Real-time enzyme kinetics monitored by dual-color fluorescence cross-correlation spectroscopy

Monitoring Enzyme Activity Using Near-Infrared Fluorescent Single-Walled Carbon Nanotubes

Enzymes serve as pivotal biological catalysts that accelerate essential chemical reactions, thereby influencing a variety of physiological processes. Consequently, the monitoring of enzyme activity and inhibition not only yields crucial insights into health and disease conditions but also forms the basis of research in drug discovery, toxicology, and the understanding of disease mechanisms. In this context, near-infrared (NIR) fluorescent single-walled carbon nanotubes (SWCNTs) have emerged as effective tools for tracking enzyme activity and inhibition through diverse strategies. This perspective explores the physicochemical attributes of SWCNTs that render them well-suited for such monitoring. Additionally, we delve into the various strategies developed so far for successfully monitoring enzyme activity and inhibition, emphasizing the distinctive features of each principle. Furthermore, we contrast the benefits of SWCNT-based NIR probes with conventional gold standards in monitoring enzyme activity. Lastly, we highlight the current challenges faced in this field and suggest potential solutions to propel it forward. This perspective aims to contribute to the ongoing progress in biodiagnostics and seeks to engage the wider community in developing and applying enzymatic assays using SWCNTs.

Objective scanning-based fluorescence cross-correlation spectroscopy (Scan-FCCS) for studying the fusion dynamics of protein phase separation

Protein phase separation plays a very important role in many biological processes and is closely related to the occurrence and development of some serious diseases. So far, the fluorescence imaging method and fluorescence correlation spectroscopy (FCS) have been frequently used to study the phase separation behavior of proteins. Due to the wide size distribution of protein condensates in phase separation from nano-scale to micro-scale in solution and living cells, it is difficult for the fluorescence imaging method and conventional FCS to fully reflect the real state of protein phase separation in the solution due to the low spatio-temporal resolution of the conventional fluorescence imaging method and the limited detection area of FCS. Here, we proposed a novel method for studying the protein phase separation process by objective scanning-based fluorescence cross-correlation spectroscopy (Scan-FCCS). In this study, CRDBP proteins were used as a model and respectively fused with fluorescent proteins (EGFP and mCherry). We first compared conventional FCS and Scan-FCS methods for characterizing the CRDBP protein phase separation behaviors and found that the reproducibility of Scan-FCS is significantly improved by the scanning mode. We studied the self-fusion process of mCherry-CRDBP and EGFP-CRDBP and observed that the phase change concentration of CRDBP was 25 nM and the fusion of mCherry-CRDBP and EGFP-CRDBP at 500 nM was completed within 70 min. We studied the effects of salt concentration and molecular crowding agents on the phase separation of CRDBP and found that salt can prevent the self-fusion of CRDBP and molecular crowding agents can improve the self-fusion of CRDBP. Furthermore, we found the recruitment behavior of CRDBP to β-catenin proteins and studied their recruitment dynamics. Compared to conventional FCS, Scan-FCCS can significantly improve the reproducibility of measurements due to the dramatic increase of detection zone, and more importantly, this method can provide information about self-fusion and recruitment dynamics in protein phase separation.

Retention of the RNA ends provides the molecular memory for maintaining the activation of the Csm complex

The type III CRISPR-Cas effector complex Csm functions as a molecular Swiss army knife that provides multilevel defense against foreign nucleic acids. The coordinated action of three catalytic activities of the Csm complex enables simultaneous degradation of the invader's RNA transcripts, destruction of the template DNA and synthesis of signaling molecules (cyclic oligoadenylates cAn) that activate auxiliary proteins to reinforce CRISPR-Cas defense. Here, we employed single-molecule techniques to connect the kinetics of RNA binding, dissociation, and DNA hydrolysis by the Csm complex from Streptococcus thermophilus. Although single-stranded RNA is cleaved rapidly (within seconds), dual-color FCS experiments and single-molecule TIRF microscopy revealed that Csm remains bound to terminal RNA cleavage products with a half-life of over 1 hour while releasing the internal RNA fragments quickly. Using a continuous fluorescent DNA degradation assay, we observed that RNA-regulated single-stranded DNase activity decreases on a similar timescale. These findings suggest that after fast target RNA cleavage the terminal RNA cleavage products stay bound within the Csm complex, keeping the Cas10 subunit activated for DNA destruction. Additionally, we demonstrate that during Cas10 activation, the complex remains capable of RNA turnover, i.e. of ongoing degradation of target RNA.

