence of oxygen. We leverage these advances to achieve direct measurements of large-scale conformational dynamics within single molecules at submillisecond resolution using wide-field illumination and camera-based detection methods. These findings demonstrate the capacity to image functionally relevant conformational processes in biological systems in the kilohertz regime at physiological oxygen concentrations and shed important light on the multivariate parameters critical to self-healing organic fluorophore design.

A Review on Schiff Base Fluorescent Chemosensors for Cell Imaging Applications

Fluorescent determinations of analytes have proven to be a powerful method due to their simplicity, low cost, detection limit, rapid photoluminescence response, and applicability to bioimaging. Fluorescence imaging as a powerful tool for monitoring biomolecules within the living systems. Schiff base has been extensively used as strongly absorbing and colorful chromophores in the design of chemosensors. In recent years, Schiff base based fluorescent probes have been developed for the detection of various toxic analytes and imaging of various analytes in biological systems. This review gives an overview of the important fluorescent sensors which are based on Schiff base, their approaches for molecular recognition, and their potential application in bioimaging studies.

Fast three-color single-molecule FRET using statistical inference

We describe theory, experiments, and analyses of three-color Förster resonance energy transfer (FRET) spectroscopy for probing sub-millisecond conformational dynamics of protein folding and binding of disordered proteins. We devise a scheme that uses single continuous-wave laser excitation of the donor instead of alternating excitation of the donor and one of the acceptors. This scheme alleviates photophysical problems of acceptors such as rapid photobleaching, which is crucial for high time resolution experiments with elevated illumination intensity. Our method exploits the molecular species with one of the acceptors absent or photobleached, from which two-color FRET data is collected in the same experiment. We show that three FRET efficiencies and kinetic parameters can be determined without alternating excitation from a global maximum likelihood analysis of two-color and three-color photon trajectories. We implement co-parallelization of CPU-GPU processing, which leads to a significant reduction of the likelihood calculation time for efficient parameter determination.

Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays

The ability to detect low concentrations of analytes and in particular low-abundance biomarkers is of fundamental importance, e.g., for early-stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single-molecule bioaffinity assays. While many review articles have highlighted the potentials of single-molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real-world applications as one should expect. This Review provides a theoretical background on single-molecule-or better digital-assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single-molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.

Prior-Apprised Unsupervised Learning of Subpixel Curvilinear Features in Low Signal/Noise Images

Many biophysical problems involve molecular and nanoscale targets moving next to a curvilinear track, e.g., a cytosolic cargo transported by motor proteins moving along a microtubule. For this type of problem, fluorescence imaging is usually the primary tool of choice. There is, however, an ∼20-fold mismatch between target-localization precision and track-imaging resolution such that questions requiring high-fidelity definition of the target's track remain inaccessible. On the other hand, if the contextual image of the tracks can be refined to a level comparable to that of the target, many intuitive yet mechanistically important issues can begin to be addressed. This work demonstrates that it is possible to statistically infer, to subpixel precision, curvilinear features in a low signal/noise image. This is achieved by a framework that consists of three stages: the Hessian-based feature enhancement, the subimage feature sampling and registration, and the statistical learning of the underlying curvilinear structure using a new, to our knowledge, method developed here for inferring the principal curves. In each stage, the descriptive prior information that the features come from curvilinear elements is explicitly taken into account. It is fully automated without user supervision, which is distinctly different from approaches that require user seeding or well-defined training data sets. Computer simulations of realistic images are used to investigate the performance of the framework and its implementation. The characterization results suggest that curvilinear features are refined to the same order of precision as that of the target and that the bootstrap confidence intervals from the analysis allow an estimate for the statistical bounds of the simulated "true" curve. Also shown are analyses of experimental images from three different microscopy modalities: two-photon laser-scanning microscopy, epifluorescence microscopy, and total internal reflection fluorescence microscopy. The practical application of this prior-apprised unsupervised learning framework as well as its potential outlook are discussed.

A 6-nm ultra-photostable DNA FluoroCube for fluorescence imaging

Photobleaching limits extended imaging of fluorescent biological samples. Here, we developed DNA based “FluoroCubes” that are similar in size to the green fluorescent protein (GFP), have single-point attachment to proteins, have a ~54-fold higher photobleaching lifetime and emit ~43-fold more photons than single organic dyes. We demonstrate that DNA FluoroCubes provide outstanding tools for single-molecule imaging, allowing the tracking of single motor proteins for >800 steps with nanometer precision.

