Fluorescence quenching: A tool for single-molecule protein-folding study

Design of Ligand-Operable Protein-Cages That Open Upon Specific Protein Binding

Protein nanocages have diverse applications in medicine and biotechnology, including molecular delivery. However, although numerous studies have demonstrated the ability of protein nanocages to encapsulate various molecular species, limited methods are available for subsequently opening a nanocage for cargo release under specific conditions. A modular platform with a specific protein-target-based mechanism of nanocage opening is notably lacking. To address this important technology gap, we present a new class of designed protein cages, the Ligand-Operable Cage (LOC). LOCs primarily comprise a protein nanocage core and a fused surface binding adaptor. The geometry of the LOC is designed so that binding of a target protein ligand (or multiple copies thereof) to the surface binder is sterically incompatible with retention of the assembled state of the cage. Therefore, the tight binding of a target ligand drives cage disassembly by mass action, subsequently exposing the encapsulated cargo. LOCs are modular; direct substitution of the surface binder sequence can reprogram the nanocage to open in response to any target protein ligand of interest. We demonstrate these design principles using both a natural and a designed protein cage as the core, with different proteins acting as the triggering ligand and with different reporter readouts─fluorescence unquenching and luminescence─for cage disassembly. These developments advance the critical problem of targeted molecular delivery and detection.

Self-quenched Fluorophore Dimers for DNA-PAINT and STED Microscopy

Super-resolution techniques like single-molecule localisation microscopy (SMLM) and stimulated emission depletion (STED) microscopy have been extended by the use of non-covalent, weak affinity-based transient labelling systems. DNA-based hybrid systems are a prominent example among these transient labelling systems, offering excellent opportunities for multi-target fluorescence imaging. However, these techniques suffer from higher background relative to covalently bound fluorophores, originating from unbound fluorophore-labelled single-stranded oligonucleotides. Here, we introduce short-distance self-quenching in fluorophore dimers as an efficient mechanism to reduce background fluorescence signal, while at the same time increasing the photon budget in the bound state by almost 2-fold. We characterise the optical and thermodynamic properties of fluorophore-dimer single-stranded DNA, and show super-resolution imaging applications with STED and SMLM with increased spatial resolution and reduced background.

Direct tool for quantitative analysis of cell/object dynamic behavior - metastasis and far beyond

INTRODUCTION

The dynamics and depth of invasion as well as the ability of cancer cells to penetrate the walls of  lymphatic or blood vessels represent critical survival-influencing factors in cancer patients. Depending on the cell type and tissue environment, cancer cell invasion differ in terms of motility mechanism and migration modes. Thus, there is the need of effective models allowing not only for single cell invasion potential assessment but also for collective migration and expansive growth evaluation in 3D microenvironment e.g. basement membranes. To meet this task, the specimens should be compared and analyzed in terms of the dynamics of movement and the evolution of the shape.

OBJECTIVES

Our main objective was development of the mathematical method that enables fast and credible calculation of parameters of shape and position, namely standard deviations (σ_X, σ_Y), centroid position (μ_X, μ_Y) and correlation coefficient ρ, based only on the contour of the aggregate.

METHODS

In order to accomplish this goal we measured geometrical properties of aggregates of RGM1 cells seeded in 3D Geltrex basement membrane. Referential microscopic images were taken 24 and 48 h after seeding and cell group dynamics was registered over 8 h periods using time lapse microscopy.

RESULTS

Based on gathered data, we managed to develop and fully test universal numerical tool allowing for estimation of statistical parameters of cell groups and aggregates which then allows for the precise evaluation of their behavior within microenvironment with time.

CONCLUSION

We conclude, that our tool is suitable for any research on the metastatic potential and motility of cancer cells in a given microenvironment, regardless of the migration mechanism, which together with the advanced analysis like cell single-cell transcriptomic, proteomic, and chromatin accessibility data may allow to identify precise targets for anti-cancer therapies, to predict the degree of malignancy of neoplastic lesions as well as it can be useful during architecting therapeutic strategies. Moreover, the developed tool seems to be broadly applicable for assessment of behavioural dynamics of any population.

Design, fabrication, and preclinical testing of a miniaturized, multispectral, chip-on-tip, imaging probe for intraluminal fluorescence imaging of the gastrointestinal tract

Gastrointestinal cancers continue to account for a disproportionately large percentage of annual cancer deaths in the US. Advancements in miniature imaging technology combined with a need for precise and thorough tumor detection in gastrointestinal cancer screenings fuel the demand for new, small-scale, and low-cost methods of localization and margin identification with improved accuracy. Here, we report the development of a miniaturized, chip-on-tip, multispectral, fluorescence imaging probe designed to port through a gastroscope working channel with the aim of detecting cancerous lesions in point-of-care endoscopy of the gastrointestinal lumen. Preclinical testing has confirmed fluorescence sensitivity and supports that this miniature probe can locate structures of interest via detection of fluorescence emission from exogenous contrast agents. This work demonstrates the design and preliminary performance evaluation of a miniaturized, single-use, chip-on-tip fluorescence imaging system, capable of detecting multiple fluorochromes, and devised for deployment via the accessory channel of a standard gastroscope.