Thermodynamic bounds on the asymmetry of cross-correlations with dynamical activity and entropy production

Entropy production and dynamical activity are two complementary aspects in nonequilibrium physics. The asymmetry of cross-correlation, serving as a distinctive feature of nonequilibrium, also finds widespread utility. In this Letter, we establish two thermodynamic bounds on the normalized asymmetry of cross-correlation in terms of dynamical activity and entropy production rate. These bounds demonstrate broad applicability and offer experimental testability.

A practical guide to time-resolved fluorescence microscopy and spectroscopy

Time-correlated single photon counting (TCSPC) coupled with confocal microscopy is a versatile biophysical tool that enables real-time monitoring of biomolecular dynamics across many timescales. With TCSPC, Fluorescence correlation spectroscopy (FCS) and pulsed interleaved excitation-Förster resonance energy transfer (PIE-FRET) are collected simultaneously on diffusing molecules to extract diffusion characteristics and proximity information. This article is a guide to calibrating FCS and PIE-FRET measurements with several biological samples including liposomes, streptavidin-coated quantum dots, proteins, and nucleic acids for reliable determination of diffusion coefficients and FRET efficiency. The FRET efficiency results are also compared to surface-attached single molecules using fluorescence lifetime imaging microscopy (FLIM-FRET). Combining the methods is a powerful approach to revealing mechanistic details of biological processes and pathways.

Three species multiplexing of fluorescent dyes and gold nanoclusters recovered with fluorescence lifetime correlation spectroscopy

Biosensor applications often require the simultaneous detection of multiple analytes, with a clear need to go beyond the traditional multiplexing relying on distinct fluorescent dyes across the visible spectrum. Fluorescence lifetime correlation spectroscopy (FLCS) is a powerful approach taking advantage of the fluorescence lifetime information to separate the contributions of different fluorescent species with overlapping emission spectra. However, so far FLCS detection has been demonstrated only on binary mixtures of two fluorescent dyes, limiting its multiplexing capabilities. Here, we report the first quantitative FLCS measurements within a ternary mixture composed of three different fluorescent emitters with near-identical emission spectra. Two organic fluorescent dyes, Alexa Fluor 647 and CF640R, are combined with water-soluble Au18(SG)14 gold nanoclusters. Our experimental data establish that FLCS allows to accurately determine individual concentrations within intricate ternary mixtures. Another major aspect of interest concerns the assessment of the suitability of gold nanoclusters for FLCS multiplexing applications. With their microsecond lifetime and stable emission characteristics, gold nanoclusters add a valuable new aspect to the array of FLCS probes. Extending FLCS multiplexing beyond binary mixtures paves the way for further progress in the simultaneous highly parallel biosensing of multiple species.

Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches

In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring-DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms.

Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity

Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.

CRDBP Protein Phase Separation and Its Recruitment to β-Catenin Protein in a Single Living Cell

The Coding Region Determinant-Binding Protein (CRDBP) is a carcinoembryonic protein, and it is overexpressed in various cancer cells in the form of granules. We speculated the formation of CRDBP granules possibly through liquid-liquid phase separation (LLPS) processes due to the existence of intrinsically disordered regions (IDRs) in CRDBP. So far, we did not know whether or how phase separation processes of CRDBP occur in single living cells due to the lack of in vivo methods for studying intracellular protein phase separation. Therefore, to develop an in situ method for studying protein phase separation in living cells is a very urgent task. In this work, we proposed an efficient method for studying phase separation behavior of CRDBP in a single living cell by combining in situ fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) with a fluorescence protein fusion technique. We first predicted and confirmed that CRDBP has phase separation in solution by conventional fluorescence imaging and FCS methods. And then, we in situ studied the phase separation behaviors of CRDBP in living cells and observed three states of CRDBP phase separation such as monomer state, cluster state, and granule state. We studied the effects of CRDBP truncated forms and its inhibitor on the CRDBP phase separation. Furthermore, we discovered the recruitment of CRDBP to β-catenin protein in living cells and investigated the effects of CRDBP structures and inhibitor on CRDBP recruitment behavior. This finding may help us to further understand the mechanism of CRDBP protein for regulating Wnt signaling pathway. Additionally, our results documented that FCS/FCCS is an efficient and alternative method for studying protein phase separation in situ in living cells.