Recent advances in bioimaging with high-speed atomic force microscopy

Among various microscopic techniques for characterizing protein structures and functions, high-speed atomic force microscopy (HS-AFM) is a unique technique in that it allows direct visualization of structural changes and molecular interactions of proteins without any labeling in a liquid environment. Since the development of the HS-AFM was first reported in 2001, it has been applied to analyze the dynamics of various types of proteins, including motor proteins, membrane proteins, DNA-binding proteins, amyloid proteins, and artificial proteins. This method has now become a versatile tool indispensable for biophysical research. This short review summarizes some bioimaging applications of HS-AFM reported in the last few years and novel applications of HS-AFM utilizing the unique ability of AFM to gain mechanical properties of samples in addition to structural information.

High-throughput single-molecule imaging system using nanofabricated trenches and fluorescent DNA-binding proteins

DNA curtain is a high-throughput system, integrating a lipid bilayer, fluorescence imaging, and microfluidics to probe protein-DNA interactions in real-time and has provided in-depth understanding of DNA metabolism. Especially, the microfluidic platform of a DNA curtain is highly suitable for a biochip. In the DNA curtain, DNA molecules are aligned along chromium nanobarriers, which are fabricated on a slide surface, and visualized using an intercalating dye, YOYO-1. Although the chromium barriers confer precise geometric alignment of DNA, reuse of the slides is limited by wear of the barriers during cleaning. YOYO-1 is rapidly photobleached and causes photocleavage of DNA under continuous laser illumination, restricting DNA observation to a brief time window. To address these challenges, we developed a new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers. The nanotrenches were robust under harsh cleaning conditions, facilitating the maintenance of surface cleanliness that is essential to slide reuse. We also stained DNA with a fluorescent protein with a DNA-binding motif, fluorescent protein-DNA binding peptide (FP-DBP). FP-DBP was slowly photobleached and did not cause DNA photocleavage. This new DNA curtain system enables a more stable and repeatable investigation of real-time protein-DNA interactions and will serve as a good platform for lab-on-a-chip.

Selective Manipulation of Biomolecules with Insulator-Based Dielectrophoretic Tweezers

Insulator-based dielectrophoretic (iDEP) trapping, separating, and concentrating nanoscale objects is carried out using a non-metal, unbiased, mobile tip acing as a tweezers. The spatial control and manipulation of fluorescently-labeled polystyrene particles and DNA were performed to demonstrate the feasibility of the iDEP tweezers. Frequency-dependent iDEP tweezers' strength and polarity were quantitatively determined using two theoretical approaches to DNA, which resulted in a factor of 2 ~ 40 differences between them. In either approach, the strength of iDEP was at least 4-order of magnitude stronger than the thermal force, indicating iDEP was a dominant force for trapping, holding, and separating DNA. The trapping strength and volume of the iDEP tweezers were also determined, which further supports direct capture and manipulation of DNA at the tip end.

Untangling the Conformational Polymorphism of Disordered Proteins Associated With Neurodegeneration at the Single-Molecule Level

A large fraction of the human genome encodes intrinsically disordered proteins/regions (IDPs/IDRs) that are involved in diverse cellular functions/regulation and dysfunctions. Moreover, several neurodegenerative disorders are associated with the pathological self-assembly of neuronal IDPs, including tau [Alzheimer's disease (AD)], α-synuclein [Parkinson's disease (PD)], and huntingtin exon 1 [Huntington's disease (HD)]. Therefore, there is an urgent and emerging clinical interest in understanding the physical and structural features of their functional and disease states. However, their biophysical characterization is inherently challenging by traditional ensemble techniques. First, unlike globular proteins, IDPs lack stable secondary/tertiary structures under physiological conditions and may interact with multiple and distinct biological partners, subsequently folding differentially, thus contributing to the conformational polymorphism. Second, amyloidogenic IDPs display a high aggregation propensity, undergoing complex heterogeneous self-assembly mechanisms. In this review article, we discuss the advantages of employing cutting-edge single-molecule fluorescence (SMF) techniques to characterize the conformational ensemble of three selected neuronal IDPs (huntingtin exon 1, tau, and α-synuclein). Specifically, we survey the versatility of these powerful approaches to describe their monomeric conformational ensemble under functional and aggregation-prone conditions, and binding to biological partners. Together, the information gained from these studies provides unique insights into the role of gain or loss of function of these disordered proteins in neurodegeneration, which may assist the development of new therapeutic molecules to prevent and treat these devastating human disorders.