Nonparametric Bayesian inference for meta-stable conformational dynamics

Analyses of structural dynamics of biomolecules hold great promise to deepen the understanding of and ability to construct complex molecular systems. To this end, both experimental and computational means are available, such as fluorescence quenching experiments or molecular dynamics simulations, respectively. We argue that while seemingly disparate, both fields of study have to deal with the same type of data about the same underlying phenomenon of conformational switching. Two central challenges typically arise in both contexts: (i) the amount of obtained data is large, and (ii) it is often unknown how many distinct molecular states underlie these data. In this study, we build on the established idea of Markov state modeling and propose a generative, Bayesian nonparametric hidden Markov state model that addresses these challenges. Utilizing hierarchical Dirichlet processes, we treat different meta-stable molecule conformations as distinct Markov states, the number of which we then do not have to set a priori. In contrast to existing approaches to both experimental as well as simulation data that are based on the same idea, we leverage a mean-field variational inference approach, enabling scalable inference on large amounts of data. Furthermore, we specify the model also for the important case of angular data, which however proves to be computationally intractable. Addressing this issue, we propose a computationally tractable approximation to the angular model. We demonstrate the method on synthetic ground truth data and apply it to known benchmark problems as well as electrophysiological experimental data from a conformation-switching ion channel to highlight its practical utility.

Investigation of the Fluorescence Turn-off Mechanism, Genome, Molecular Docking In Silico and In Vitro Studies of 2-Acetyl-3H-benzo[f]chromen-3-one

The present study harnesses fluorescence quenching between a nonfluorescent aniline and fluorophore 2-acetyl-3H-benzo[f]chromen-3-one [2AHBC] in binary solvent mixtures of acetonitrile and 1,4-dioxane at room temperature and explores the fluorophore as an antimicrobial material. Our findings throw light on the key performance of organic molecules in the medicinal and pharmaceutical fields, which are considered as the most leading drives in therapeutic applications. In view of that, fluorescence quenching data have been interpreted by various quenching models. This demonstrates that the sphere of action holds very well in the present work and also confirms the presence of static quenching reactions. Additionally, the fluorophore was first investigated for druglike activity with the help of in silico tools, and then it was investigated for antimicrobial activity through bioinformatics tools, which has shown promising insights.

BODIPY-Based Polymers of Intrinsic Microporosity for the Photocatalytic Detoxification of a Chemical Threat

Effective heterogeneous photocatalysts capable of detoxifying chemical threats in practical settings must exhibit outstanding device integrity. We report a copolymerization that yields robust, porous, processible, chromophoric BODIPY (BDP; boron-dipyrromethene)-containing polymers of intrinsic microporosity (BDP-PIMs). Installation of a pentafluorophenyl at the meso position of a BDP produced reactive monomer that when combined with 5,5,6,6-tetrahydroxy-3,3,3,3-tetramethyl-1,1-spirobisindane (TTSBI) and tetrafluoroterephthalonitrile (TFTPN) yields PIM-1. Postsynthetic modification of these polymers yields Br-BDP-PIM-1a and -1b─polymers containing bromine at the 2,6-positions. Remarkably, the brominated polymers display porosity and processability features similar to those of H-BDP-PIMs. Gas adsorption reveals molecular-scale porosity and Brunette-Emmet-Teller surface areas as high as 680 m² g^-1. Electronic absorption spectra reveal charge-transfer (CT) bands centered at 660 nm, while bands arising from local excitations, LE, of BDP and TFTPN units are at 530 and 430 nm, respectively. Fluorescence spectra of the polymers reveal a Förster resonance energy-transfer (FRET) pathway to BDP units when TFTPN units are excited at 430 nm; weak phosphorescence at room temperature indicates a singlet-to-triplet intersystem crossing. The low-lying triplet state is well positioned energetically to sensitize the conversion of ground-state (triplet) molecular oxygen to electronically excited singlet oxygen. Photosensitization capabilities of these polymers toward singlet-oxygen-driven detoxification of a sulfur-mustard simulant 2-chloroethyl ethyl sulfide (CEES) have been examined. While excitation of CT and LE_BDP bands yields weak catalytic activity (t_1/2 > 15 min), excitation to higher energy states of TFTPN induces significant increases in photoactivity (t_1/2 ≅ 5 min). The increase is attributable to (i) enhanced light collection, (ii) FRET between TFTPN and BDP, (iii) the presence of heavy atoms (bromine) having large spin-orbit coupling energies that can facilitate intersystem crossing from donor-acceptor CT-, FRET-, or LE-generated BDP singlet states to BDP-related triplet states, and (iv) polymer triplet excited-state sensitization of the formation of CEES-reactive, singlet oxygen.