Transition between Random and Periodic Electron Currents on a DNA Chain

By resorting to a model inspired to the standard Davydov and Holstein-Fröhlich models, in the present paper we study the motion of an electron along a chain of heavy particles modeling a sequence of nucleotides proper to a DNA fragment. Starting with a model Hamiltonian written in second quantization, we use the Time Dependent Variational Principle to work out the dynamical equations of the system. It can be found that, under the action of an external source of energy transferred to the electron, and according to the excitation site, the electron current can display either a broad frequency spectrum or a sharply peaked frequency spectrum. This sequence-dependent charge transfer phenomenology is suggestive of a potentially rich variety of electrodynamic interactions of DNA molecules under the action of electron excitation. This could imply the activation of interactions between DNA and transcription factors, or between DNA and external electromagnetic fields.

Quantification of the effect of site-specific histone acetylation on chromatin transcription rate

Eukaryotic transcription is epigenetically regulated by chromatin structure and post-translational modifications (PTMs). For example, lysine acetylation in histone H4 is correlated with activation of RNA polymerase I-, II- and III-driven transcription from chromatin templates, which requires prior chromatin remodeling. However, quantitative understanding of the contribution of particular PTM states to the sequential steps of eukaryotic transcription has been hampered partially because reconstitution of a chromatin template with designed PTMs is difficult. In this study, we reconstituted a di-nucleosome with site-specifically acetylated or unmodified histone H4, which contained two copies of the Xenopus somatic 5S rRNA gene with addition of a unique sequence detectable by hybridization-assisted fluorescence correlation spectroscopy. Using a Xenopus oocyte nuclear extract, we analyzed the time course of accumulation of nascent 5S rRNA-derived transcripts generated on chromatin templates in vitro. Our mathematically described kinetic model and fitting analysis revealed that tetra-acetylation of histone H4 at K5/K8/K12/K16 increases the rate of transcriptionally competent chromatin formation ∼3-fold in comparison with the absence of acetylation. We provide a kinetic model for quantitative evaluation of the contribution of epigenetic modifications to chromatin transcription.

A single-molecule counting approach for convenient and ultrasensitive measurement of restriction digest efficiencies

Restriction endonucleases play a central role in the microbial immune system against viruses and are widely used in DNA specific cleavage, which is called restriction digestion, for genetic engineering. Herein, we applied digital cell-free protein synthesis as an easy-to-use orthogonal readout means to assess the restriction digest efficiency, a new application of digital bioassays. The digital counting principle enabled an unprecedentedly sensitive trace analysis of undigested DNA at the single-molecule level in a PCR-free manner. Our approach can quantify the template DNA of much lower concentrations that cannot be detected by ensemble-based methods such as gold-standard DNA electrophoresis techniques. The sensitive and quantitative measurements revealed a considerable variation in the digest efficiency among restriction endonucleases, from less than 70% to more than 99%. Intriguingly, none of them showed truly complete digestion within reasonably long periods of reaction time. The same rationale was extended to a multiplexed assay and applicable to any DNA-degrading or genome-editing enzymes. The enzyme kinetic parameters and the flanking sequence-dependent digest efficiency can also be interrogated with the proposed digital counting method. The absolute number of residual intact DNA molecules per microliter was concluded to be at least 10⁷, drawing attention to the residual issue of genetic materials associated with the interpretation of nucleases’ behaviors and functions in daily genetic engineering experiments.