Approaches for measuring the dynamics of RNA-protein interactions

RNA-protein interactions are pivotal for the regulation of gene expression from bacteria to human. RNA-protein interactions are dynamic; they change over biologically relevant timescales. Understanding the regulation of gene expression at the RNA level therefore requires knowledge of the dynamics of RNA-protein interactions. Here, we discuss the main experimental approaches to measure dynamic aspects of RNA-protein interactions. We cover techniques that assess dynamics of cellular RNA-protein interactions that accompany biological processes over timescales of hours or longer and techniques measuring the kinetic dynamics of RNA-protein interactions in vitro. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Evolution and Genomics > Ribonomics.

Hybrid 3,4-dihydropyrimidin-2-(thi)ones as dual-functional bioactive molecules: fluorescent probes and cytotoxic agents to cancer cells

A series of new hybrid fluorescent Biginelli compounds, including a Monastrol derivative, were designed and synthesized with good yields.

Advancing Wireframe DNA Nanostructures Using Single-Molecule Fluorescence Microscopy Techniques

DNA nanotechnology relies on the molecular recognition properties of DNA to produce complex architectures through self-assembly. The resulting DNA nanostructures allow scientists to organize functional materials at the nanoscale and have therefore found applications in many domains of materials science over the past several years. These scaffolds have been used to position proteins, nanoparticles, carbon nanotubes, and other nanomaterials with high spatial resolution. In addition to their remarkable performance as frameworks for other species, DNA constructs also possess interesting dynamic properties, which have led to their use in logic circuits, drug delivery vehicles, and molecular walkers. Although DNA nanostructures have become increasingly complex, the development of tools to study them has lagged. Currently, gel electrophoresis, dynamic light scattering, and ensemble fluorescence measurements are widely used to characterize DNA-based assemblies. Unfortunately, ensemble averaging in these methods obscures malformed structures and may mask properties associated with structure, length, and shape in polydisperse samples. While atomic force microscopy allows for the determination of morphology at the single-molecule level, this technique cannot typically be used to assess the dynamic properties of these constructs. To analyze the function of DNA-based devices such as molecular motors and reconfigurable nanostructures in real time, new single-molecule techniques are required. This Account details the work from our laboratories toward developing single-molecule fluorescence (SMF) methodologies for the structural and dynamic characterization of wireframe DNA nanostructures, one at a time. The methods described herein provide us with two separate yet related sets of information: First, we can statically examine the nanostructures one by one to assess their robustness, structural fidelity, and morphology. This is primarily done using two-color stepwise photobleaching, wherein we can examine the subunit stoichiometry of our assemblies before and after various perturbations to the structures. For example, we can introduce length mismatches to cause the nanotube to bend or perform strand displacement reactions to generate single-stranded, flexible analogues of our materials. Second, due to the unmatched spatiotemporal resolution of SMF techniques, we can study the dynamic character of these assemblies by implementing structural changes to the nanotube and monitoring them in real time. With this structural and dynamic information in hand, our groups have additionally developed new tools for the improved construction of DNA nanotubes, inspired by solid-phase DNA synthesis. By assembling the nanotubes in a stepwise manner, highly monodisperse nanostructures of any desired length can be made without a template strand. In this way, unique building blocks can also be added sequence-specifically, allowing for the production of user-defined scaffolds to organize nanoscale materials in three dimensions. This method, in combination with our imaging and analysis protocols, may be extended to assemble and inspect other supramolecular constructs in a controlled manner. Overall, by combining synthesis, characterization, and analysis, these single-molecule techniques hold the potential to advance the study of DNA nanostructures and dynamic DNA-based devices.

Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP-DNA dissociation

The TATA-box Binding Protein (TBP) plays a central role in regulating gene expression and is the first step in the process of pre-initiation complex (PIC) formation on promoter DNA. The lifetime of TBP at the promoter site is controlled by several cofactors including the Modifier of transcription 1 (Mot1), an essential TBP-associated ATPase. Based on ensemble measurements, Mot1 can use adenosine triphosphate (ATP) hydrolysis to displace TBP from DNA and various models for how this activity is coupled to transcriptional regulation have been proposed. However, the underlying molecular mechanism of Mot1 action is not well understood. In this work, the interaction of Mot1 with the DNA/TBP complex was investigated by single-pair Förster resonance energy transfer (spFRET). Upon Mot1 binding to the DNA/TBP complex, a transition in the DNA/TBP conformation was observed. Hydrolysis of ATP by Mot1 led to a conformational change but was not sufficient to efficiently disrupt the complex. SpFRET measurements of dual-labeled DNA suggest that Mot1's ATPase activity primes incorrectly oriented TBP for dissociation from DNA and additional Mot1 in solution is necessary for TBP unbinding. These findings provide a framework for understanding how the efficiency of Mot1's catalytic activity is tuned to establish a dynamic pool of TBP without interfering with stable and functional TBP-containing complexes.

Robustness of FCS (Fluorescence Correlation Spectroscopy) with Quenchers Present

Inspired by recent publications doubtful of the FCS technique, we scrutinize how irreversible ("static") and reversible ("dynamic") quenching can influence the interpretation of such data. Textbook presentations often emphasize only how to analyze data in extremes, the absence of quenching or the presence of substantial quenching. Here, we consider intermediate cases where the assessment of photophysics (static quenching, blinking-like triplet-state relaxation) influence on autocorrelation curves can be delicate if dye-labeled objects diffuse on comparably rapid time scales. We used the amino acid, tryptophan, as the quencher. As our example of small-molecule dye that diffuses rapidly, we mix the quencher with the fluorescence dye, Alexa 488. The translational diffusion coefficient, inferred from fit to the standard one-component Fickian diffusion model, speeds up without the loss of quality of fit, but quenching is reflected in the fact that the data become exceptionally noisy. This reflects the bidisperse population of quenched and unquenched dyes when the time scales overlap between the processes of translational diffusion, quenching, and blinking. As our example of the large-molecule dye-labeled object that diffuses relatively slowly, we mixed the quencher with dye-labeled BSA, bovine serum albumin. Diffusion, static quenching, and blinking time scales are now separated. In spite of quenching contribution to the autocorrelation function when the delay time is relatively short, the inferred translational diffusion coefficient now depends weakly on the presence of a quencher. We conclude that when the diffusing molecule is substantially slower to diffuse than the time scale of photophysical processes of the fluorescent dye to which it is attached, the influence of quenching is self-evident and the FCS autocorrelation curves give an appropriate diffusion coefficient if correct fitting functions are chosen in the analysis.

Conjugation of Fab' Fragments with Fluorescent Dyes for Single-Molecule Tracking On Live Cells

Our understanding of the regulation and functions of cell-surface proteins has progressed rapidly with the advent of advanced optical imaging techniques. In particular, single-molecule tracking (SMT) using bright fluorophores conjugated to antibodies and wide-field microscopy methods such as total internal reflection fluorescence microscopy have become valuable tools to discern how endogenous proteins control cell biology. Yet, some technical challenges remain; in SMT, these revolve around the characteristics of the labeling reagent. A good reagent should have neutrality (in terms of not affecting the target protein's functions), tagging specificity, and a bright fluorescence signal. In addition, a long shelf-life is desirable due to the time and monetary costs associated with reagent preparation. Semiconductor-based quantum dots (Qdots) or Janelia Fluor (JF) dyes are bright and photostable, and are thus excellent candidates for SMT tagging. Neutral, high-affinity antibodies can selectively bind to target proteins. However, the bivalency of antibodies can cause simultaneous binding to two proteins, and this bridging effect can alter protein functions and behaviors. Bivalency can be avoided using monovalent Fab fragments generated by enzymatic digestion of neutral antibodies. However, conjugation of a Fab with a dye using the chemical cross-linking agent SMCC (succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate) requires reduction of the interchain disulfide bond within the Fab fragment, which can decrease the structural stability of the Fab and weaken its antigen-binding capability. To overcome this problem, we perform limited reduction of F(ab')2 to generate Fab' fragments using a weak reducer, cysteamine, which yields free sulfhydryl groups in the hinge region, while the interchain disulfide bond in Fab' is intact. Here, we describe a method that generates Fab' with high yield from two isoforms of IgG and conjugates the Fab' fragments with Qdots. This conjugation scheme can be applied easily to other types of dyes with similar chemical characteristics.