Direct evaluation of self-quenching behavior of fluorophores at high concentrations using an evanescent field

The quantum yield of a fluorophore is reduced when two or more identical fluorophores are in close proximity to each other. The study of protein folding or particle aggregation is can be done based on this above-mentioned phenomenon—called self-quenching. However, it is challenging to characterize the self-quenching of a fluorophore at high concentrations because of the inner filter effect, which involves depletion of excitation light and re-absorption of emission light. Herein, a novel method to directly evaluate the self-quenching behavior of fluorophores was developed. The evanescent field from an objective-type total internal reflection fluorescence (TIRF) microscope was used to reduce the path length of the excitation and emission light to ~100 nm, thereby supressing the inner filter effect. Fluorescence intensities of sulforhodamine B, fluorescein isothiocyanate (FITC), and calcein solutions with concentrations ranging from 1 μM to 50 mM were directly measured to evaluate the concentration required for 1000-fold degree of self-quenching and to examine the different mechanisms through which the fluorophores undergo self-quenching.

Development and application of a high throughput assay system for the detection of Rieske dioxygenase activity

Herein we report the development of a new periodate-based reactive assay system for the fluorescent detection of the cis-diol metabolites produced by Rieske dioxygenases. This sensitive and diastereoselective assay system successfully evaluates the substrate scope of Rieske dioxygenases and determines the relative activity of a rationally designed Rieske dioxygenase variant library. The high throughput capacity of the assay system enables rapid and efficient substrate scope investigations and screening of large dioxygenase variant libraries.

FRACTAL: Signal amplification of immunofluorescence via cyclic staining of target molecules

In this article, we demonstrate fluorescent signal amplification via cyclic staining of target molecules (FRACTAL), a technique that can amplify the signal intensity of immunofluorescence staining more than nine-fold via simple cyclic staining of secondary antibodies. We also show that FRACTAL is compatible with four-color imaging and expansion microscopy imaging.

Amphiphilic "Like-a-Brush" Oligonucleotide Conjugates with Three Dodecyl Chains: Self-Assembly Features of Novel Scaffold Compounds for Nucleic Acids Delivery

The conjugation of lipophilic groups to oligonucleotides is a promising approach for improving nucleic acid-based therapeutics' intracellular delivery. Lipid oligonucleotide conjugates can self-aggregate in aqueous solution, which gains much attention due to the formation of micellar particles suitable for cell endocytosis. Here, we describe self-association features of novel "like-a-brush" oligonucleotide conjugates bearing three dodecyl chains. The self-assembly of the conjugates into 30-170 nm micellar particles with a high tendency to aggregate was shown using dynamic light scattering (DLS), atomic force (AFM), and transmission electron (TEM) microscopies. Fluorescently labeled conjugates demonstrated significant quenching of fluorescence intensity (up to 90%) under micelle formation conditions. The conjugates possess increased binding affinity to serum albumin as compared with free oligonucleotides. The dodecyl oligonucleotide conjugate and its duplex efficiently internalized and accumulated into HepG2 cells' cytoplasm without any transfection agent. It was shown that the addition of serum albumin or fetal bovine serum to the medium decreased oligonucleotide uptake efficacy (by 22.5-36%) but did not completely inhibit cell penetration. The obtained results allow considering dodecyl-containing oligonucleotides as scaffold compounds for engineering nucleic acid delivery vehicles.

Apolipoprotein E4 exhibits intermediates with domain interaction

ApoE4(C112R) is the strongest risk factor for Alzheimer's disease, while apoE3(C112) is considered normal. The C112R substitution is believed to alter the interactions between the N-terminal (NTD) and the C-terminal domain (CTD) leading to major functional differences. Here we investigate how the molecular property of the residue at position 112 affects domain interaction using an array of C112X substitutions with arginine, alanine, threonine, valine, leucine and isoleucine as 'X'. We attempt to determine the free energy of domain interaction (∆G_INT) from stabilities of the NTD (∆G_NTD) and CTD (∆G_CTD) in the full-length apoE, and the stabilities of fragments of the NTD (∆G_NTF) and CTD (∆G_CTF), using the relationship, ∆G_INT = ∆G_NTD + ∆G_CTD - ∆G_NTF - ∆G_CTF. We find that although ∆G_NTD is strongly dependent on the C112X substitutions, ∆G_NTD - ∆G_NTF is small. Furthermore, ∆G_CTD remains nearly the same as ∆G_CTF. Therefore, ∆G_INT is estimated to be small and similar for the apoE isoforms. However, stability of domain interaction monitored by urea dependent changes in interdomain Forster Resonance Energy Transfer (FRET) is found to be strongly dependent on C112X substitutions. ApoE4 exhibits the highest mid-point of denaturation of interdomain FRET. To resolve the apparently contradictory observations, we hypothesize that higher interdomain FRET in apoE4 in urea may involve 'intermediate' states. Enhanced fluorescence of bis-ANS and susceptibility to proteolytic cleavage support that apoE4, specifically, the NTD of apoE4 harbor 'intermediates' in both native and mildly denaturing conditions. The intermediates could hold key to the pathological functions of apoE4.