Dimerization of Human Drebrin-like Protein Governs Its Biological Activity

Drebrin-like protein (DBNL) is a multidomain F-actin-binding protein, which also interacts with other molecules within different intracellular pathways. Here, we present quantitative measurements on the size and conformation of human DBNL. Using dual-focus fluorescence correlation spectroscopy, we determined the hydrodynamic radius of the DBNL monomer. Native gel electrophoresis and dual-color fluorescence cross-correlation spectroscopy show that both endogenous DBNL and recombinant DBNL exist as dimers under physiological conditions. We demonstrate that C-terminal truncations of DBNL downstream of the coiled-coil domain result in its oligomerization at nanomolar concentrations. In contrast, the ADF-H domain alone is a monomer, which displays a concentration-dependent self-assembly. In vivo FLIM-FRET imaging shows that the presence of only actin-binding domains is not sufficient for DBNL to localize properly at the actin filament inside the cell. In summary, our work provides detailed insight into the structure-function relationship of human drebrin-like protein.

Laboratory Exercise To Measure Restriction Enzyme Kinetics

Enzymes are ubiquitous in the fields of biology and microbiology, catalyzing critical reactions and enabling a broad range of biotechnological applications. Despite the important role that enzyme catalysis plays in biological processes, undergraduate students often struggle to understand enzyme kinetics in the classroom. In an attempt to improve students’ understanding of the topic, we present a relatively short and inexpensive laboratory activity designed to give students hands-on experience with generating and manipulating enzyme kinetic data. Students perform restriction digests of DNA at various time points, visualize the reaction products on an agarose gel, and quantify their data in order to construct Lineweaver-Burk plots which compare the effects of a restriction enzyme and its engineered version. The activity may be completed in a single two-hour lab session and, unlike other enzyme assays designed for laboratory courses, does not require a microplate reader to complete. The activity allows students to see connections between a visual data set and quantitative kinetic data, in order to solidify their understanding of enzyme kinetics. Students also learn the skills of gel electrophoresis and image quantification using ImageJ software. This lab activity is ideal for undergraduate laboratory courses which address enzyme kinetics and DNA technology.

Deep Tumor Penetration of Drug-Loaded Nanoparticles by Click Reaction-Assisted Immune Cell Targeting Strategy

Nanoparticles have been extensively used to deliver therapeutic drugs to tumor tissues through the extravasation of a leaky vessel via enhanced permeation and retention effect (EPR, passive targeting) or targeted interaction of tumor-specific ligands (active targeting). However, the therapeutic efficacy of drug-loaded nanoparticles is hampered by its heterogeneous distribution owing to limited penetration in tumor tissue. Inspired by the fact that cancer cells can recruit inflammatory immune cells to support their survival, we developed a click reaction-assisted immune cell targeting (CRAIT) strategy to deliver drug-loaded nanoparticles deep into the avascular regions of the tumor. Immune cell-targeting CD11b antibodies are modified with trans-cyclooctene to enable bioorthogonal click chemistry with mesoporous silica nanoparticles functionalized with tetrazines (MSNs-Tz). Sequential injection of modified antibodies and MSNs-Tz at intervals of 24 h results in targeted conjugation of the nanoparticles onto CD11b⁺ myeloid cells, which serve as active vectors into tumor interiors. We show that the CRAIT strategy allows the deep tumor penetration of drug-loaded nanoparticles, resulting in enhanced therapeutic efficacy in an orthotopic 4T1 breast tumor model. The CRAIT strategy does not require ex vivo manipulation of cells and can be applied to various types of cells and nanovehicles.