Facilitated diffusion of Argonaute-mediated target search

Argonaute (Ago) proteins are of key importance in many cellular processes. In eukaryotes, Ago can induce translational repression followed by deadenylation and degradation of mRNA molecules through base pairing of microRNAs (miRNAs) with a complementary target on a mRNA sequence. In bacteria, Ago eliminates foreign DNA through base pairing of siDNA (small interfering DNA) with a target on a DNA sequence. Effective targeting activities of Ago require fast recognition of the cognate target sequence among numerous off-target sites. Other target search proteins such as transcription factors (TFs) are known to rely on facilitated diffusion for this goal, but it is undetermined to what extent these small nucleic acid-guided proteins utilize this mechanism. Here, we review recent single-molecule studies on Ago target search. We discuss the consequences of the recent findings on the search mechanism. Furthermore, we discuss the open standing research questions that need to be addressed for a complete picture of facilitated target search by small nucleic acids.

Co-temporal Force and Fluorescence Measurements Reveal a Ribosomal Gear Shift Mechanism of Translation Regulation by Structured mRNAs

The movement of ribosomes on mRNA is often interrupted by secondary structures that present mechanical barriers and play a central role in translation regulation. We investigate how ribosomes couple their internal conformational changes with the activity of translocation factor EF-G to unwind mRNA secondary structures using high-resolution optical tweezers with single-molecule fluorescence capability. We find that hairpin opening occurs during EF-G-catalyzed translocation and is driven by the forward rotation of the small subunit head. Modulating the magnitude of the hairpin barrier by force shows that ribosomes respond to strong barriers by shifting their operation to an alternative 7-fold-slower kinetic pathway prior to translocation. Shifting into a slow gear results from an allosteric switch in the ribosome that may allow it to exploit thermal fluctuations to overcome mechanical barriers. Finally, we observe that ribosomes occasionally open the hairpin in two successive sub-codon steps, revealing a previously unobserved translocation intermediate.

Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes

Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ⁷⁰ region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation.

Reactive oxygen species-mediated BIN2 activity revealed by single-molecule analysis

Much evidence has shown that reactive oxygen species (ROS) regulate several plant hormone signaling cascades, but little is known about the real-time kinetics and the underlying molecular mechanisms of the target proteins in the brassinosteroid (BR) signaling pathway. In this study, we used single-molecule techniques to investigate the true signaling timescales of the major BR signaling components BRI1-EMS-SUPPRESSOR 1 (BES1) and BRASSINOSTEROID INSENSITIVE 2 (BIN2) of Arabidopsis thaliana. The rate constants of BIN2 associating with ATP and phosphorylating BES1 were determined to be 0.7 ± 0.4 mM^-1  s^-1 and 2.3 ± 1.4 s^-1 , respectively. Interestingly, we found that the interaction of BIN2 and BES1 was oxygen-dependent, and oxygen can directly modify BIN2. The activity of BIN2 was switched on via modification of specific cysteine (Cys) residues, including C59, C95, C99 and C162. The mutation of these Cys residues inhibited the BR signaling outputs. These findings demonstrate the power of using single-molecule techniques to study the dynamic interactions of signaling components, which is difficult to be discovered by conventional physiological and biochemical methods.

Construction of Tetrahedral DNA-Quantum Dot Nanostructure with the Integration of Multistep Förster Resonance Energy Transfer for Multiplex Enzymes Assay

Three-dimensional (3D) DNA scaffolds with well-defined structure and high controllability hold promising potentials for biosensing and drug delivery. However, most of 3D DNA scaffolds can detect only a single type of molecule with the involvement of complex logic operations. Herein, we develop a 3D DNA nanostructure with the capability of multiplexed detection by exploiting a multistep Förster resonance energy transfer (FRET). The tetrahedron-structured DNA is constructed by four oligonucleotide strands and is subsequently conjugated to a streptavidin-coated quantum dot (QD) to obtain a QD-Cy3-Texas Red-Cy5 tetrahedron DNA. This QD-Cy3-Texas Red-Cy5 tetrahedral DNA nanostructure has well-defined dye-to-dye spacing and high controllability for energy transfer between intermediary acceptors and terminal acceptors, enabling the generation of multistep FRET between the QD and three dyes (i.e., Cy3, Texas Red, and Cy5) for simultaneous detection of multiple endonucleases and methyltransferases even in complex biological samples as well as the screening of multiple enzyme inhibitors.