A Single-Molecule Surface-Based Platform to Detect the Assembly and Function of the Human RNA Polymerase II Transcription Machinery

Single-molecule detection and manipulation is a powerful tool for unraveling dynamic biological processes. Unfortunately, success in such experiments is often challenged by tethering the biomolecule(s) of interest to a biocompatible surface. Here, we describe a robust surface passivation method by dense polymer brush grafting, based on optimized polyethylene glycol (PEG) deposition conditions, exactly at the lower critical point of an aqueous biphasic PEG-salt system. The increased biocompatibility achieved, compared with PEG deposition in sub-optimal conditions away from the critical point, allowed us to successfully detect the assembly and function of a large macromolecular machine, a fluorescent-labeled multi-subunit, human RNA Polymerase II Transcription Pre-Initiation Complex, on single, promoter-containing, surface-immobilized DNA molecules. This platform will enable probing the complex biochemistry and dynamics of large, multi-subunit macromolecular assemblies, such as during the initiation of human RNA Pol II transcription, at the single-molecule level.

Adhesive stem cell coatings for enhanced retention in the heart tissue

Injection into the heart tissue is a direct route for optimally placing mesenchymal stem cells (MSC) to regulate local inflammation following a heart attack. The retention of MSCs at the injection site is severely limited by the fluid flows that rapidly wash cells away and minimize their capacity to modulate cardiac inflammation. To prevent this loss of MSCs and their function, antibody coatings were designed for the surface of MSCs to enhance their adhesion to the inflamed tissue. MSCs were biotinylated, and biotinylated antibodies against intercellular cell adhesion molecules were conjugated to the cell surface through an intermediate layer of streptavidin. MSC surfaces were modified with ~7,000 biotin/μm² and ~23 antibodies/μm². The heart tissue injection of antibody-coated MSCs offered a 3-fold increase of cell retention in an infarcted heart over the injection of uncoated MSCs. We supported the mechanism of adhesion through analysis of MSC adhesion to inflamed endothelial cells and also surfaces of purified adhesion molecules on glass under microfluidic shear flow.

Label-Free Analysis of Protein Aggregation and Phase Behavior

Phase transitions of protein molecules are central to biological function and malfunction. One such transition commonly encountered in nature is the conversion of soluble monomeric states into solid phases, which include crystals and amyloid fibrils, the latter of which are associated with the onset and development of neurodegenerative diseases. Monitoring aggregate formation and protein phase behavior is essential in gaining mechanistic insights into these fundamental processes. Fluorescence techniques have proven invaluable in observing biological molecules; yet, most such approaches rely on the use of an extrinsic fluorophore that binds to the molecule of interest, the installation of which can perturb the molecular systems under study. However, most proteins also possess aromatic amino acids within their peptide sequence and therefore exhibit intrinsic fluorescence. Here, we show that by measuring in space and time tryptophan autofluorescence for three proteins, reconstituted silk fibroin, β-lactoglobulin, and lysozyme, fibrillar self-assembly can be monitored accurately and without the need for extrinsic dyes. When fibrillar protein self-assembly takes place, hydrophobic burial occurs, resulting in the minimization of exposed tryptophan residues to the solvent and consequently leading to an increase in protein autofluorescence. Moreover, by employing a droplet-microfluidic approach to confine protein self-assembly in space, we demonstrate that intrinsic fluorescence can be used to image protein nanofibrils in a label-free manner and that the microstructural analysis obtained from intrinsic fluorescence microscopy correlates well with that from samples treated with extrinsic dyes. Finally, our results show that protein autofluorescence is not limited to the observation of β-sheet-rich structures, but can also be used to distinguish between different types of solid phases including spherulites and crystals, making this approach suitable for overall characterization of protein phase transition phenomena.

High Potency of SN-38-Loaded Bovine Serum Albumin Nanoparticles Against Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer with a worse prognosis than other types. There are currently no specific approved treatments for TNBC. Albumin is a promising biomimetic material that may be fabricated into nanoparticles to possibly exert passive effects on targeted tumors. Irinotecan has been extensively used in clinical settings, although a high dosage is required due to its low efficiency of conversion into the active metabolite SN-38, also known as 7-ethyl-10-hydroxy-camptothecin. The aim of this work was to optimize SN-38-loaded bovine serum albumin nanoparticles (sBSANPs) and evaluate their potency against TNBC. The sBSANPs were characterized by a small size of about 134-264 nm, a negative charge of -37 to -40 mV, an entrapment efficiency of 59-71%, and a particle yield of 65-86%. The cytotoxicity assays using sBSANPs showed a higher potency specifically against both MDA-MB-468 and MDA-MB-231 cells (ER-, PR-, HER2-) compared to MCF-7 (ER+, PR+, HER2-), and exhibited an extremely low IC₅₀ at the nanomolar levels (2.01-6.82 nM). The release profiles indicated that SN-38 presented an initial burst release within 12 h, and sBSANPs had a slow release pattern. Flow cytometry results showed that the fluorescence intensity of sBSANPs was significantly higher than that of the control group. The confocal images also confirmed that sBSANPs were taken up by MDA-MB-468 cells. Moreover, we found that a larger BSANP size resulted in an increased hemolytic effect. In vivo animal studies demonstrated that loading of SN-38 into bovine serum albumin nanoparticles could minimize the initial concentration without extending the elimination half-life, but significantly minimized the Cmax (p < 0.001) as compared with irinotecan treatment.