Fluorescent determination of micro-quantities of RNA using Hoechst 33258 and binase

Detection of small amounts of RNA in various biological samples is an important applied task. Using fluorescence spectroscopy, the hydrolysis by binase of rRNA and tRNA, stained with Hoechst 33258, in aqueous solutions was investigated. The binding constant of Hoechst with rRNA is 10⁶ M^-1. Specific hydrolysis of rRNA and tRNA by binase during 1-2 min at room temperature leads to a multiple decrease in fluorescence of the dye. This rapid hydrolysis goes to large polynucleotide fragments, but not to short oligonucleotides. The binding constant of binase with rRNA is about of 2.5 × 10⁶ M^-1, which is several dozen times higher than with oligonucleotides. The susceptibility to binase attack depends on the secondary structure of RNA, determined by non-canonical ribonucleotides. The developed highly sensitive fluorescent method can be used for the rapid selective detection of trace amounts of rRNA or tRNA, as well as for studying the physicochemical properties of these RNAs. Using the proposed method, one can confidently detect RNA from 10^-7 M.

Non-Steady State Analysis of Enzyme Kinetics in Real Time Elucidates Substrate Association and Dissociation Rates: Demonstration with Analysis of Firefly Luciferase Mutants

Firefly luciferase has been widely used in biotechnology and biophotonics due to photon emission during enzymatic activity. In the past, the effect of amino acid substitutions (mutants) on the enzymatic activity of firefly luciferase has been characterized by the Michaelis constant, KM. The KM is obtained by plotting the maximum relative luminescence units (RLU) detected for several concentrations of the substrate (luciferin or luciferyl-adenylate). The maximum RLU is used because the assay begins to violate the quasi-steady state approximation when RLU decays as a function of time. However, mutations also affect the time to reach and decay from the maximum RLU. These effects are not captured when calculating the KM. To understand changes in the RLU kinetics of firefly luciferase mutants, we used a Michaelis-Menten model with the non-steady state approximation. In this model, we do not assume that the amount of enzyme-substrate complex is at equilibrium throughout the course of the experiment. We found that one of the two mutants analyzed in this study decreases not only the dissociation rate ( koff) but also the association rate ( kon) of luciferyl-adenylate, suggesting the narrowing of the structural pocket containing the catalytic amino acids. Furthermore, comparative analysis of the nearly complete oxidation of luciferyl-adenylate with wild-type and mutant firefly luciferase reveals that the total amount of photons emitted with the mutant is 50-fold larger than that with the wild type, on average. These two results together indicate that the slow supply of luciferyl-adenylate to the enzyme increases the total number of photons emitted from the substrate, luciferyl-adenylate. Analysis with the non-steady state approximation model is generally applicable when enzymatic production kinetics are monitored in real time.

Determination of Micro-Quantities of DNA Using DNAse and Fluorescence of Hoechst 33258 and Light-Scattering

The DNA hydrolysis by deoxyribonuclease (DNAse I) in aqueous solution was studied, using fluorescence spectroscopy and high-sensitive light-scattering detection. Specific hydrolysis of high-polymer DNA or fragmented DNA by the enzyme led to a strong decrease in the fluorescence of the Hoechst dye. The hydrolysis of mitochondrial DNA was accompanied by a decrease in the fluorescence of the dye only in 1.6 times. Hydrolysis within minutes and even hours led to appearance of large polynucleotide fragments, but not to short oligonucleotides, that was confirmed using polarized fluorescence and highly sensitive measurement of light-scattering. At the moment of the time of formation of a complex between DNA and DNAse I, a strong light-scattering occurred, which then dropped sharply during hydrolysis of high-molecular DNA, and slowly decreased during hydrolysis of fragmented DNA. The proposed methods can be applied for selective detection of trace amounts of various types of DNA, as well as for studying their physic-chemical properties.

pH-Sensitive Polymers as Dynamic Mediators of Barriers to Nucleic Acid Delivery

The nonviral delivery of exogenous nucleic acids (NA) into cells for therapeutic purposes has rapidly matured into tangible clinical impact. Synthetic polymers are particularly attractive vectors for NA delivery due to their relatively inexpensive production compared to viral alternatives and their highly tailorable chemical properties; indeed, many preclinical investigations have revealed the primary biological barriers to nonviral NA delivery by systematically varying polymeric material properties. This review focuses on applications of pH-sensitive chemistries that enable polymeric vectors to serially address multiple biological barriers to NA delivery. In particular, we focus on recent innovations with in vivo evaluation that dynamically enable colloidal stability, cellular uptake, endosomal escape, and nucleic acid release. We conclude with a summary of successes to date and projected areas for impactful future research.