Simple mechanics of protein machines

While belonging to the nanoscale, protein machines are so complex that tracing even a small fraction of their cycle requires weeks of calculations on supercomputers. Surprisingly, many aspects of their operation can be however already reproduced by using very simple mechanical models of elastic networks. The analysis suggests that, similar to other self-organized complex systems, functional collective dynamics in such proteins is effectively reduced to a low-dimensional attractive manifold.

Fluorescence microscopy for visualizing single-molecule protein dynamics

BACKGROUND

Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically.

SCOPE OF REVIEW

This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy.

MAJOR CONCLUSIONS

smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on.

GENERAL SIGNIFICANCE

Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.

Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation

Intrinsically disordered proteins (IDPs) are ubiquitous in proteomes and serve in a range of cellular functions including signaling, regulation, transport and enzyme function. IDP misfunction and aggregation are also associated with several diseases including neurodegenerative diseases and cancer. During the past decade, single-molecule methods have become popular for detailed biophysical and structural studies of these complex proteins. This work has included recent applications to cellular liquid-liquid phase separation (LLPS), relevant for functional dynamics of membraneless organelles such as the nucleolus and stress granules. In this concise review, we cover the conceptual motivations for development and application of single-molecule fluorescence methods for such IDP studies. We follow with a few key examples of systems and biophysical problems that have been addressed, and conclude with thoughts for emerging and future directions.

Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy

G-quadruplexes (GQs) can adopt diverse structures and are functionally implicated in transcription, replication, translation, and maintenance of telomere. Their conformational diversity under physiological levels of mechanical stress, however, is poorly understood. We used single-molecule fluorescence-force spectroscopy that combines fluorescence resonance energy transfer with optical tweezers to measure human telomeric sequences under tension. Abrupt GQ unfolding with K⁺ in solution occurred at as many as four discrete levels of force. Added to an ultrastable state and a gradually unfolding state, there were six mechanically distinct structures. Extreme mechanical diversity was also observed with Na⁺, although GQs were mechanically weaker. Our ability to detect small conformational changes at low forces enabled the determination of refolding forces of about 2 pN. Refolding was rapid and stochastically redistributed molecules to mechanically distinct states. A single guanine-to-thymine substitution mutant required much higher ion concentrations to display GQ-like unfolding and refolded via intermediates, contrary to the wild type. Contradicting an earlier proposal, truncation to three hexanucleotide repeats resulted in a single-stranded DNA-like mechanical behavior under all conditions, indicating that at least four repeats are required to form mechanically stable structures.

SMALL-LABS: Measuring Single-Molecule Intensity and Position in Obscuring Backgrounds

Single-molecule and super-resolution imaging relies on successful, sensitive, and accurate detection of the emission from fluorescent molecules. Yet, despite the widespread adoption of super-resolution microscopies, single-molecule data processing algorithms can fail to provide accurate measurements of the brightness and position of molecules in the presence of backgrounds that fluctuate significantly over time and space. Thus, samples or experiments that include obscuring backgrounds can severely, or even completely, hinder this process. To date, no general data analysis approach to this problem has been introduced that is capable of removing obscuring backgrounds for a wide variety of experimental modalities. To address this need, we present the Single-Molecule Accurate LocaLization by LocAl Background Subtraction (SMALL-LABS) algorithm, which can be incorporated into existing single-molecule and super-resolution analysis packages to accurately locate and measure the intensity of single molecules, regardless of the shape or brightness of the background. Accurate background subtraction is enabled by separating the foreground from the background based on differences in the temporal variations of the foreground and the background (i.e., fluorophore blinking, bleaching, or moving). We detail the function of SMALL-LABS here, and we validate the SMALL-LABS algorithm on simulated data as well as real data from single-molecule imaging in living cells.

Single-Molecule Techniques and Cell-Free Protein Synthesis: A Perfect Marriage

Single-molecule techniques are currently an essential tool to study conformational changes as well as the synthesis and folding of proteins. However, the preparation of suitable protein samples is often time-consuming and demanding. The rapid development of cell-free protein synthesis over the last few years opened new perspectives for fast and easy sample preparation, but this was not fully exploited until now. Here, we take a look at the advancements in sample preparation as well as in the development of technical approaches and analytical tools, which unavoidably lead to the combination of single-molecule techniques and cell-free protein synthesis. It is an ideal combination that can unlock the full potential of studying complex biological processes in the near future.