Extending Single Molecule Imaging to Proteome Analysis by Quantitation of Fluorescent Labeling Homogeneity in Complex Protein Samples

Fluorescence-based electrophoresis has been widely used for proteome analysis in which every protein species in cells is labeled with a fluorescent dye, separated by electric migration, and quantified using fluorescence detection. The ultimate limit of sensitivity for this approach could be reached by single-molecule fluorescence imaging and counting individual proteins, requiring exhaustive fluorescent labeling of proteins across molecular populations and species. However, it remains unclear how homogeneous the fluorescence labeling of individual protein molecules of each species is across the proteome. To address this question, we developed a method to measure the labeling homogeneity based on a single-molecule fluorescence counting assay. Our results reveal that the proportion of proteins labeled with at least one dye, called labeling occupancy (LO), was 35% for fluorescently labeled BSA using existing protocols. We then found that the LO could be improved to 82% under high pH and surfactant-rich conditions. Furthermore, when a proteome sample from a human cell lysate was analyzed, the total LO was 71%, whereby the values varied between 50 and 90% for low and high molecular weight proteome fractions, respectively. The results support the possibility of sensitive detection of proteins using single-molecule counting with fluorescent labeling at the proteome scale.

State-of-the-Art Fluorescence Fluctuation-Based Spectroscopic Techniques for the Study of Protein Aggregation

Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, are devastating proteinopathies with misfolded protein aggregates accumulating in neuronal cells. Inclusion bodies of protein aggregates are frequently observed in the neuronal cells of patients. Investigation of the underlying causes of neurodegeneration requires the establishment and selection of appropriate methodologies for detailed investigation of the state and conformation of protein aggregates. In the current review, we present an overview of the principles and application of several methodologies used for the elucidation of protein aggregation, specifically ones based on determination of fluctuations of fluorescence. The discussed methods include fluorescence correlation spectroscopy (FCS), imaging FCS, image correlation spectroscopy (ICS), photobleaching ICS (pbICS), number and brightness (N&B) analysis, super-resolution optical fluctuation imaging (SOFI), and transient state (TRAST) monitoring spectroscopy. Some of these methodologies are classical protein aggregation analyses, while others are not yet widely used. Collectively, the methods presented here should help the future development of research not only into protein aggregation but also neurodegenerative diseases.

On-chip measurements of protein unfolding from direct observations of micron-scale diffusion

The unfolding process of BSA in solution as a function of pH was studied by microfluidic diffusional sizing device.

Investigations of protein folding, unfolding and stability are critical for the understanding of the molecular basis of biological structure and function. We describe here a microfluidic approach to probe the unfolding of unlabelled protein molecules in microliter volumes. We achieve this objective through the use of a microfluidic platform, which allows the changes in molecular diffusivity upon folding and unfolding to be detected directly. We illustrate this approach by monitoring the unfolding of bovine serum albumin in solution as a function of pH. These results show the viability of probing protein stability on chip in small volumes.

Optimized Streptavidin for Fluorescent Labeling of Biotinylated Targets

In order to develop a streptavidin-biotin system with optimal performance in fluorescent labeling, in this issue of Cell Chemical Biology, Jacobsen et al. (2017) focused on changing the surface density of amino groups present on streptavidin via lysine mutagenesis. The streptavidin mutant containing only one free amino group was found superior to other streptavidin variants and was named Flavidin for fluorophore-friendly streptavidin.

UbFluor: A Fluorescent Thioester to Monitor HECT E3 Ligase Catalysis

HECT E3 ubiquitin ligases (∼28 are known) are associated with many phenotypes in eukaryotes and are important drug targets. However, assays used to screen for small molecule inhibitors of HECT E3s are complex and require ATP, Ub, E1, E2, and HECT E3 enzymes, producing three covalent thioester enzyme intermediates E1∼Ub, E2∼Ub, and HECT E3∼Ub (where ∼ indicates a thioester bond), and mixtures of polyubiquitin chains. To reduce the complexity of the assay, we developed a novel class of fluorescent probes, UbFluor, that act as mechanistically relevant pseudosubstrates of HECT E3s. These probes undergo a direct transthiolation reaction with the catalytic cysteine of HECT E3s, producing the catalytically active HECT E3∼Ub thioester accompanied by fluorophore release. Thus, a fluorescence polarization assay can continuously monitor UbFluor consumption by HECT E3s, and changes in UbFluor consumption rendered by biochemical point mutations or small molecule modulation of HECT E3 activity. © 2017 by John Wiley & Sons, Inc.

Synthesis and evaluation of benzothiazole-triazole and benzothiadiazole-triazole scaffolds as potential molecular probes for amyloid-β aggregation

Fluorescent scaffolds that can be easily modifiedviaclick chemistry were investigated as probes for Aβ-plaque deposits in mouse tissue.