Kinetics in the real world: linking molecules, processes, and systems

Unravelling elementary steps, reaction pathways, and kinetic mechanisms is key to understanding the behaviour of many real-world chemical systems that span from the troposphere or even interstellar media to engines and process reactors. Recent work in chemical kinetics provides detailed information on the reactive changes occurring in chemical systems, often on the atomic or molecular scale. The optimisation of practical processes, for instance in combustion, catalysis, battery technology, polymerisation, and nanoparticle production, can profit from a sound knowledge of the underlying fundamental chemical kinetics. Reaction mechanisms can combine information gained from theory and experiments to enable the predictive simulation and optimisation of the crucial process variables and influences on the system's behaviour that may be exploited for both monitoring and control. Chemical kinetics, as one of the pillars of Physical Chemistry, thus contributes importantly to understanding and describing natural environments and technical processes and is becoming increasingly relevant for interactions in and with the real world.

There and back again: from the origin of life to single molecules

What is life? There is hardly a more fundamental question raised by aspiring researchers, and one less prone to ever be answered in a scientifically satisfying way. In the long, productive and highly influential period of research following his Nobel-recognised work on relaxation kinetics, Manfred Eigen made seminal contributions towards a quantifiable definition of life, with a strong focus on its evolutionary character. In the last years of his time as an active researcher, however, he devoted himself to another, purely experimental topic: the detection and analysis of single biomolecules in aqueous solution. In this short review, I will give an overview of the groundbreaking contributions to the field of single molecule research made by Eigen and coworkers, and show that both, in its intrinsic motivation, and in its consequences, single molecule research strongly relates to the question of the physical-chemical essence of life. In fact, research on living systems with single molecule sensitivity will always refer the researcher to the question of the simplest possible representation, and thus the origin, of any biological phenomenon.

Quantifying membrane protein oligomerization with fluorescence cross-correlation spectroscopy

Fluorescence cross-correlation spectroscopy (FCCS) is an advanced fluorescence technique that can quantify protein-protein interactions in vivo. Due to the dynamic, heterogeneous nature of the membrane, special considerations must be made to interpret FCCS data accurately. In this study, we describe a method to quantify the oligomerization of membrane proteins tagged with two commonly used fluorescent probes, mCherry (mCH) and enhanced green (eGFP) fluorescent proteins. A mathematical model is described that relates the relative cross-correlation value (f_c) to the degree of oligomerization. This treatment accounts for mismatch in the confocal volumes, combinatoric effects of using two fluorescent probes, and the presence of non-fluorescent probes. Using this model, we calculate a ladder of f_c values which can be used to determine the oligomer state of membrane proteins from live-cell experimental data. Additionally, a probabilistic mathematical simulation is described to resolve the affinity of different dimeric and oligomeric protein controls.

Simultaneous enzymatic activity modulation and rapid determination of enzyme kinetics by highly crystalline graphite dots

The research field in enzyme-based biotechnology urgently requires the discovery of new materials and methods with high-performance. Here we report that highly crystalline graphite dots (GDs) can modulate enzyme activities, and simultaneously allow for real-time measurements on enzyme kinetics in combination with mass spectrometry (MS). A well-defined modulation of lipolytic activities from inhibition to enhancement can be realized by selectively coupling lipase enzymes with GDs containing specific functional groups on the surface. As a unique feature of our approach, GDs in the enzyme reaction can simultaneously serve as a versatile matrix for rapid and sensitive detection of the residual enzyme substrate, the intermediate or final product of lipolytic digestion using MS technology. Therefore, enzyme kinetic data can be collected in a real-time, high-throughput format. This work provides a new platform for enzymological research in hybrid bio-catalytic processes with advanced nanotechnology.