Single-Molecule Fluorescence Measurement of SNARE-Mediated Vesicle Fusion

This chapter expounds the single vesicle-vesicle fluorescence resonance energy transfer (FRET) measurement to study the membrane fusion mediated by SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. The formation of a four-α-helix bundle of SNARE proteins can drive two membranes to a close proximity for fusion. Through single-molecule FRET-based microscopy, the lipid-mixing process at the single-vesicle level can be tracked in real time. This reconstitution system is applicable to study the molecular mechanism of SNAREs during different membrane fusion stages, such as docking, hemifusion, and full fusion. Four main parts are described in this chapter, including SNARE reconstitution, imaging preparation, data collection, and analysis.

Redefining the photo-stability of common fluorophores with triplet state quenchers: mechanistic insights and recent updates

Light microscopy can offer certain advantages over electron microscopy in terms of acquiring detailed insights into the biological/intra-cellular milieu. In recent years, with the development of new fluorescence imaging technologies, it has become extremely important to assess the role of designing appropriate fluorophores in acquiring desired biological information without encountering any untoward hitches. Over the years, external fluorophores have been prevalently used in fluorescence microscopy and single-molecule fluorescence microscopy-based studies. Photostable fluorogenic probes with high extinction coefficients and quantum yields, exhibiting minimum autofluorescence and photobleaching properties, are preferred in single-molecule microscopy as they can tolerate long-term laser exposure. Therefore, the development of triplet state quenchers and/or any other suitable new strategy to ensure the photo-stability of the fluorophores during long-term live cell imaging exercises is highly anticipated. In this feature article, various strategies for stabilizing fluorophores, including the mechanisms of TSQ-induced stabilization, have been thoroughly reviewed considering contemporary literature reports and applications.

High-throughput, non-equilibrium studies of single biomolecules using glass-made nanofluidic devices

Single-molecule detection schemes offer powerful means to overcome static and dynamic heterogeneity inherent to complex samples. However, probing biomolecular interactions and reactions with high throughput and time resolution remains challenging, often requiring surface-immobilized entities. Here, we introduce glass-made nanofluidic devices for the high-throughput detection of freely-diffusing single biomolecules by camera-based fluorescence microscopy. Nanochannels of 200 nm height and a width of several micrometers confine the movement of biomolecules. Using pressure-driven flow through an array of parallel nanochannels and by tracking the movement of fluorescently labelled DNA oligonucleotides, we observe conformational changes with high throughput. In a device geometry featuring a T-shaped junction of nanochannels, we drive steady-state non-equilibrium conditions by continuously mixing reactants and triggering chemical reactions. We use the device to probe the conformational equilibrium of a DNA hairpin as well as to continuously observe DNA synthesis in real time. Our platform offers a straightforward and robust method for studying reaction kinetics at the single-molecule level.

Tracking DNA Synthesis with Single-Molecule Strand Displacement

We have previously shown that double-stranded DNA labeled with a periodic series of fluorescent dyes can be used to track a single helicase. Here we demonstrate how this technique can be adapted to follow processive DNA synthesis. By monitoring strand displacement, we track the motion of a single ϕ29 DNA polymerase without labeling or altering the enzyme or the template strand, and without applying any force. We observe a wide range of speeds, with the highest exceeding by several times those observed in earlier in vitro single-molecule experiments. Because this method enables repeated observations of the same polymerase traversing identical segments of DNA, it should prove useful for determining the effects of sequence on DNA replication and transcription. In addition, future measurements of this type may allow us to examine in detail the interactions of individual DNA polymerases with other components of the replisome.

Integration of sample preparation and analysis into an optofluidic chip for multi-target disease detection

Detection of molecular biomarkers with high specificity and sensitivity from biological samples requires both sophisticated sample preparation and subsequent analysis. These tasks are often carried out on separate platforms which increases required sample volumes and the risk of errors, sample loss, and contamination. Here, we present an optofluidic platform which combines an optical detection section with single nucleic acid strand sensitivity, and a sample processing unit capable of on-chip, specific extraction and labeling of nucleic acid and protein targets in complex biological matrices. First, on-chip labeling and detection of individual lambda DNA molecules down to concentrations of 8 fM is demonstrated. Subsequently, we demonstrate the simultaneous capture, fluorescence tagging and detection of both Zika specific nucleic acid and NS-1 protein targets in both buffer and human serum. We show that the dual DNA and protein assay allows for successful differentiation and diagnosis of Zika against cross-reacting species like dengue.

Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts

Cellular protein-RNA complexes assemble on nascent transcripts, but methods to observe transcription and protein binding in real time and at physiological concentrations are not available. Here, we report a single-molecule approach based on zero-mode waveguides that simultaneously tracks transcription progress and the binding of ribosomal protein S15 to nascent RNA transcripts during early ribosome biogenesis. We observe stable binding of S15 to single RNAs immediately after transcription for the majority of the transcripts at 35 °C but for less than half at 20 °C. The remaining transcripts exhibit either rapid and transient binding or are unable to bind S15, likely due to RNA misfolding. Our work establishes the foundation for studying transcription and its coupled co-transcriptional processes, including RNA folding, ligand binding, and enzymatic activity such as in coupling of transcription to splicing, ribosome assembly or translation.

The early steps of ribosome assembly occur co-transcriptionally on the nascent ribosomal RNA. Here the authors demonstrate an approach that allows simultaneous monitoring of transcription and ribosomal protein assembly at the single-molecule level in real time.

Efficient One-Step PEG-Silane Passivation of Glass Surfaces for Single-Molecule Fluorescence Studies

Surface passivation to inhibit nonspecific interactions is a key requirement for in vitro single-molecule fluorescent studies. Although the standard passivation methods involve the covalent attachment of poly(ethylene glycol) (PEG) in two steps preferably over quartz surfaces, this protocol and improvements thereon require extensive labor and chemicals. Herein, we report an efficient one-step surface grafting of PEG-silane that yields enhanced passivation, as evidenced by reduced nonspecific interactions, over the conventional method at a minimal time and reagent cost and on glass surfaces. Our method is rooted in a mechanistic understanding of the silane reaction with the silanol groups on the glass surface. Single-molecule fluorescence studies with fluorescently tagged proteins and DNA on PEG-silane-functionalized glass surfaces validate the enhanced performance of the method. Combined with atomic force microscopy surface characterization, our study further illustrates that few remaining pinhole defects, plausibly from defects on the glass, on PEG-silane glass-coated surfaces account for the minimal background, where typically no more than one molecule is nonspecifically attached in a given diffraction-limited spot on the surface.

Single-Particle Tracking for the Quantification of Membrane Protein Dynamics in Living Plant Cells

The plasma membrane is a sophisticated, organized, and highly heterogeneous structure that compartmentalizes cellular processes. To decipher the biological processes involving membrane proteins, it is necessary to analyze their spatiotemporal dynamics. However, it is difficult to directly assess the dynamics and interactions of biomolecules in living cells using traditional biochemical methods. Single-particle tracking (SPT) methods for imaging and tracking single particles conjugated with fluorescent probes offer an ideal approach to acquire valuable and complementary information about dynamic intracellular processes. SPT can be used to quantitatively monitor the diverse motions of individual particles in living cells. SPT also provides super-spatiotemporal resolution that allows early-stage or rapid response information to be obtained for a better understanding of molecular basis of associated signal transduction processes. More importantly, SPT can be used to detect the motion paths of individual biomolecules in vivo and in situ, thus unveiling the dynamic behavior of the biomolecules that support developmental processes in living cells. In this review, we give an overview of SPT methods, from image acquisition to the detection of single particles, as well as tracking and data analysis. We also discuss recent applications of SPT methods in the field of plant biology to reveal the complex biological functions of membrane proteins.

Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics

Riboswitches are dynamic RNA motifs that are mostly embedded in the 5'-untranslated regions of bacterial mRNAs, where they regulate gene expression transcriptionally or translationally by undergoing conformational changes upon binding of a small metabolite or ion. Due to the small size of typical ligands, relatively little free energy is available from ligand binding to overcome the often high energetic barrier of reshaping RNA structure. Instead, most riboswitches appear to take advantage of the directional and hierarchical folding of RNA by employing the ligand as a structural 'linchpin' to adjust the kinetic partitioning between alternate folds. In this model, even small, local structural and kinetic effects of ligand binding can cascade into global RNA conformational changes affecting gene expression. Single-molecule (SM) microscopy tools are uniquely suited to study such kinetically controlled RNA folding since they avoid the ensemble averaging of bulk techniques that loses sight of unsynchronized, transient, and/or multi-state kinetic behavior. This review summarizes how SM methods have begun to unravel riboswitch-mediated gene regulation.