Time-resolved homo-FRET studies of biotin-streptavidin complexes

Förster resonance energy transfer is a mechanism of fluorescence quenching that is notably useful for characterizing properties of biomolecules and/or their interactions. Here we study water-solutions of Biotin-Streptavidin complexes, in which Biotin is labeled with a rigidly-bound fluorophore that can interact by Förster resonance energy transfer with the fluorophores labeling the other, up to three, Biotins of the same complex. The fluorophore, Atto550, is a Rhodamine analogue. We detect the time-resolved fluorescence decay of the fluorophores with an apparatus endowed with single-photon sensitivity and temporal resolution of ~30ps. The decay profiles we observe for samples containing constant Biotin-Atto550 conjugates and varying Streptavidin concentrations are multi-exponential. Each decay component can be associated with the rate of quenching exerted on each donor by each of the acceptors that label the other Biotin molecules, depending on the binding site they occupy. The main features that lead to this result are that (i) the transition dipole moments of the up-to-four Atto550 fluorophores that label the complexes are fixed as to both relative positions and mutual orientations; (ii) the fluorophores are identical and the role of donor in each Biotin-Streptavidin complex is randomly attributed to the one that has absorbed the excitation light (homo-FRET). Obviously the high-temporal resolution of the excitation-detection apparatus is necessary to discriminate among the fluorescence decay components.

Morphology-Specific Inhibition of β-Amyloid Aggregates by 17β-Hydroxysteroid Dehydrogenase Type 10

A major hallmark of Alzheimer's disease (AD) is the formation of toxic aggregates of the β-amyloid peptide (Aβ). Given that Aβ peptides are known to localise within mitochondria and interact with 17β-HSD10, a mitochondrial protein expressed at high levels in AD brains, we investigated the inhibitory potential of 17β-HSD10 against Aβ aggregation under a range of physiological conditions. Fluorescence self-quenching (FSQ) of Aβ(1-42) labelled with HiLyte Fluor 555 was used to evaluate the inhibitory effect under conditions established to grow distinct Aβ morphologies. 17β-HSD10 preferentially inhibits the formation of globular and fibrillar-like structures but has no effect on the growth of amorphous plaque-like aggregates at endosomal pH 6. This work provides insights into the dependence of the Aβ-17β-HSD10 interaction with the morphology of Aβ aggregates and how this impacts enzymatic function.

Colorimetric and fluorometric monitoring of the helix composition of collagen-like peptides at the nM level

We have demonstrated that the incorporation of a dye-labeled collagen-like peptide in the homotrimeric versus heterotrimeric context results in visible color changes and distinct fluorescence. The unique fluorescence self-quenching assay can unambiguously determine the helix composition of heterotrimers at the nM level, far extending our capability to characterize a collagen triple helix.

Type 3 Secretion Translocators Spontaneously Assemble a Hexadecameric Transmembrane Complex

A type 3 secretion system is used by many bacterial pathogens to inject proteins into eukaryotic cells. Pathogens insert a translocon complex into the target eukaryotic membrane by secreting two proteins known as translocators. How these translocators form a translocon in the lipid bilayer and why both proteins are required remains elusive. Pseudomonas aeruginosa translocators PopB and PopD insert pores into membranes forming homo- or hetero-complexes of undetermined stoichiometry. Single-molecule fluorescence photobleaching experiments revealed that PopD formed mostly hexameric structures in membranes, whereas PopB displayed a bi-modal distribution with 6 and 12 subunits peaks. However, individually the proteins are not functional for effector translocation. We have found that when added together, the translocators formed distinct hetero-complexes containing 8 PopB and 8 PopD molecules. Thus, the interaction between PopB and PopD guide the assembly of a unique hetero-oligomer in membranes.

Synthesis, Spectral Characteristics and DFT Studies of the New Dye 2,7-diacetyl-9-((dimethylamino)methylene)-9H-fluorene (DMMF) in Different Solvents

The photophysical parameters such as electronic absorption spectra, molar absorptivity(ε), fluorescence spectra and fluorescence quantum yield (φf) of a new dye namely 2,7-diacetyl-9-((dimethylamino)methylene)-9H-fluorene (DMMF) were determined in different solvents. The electronic absorption are less sensitive to medium polarity. A bathochromic shift was observed in emission spectra(ca. 50 nm) upon increase of solvent polarity, which indicates that the singlet excited state (S1) of DMMF is more polar than the singlet ground state (So). Solid crystals of DMMF exhibit intense yellow fluorescence maximum at 550 nm with bandwidth equal 64 nm upon excitation at wavelength 365 nm. The change in dipole moment value (Δμ) was calculated by using the variation of Stokes shift with solvent polarizability (Δf) (Lippert - Mataga plot) and was found to be 7.22 and 5.5 Debye for higher and lower energy of So - S1 (π-π*) H-1 → L and So - S1 (π-π*) H → L, respectively. These results show that, the excited state is more polar than the ground state. The net photochemical quantum yields of photodecomposition of DMMF (φc) were calculated as 7.2 × 10(-5), 1.14 × 10(-4), 1.44 × 10(-4) and 2.11 × 10(-4) in different solvents such as MeOH, CH2Cl2, CHCl3 and CCl4, respectively. DFT/TD-DFT methods were used to study the geometric and electronic structures of DMMF in different solvents. A good agreement was found between the experimental and theoretical results.

Aggregation of nitroaniline in tetrahydrofuran through intriguing H-bond formation by sodium borohydride

The participation of sodium borohydride (NaBH4) in hydrogen bonding interactions and transient anion radical formation has been proved. Thus, the properties of NaBH4 are extended beyond the purview of its normal reducing capability and nucleophilic property. It is reported that ortho- and para-nitroanilines (NAs) form stable aggregates only in tetrahydrofuran (THF) in the presence of NaBH4 and unprecedented orange/red colorations are observed. The same recipe with nitrobenzene instead of nitroanilines (NAs) in the presence of NaBH4 evolves a transient rose red solution due to the formation of a highly fluorescent anion radical. Spectroscopic studies (UV-vis, fluorescence, RLS, Raman, NMR etc.) as well as theoretical calculations supplement the J-aggregate formation of NAs due to extensive hydrogen bonding. This is the first report where BH4(-) in THF has been shown to support such an aggregation process through H-bonding. It is further confirmed that stable intermolecular hydrogen bond-induced aggregation requires a geometrical match in both the nitro- and amino-functionalities attached to the phenyl ring with proper geometry. On the contrary, meta-nitroaniline remains as the odd man out and does not take part in such aggregation. Surprisingly, Au nanoparticles dismantle the J-aggregates of NA in THF. Explicit hydrogen bond formation in NA has been confirmed experimentally considering its promising applications in different fields including non-linear optics.

Ultrasound-modulated fluorescence based on donor-acceptor-labeled microbubbles

A fluorescence resonance energy transfer (FRET)-based microbubble contrast agent system was designed to experimentally demonstrate the concept of ultrasound-modulated fluorescence (UMF). Microbubbles were simultaneously labeled with donor and acceptor fluorophores on the surface to minimize self-quenching and maximize FRET. In response to ultrasound, the quenching efficiency was greatly modulated by changing the distance between the donor and acceptor molecules through microbubble size oscillations. Both donors and acceptors exhibited UMF on individual microbubbles. The UMF strength of the donor was more significant compared to that of the acceptor. Furthermore, the UMF of the donor was observed from a microbubble solution in a turbid media. This study exploits the feasibility of donor–acceptor labeled microbubbles as UMF contrast agents.

Extracting physics of life at the molecular level: A review of single-molecule data analyses

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.

Mucus barrier-triggered disassembly of siRNA nanocarriers

The mucus overlying mucosal epithelial surfaces presents not only a biological barrier to the penetration of potential pathogens, but also therapeutic modalities including RNAi-based nanocarriers. Movement of nanomedicines across the mucus barriers of the gastrointestinal mucosa is modulated by interactions of the nanomedicine carriers with mucin glycoproteins inside the mucus, potentiated by the large surface area of the nanocarrier. We have developed a fluorescence activation-based reporter system showing that the interaction between polyanionic mucins and the cationic chitosan/small interfering RNA (siRNA) nanocarriers (polyplexes) results in the disassembly and consequent triggered release of fluorescent siRNA. The quantity of release was found to be dependent on the molar ratio between chitosan amino groups and siRNA phosphate groups (NP ratio) of the polyplexes with a maximal estimated 48.6% release of siRNA over 30 min at NP 60. Furthermore, a microfluidic in vitro model of the gastrointestinal mucus barrier was used to visualize the dynamic interaction between chitosan/siRNA nanocarriers and native purified porcine stomach mucins. We observed strong interactions and aggregations at the mucin-liquid interface, followed by an NP ratio dependent release and consequent diffusion of siRNA across the mucin barrier. This work describes a new model of interaction at the nanocarrier-mucin interface and has important implications for the design and development of nucleic acid-based nanocarrier therapeutics for mucosal disease treatments and also provides insights into nanoscale pathogenic processes.

Single-molecule patch-clamp FRET microscopy studies of NMDA receptor ion channel dynamics in living cells: revealing the multiple conformational states associated with a channel at its electrical off state

Conformational dynamics plays a critical role in the activation, deactivation, and open-close activities of ion channels in living cells. Such conformational dynamics is often inhomogeneous and extremely difficult to be directly characterized by ensemble-averaged spectroscopic imaging or only by single channel patch-clamp electric recording methods. We have developed a new and combined technical approach, single-molecule patch-clamp FRET microscopy, to probe ion channel conformational dynamics in living cell by simultaneous and correlated measurements of real-time single-molecule FRET spectroscopic imaging with single-channel electric current recording. Our approach is particularly capable of resolving ion channel conformational change rate process when the channel is at its electrically off states and before the ion channel is activated, the so-called "silent time" when the electric current signals are at zero or background. We have probed NMDA (N-methyl-D-aspartate) receptor ion channel in live HEK-293 cell, especially, the single ion channel open-close activity and its associated protein conformational changes simultaneously. Furthermore, we have revealed that the seemingly identical electrically off states are associated with multiple conformational states. On the basis of our experimental results, we have proposed a multistate clamshell model to interpret the NMDA receptor open-close dynamics.

Ultrasound-modulated fluorescence based on fluorescent microbubbles

Ultrasound-modulated fluorescence (UMF) imaging has been proposed to provide fluorescent contrast while maintaining ultrasound resolution in an optical-scattering medium (such as biological tissue). The major challenge is to extract the weakly modulated fluorescent signal from a bright and unmodulated background. UMF was experimentally demonstrated based on fluorophore-labeled microbubble contrast agents. These contrast agents were produced by conjugating N-hydroxysuccinimide (NHS)-ester-attached fluorophores on the surface of amine-functionalized microbubbles. The fluorophore surface concentration was controlled so that a significant self-quenching effect occurred when no ultrasound was applied. The intensity of the fluorescent emission was modulated when microbubbles were oscillated by ultrasound pulses, presented as UMF signal. Our results demonstrated that the UMF signals were highly dependent on the microbubbles' oscillation amplitude and the initial surface fluorophore-quenching status. A maximum of ∼42% UMF modulation depth was achieved with a single microbubble under an ultrasound peak-to-peak pressure of 675 kPa. Further, UMF was detected from a 500-μm tube filled with contrast agents in water and scattering media with ultrasound resolution. These results indicate that ultrasound-modulated fluorescent microbubble contrast agents can potentially be used for fluorescence-based molecular imaging with ultrasound resolution in the future.

DNA origami-based standards for quantitative fluorescence microscopy

Validating and testing a fluorescence microscope or a microscopy method requires defined samples that can be used as standards. DNA origami is a new tool that provides a framework to place defined numbers of small molecules such as fluorescent dyes or proteins in a programmed geometry with nanometer precision. The flexibility and versatility in the design of DNA origami microscopy standards makes them ideally suited for the broad variety of emerging super-resolution microscopy methods. As DNA origami structures are durable and portable, they can become a universally available specimen to check the everyday functionality of a microscope. The standards are immobilized on a glass slide, and they can be imaged without further preparation and can be stored for up to 6 months. We describe a detailed protocol for the design, production and use of DNA origami microscopy standards, and we introduce a DNA origami rectangle, bundles and a nanopillar as fluorescent nanoscopic rulers. The protocol provides procedures for the design and realization of fluorescent marks on DNA origami structures, their production and purification, quality control, handling, immobilization, measurement and data analysis. The procedure can be completed in 1-2 d.

Single-molecule studies of riboswitch folding

The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.

Conformational dynamics of an ATP-binding DNA aptamer: a single-molecule study

Nucleic acid aptamers are single-stranded RNA or DNA molecules that bind to their targets with high specificity and affinity. Although their biomedical applications have been booming, it is still debatable whether an aptamer recognizes its target through "induced fit" or "conformational selection", a central question in molecular recognition. To address this question, an ATP-binding DNA aptamer was selected as a model system and the conformational properties of this aptamer with and without the presence of ATP were investigated by single-pair Förster resonance energy transfer (spFRET) spectroscopy. The single-molecule results indicate that the aptamer can fold into a double-stranded-like structure, similar to the ligand-bound conformation, even without the presence of ATP. The folded structure is thermally stable at high salt concentrations and becomes rather dynamic at low salt concentrations. Although in the latter condition, the aptamer prefers unfolded structures, it can occasionally migrate to the folded conformation for a short time before being unfolded again. The binding of ATP to the aptamer stabilizes the folded structure, which populates the ligand-bound state of the aptamer, thus shifting the conformational equilibrium. Collectively, our data support that the ATP-binding DNA aptamer recognizes ATP ligand through "conformational selection".

tRNA binding to antitumor drug doxorubicin and its analogue

The binding sites of antitumor drug doxorubicin (DOX) and its analogue N-(trifluoroacetyl) doxorubicin (FDOX) with tRNA were located, using FTIR, CD, fluorescence spectroscopic methods and molecular modeling. Different binding sites are involved in drug-tRNA adducts with DOX located in the vicinity of A-29, A-31, A-38, C-25, C-27, C-28, G-30 and U-41, while FDOX bindings involved A-23, A-44, C-25, C-27, G-24, G-42, G-53, G-45 and U-41 with similar free binding energy (-4.44 for DOX and -4.41 kcal/mol for FDOX adducts). Spectroscopic results showed that both hydrophilic and hydrophobic contacts are involved in drug-tRNA complexation and FDOX forms more stable complexes than DOX with K DOX-tRNA=4.7 (± 0.5)× 10(4) M(-1) and K FDOX-tRNA=6.3 (± 0.7)× 10(4) M(-1). The number of drug molecules bound per tRNA (n) was 0.6 for DOX and 0.4 for FDOX. No major alterations of tRNA structure were observed and tRNA remained in A-family conformation, while biopolymer aggregation and particle formation occurred at high drug concentrations.