Dopamine Receptor Signaling in MIN6 β-Cells Revealed by Fluorescence Fluctuation Spectroscopy

Insulin secretion defects are central to the development of type II diabetes mellitus. Glucose stimulation of insulin secretion has been extensively studied, but its regulation by other stimuli such as incretins and neurotransmitters is not as well understood. We investigated the mechanisms underlying the inhibition of insulin secretion by dopamine, which is synthesized in pancreatic β-cells from circulating L-dopa. Previous research has shown that this inhibition is mediated primarily by activation of the dopamine receptor D3 subtype (DRD3), even though both DRD2 and DRD3 are expressed in β-cells. To understand this dichotomy, we investigated the dynamic interactions between the dopamine receptor subtypes and their G-proteins using two-color fluorescence fluctuation spectroscopy (FFS) of mouse MIN6 β-cells. We show that proper membrane localization of exogenous G-proteins depends on both the Gβ and Gγ subunits being overexpressed in the cell. Triple transfections of the dopamine receptor subtype and Gβ and Gγ subunits, each labeled with a different-colored fluorescent protein (FP), yielded plasma membrane expression of all three FPs and permitted an FFS evaluation of interactions between the dopamine receptors and the Gβγ complex. Upon dopamine stimulation, we measured a significant decrease in interactions between DRD3 and the Gβγ complex, which is consistent with receptor activation. In contrast, dopamine stimulation did not cause significant changes in the interactions between DRD2 and the Gβγ complex. These results demonstrate that two-color FFS is a powerful tool for measuring dynamic protein interactions in living cells, and show that preferential DRD3 signaling in β-cells occurs at the level of G-protein release.

Fluorescence and Scattering Light Cross Correlation Spectroscopy and Its Applications in Homogeneous Immunoassay

In this work, we propose fluorescence and scattering light cross-correlation spectroscopy (FSCCS) based on laser confocal configuration using silver nanoparticle (SNPs) and Alexa Fluor 488 (Alexa) as probe pairs. FSCCS is a single molecule (particle) method, and its principle is similar to that of fluorescence cross-correlation spectroscopy (FCCS). We established the setup of FSCCS using single wavelength laser and developed an immunoassay model of FSCCS. The reliability and adaptability of FSCCS method were evaluated by homogeneous sandwich immunoassay mode. In the study, liver cancer biomarker alpha-fetoprotein (AFP) was used as an assay model, two different antibodies were labeled with SNPs and fluorophore Alexa Fluor 488, respectively. In the optimal conditions, the linear range of AFP covers 5 pM to 580 pM and the detection limit is 3.1 pM. This method was successfully applied for direct determination of AFP levels in human serum samples, and the obtained results were in good agreement with data obtained via ELISAs. The advantage of this method lies in its simplicity, attractive SNPs probes, high sensitivity and selectivity and high efficiency. We believe that FSCCS method exhibits promising potential applications in homogeneous bioassays and study on the molecular interaction and nanoparticle-molecule interaction.

Influence of bile salt on vitamin E derived vesicles involving a surface active ionic liquid and conventional cationic micelle

This study has been actually performed with the aim to develop vitamin E derived vesicles individually from a surface active ionic liquid (1-Hexadecyl-3-Methylimidazolium chloride ([C₁₆mim]Cl)) and a common cationic amphiphile (benzyldimethylhexadecylammonium chloride (BHDC)) and also to investigate their consequent breakdown in presence of bile salt molecule. From this study, it is revealed that the rotational motion of coumarin 153 (C153) molecule is hindered as the vitamin E content is increased in the individual micellar solution of [C₁₆mim]Cl and BHDC. The extent of enhancement in rotational relaxation time is more pronounced in case of [C₁₆mim]Cl-vitamin E solutions than in the BHDC-vitamin E vesicular aggregates which confirms the greater rigidity of the former vesicular system than the later one. Moreover, the effect of bile salt in the vitamin E forming vesicular assemblies have also been unravelled. It is found that the large area occupancy by the steroidal backbone of the bile salt plays a crucial role towards the enlargement of the average surfactant head group area. This results in disintegration of the vesicles composed of vitamin E and consequently, vesicles are transformed into mixed micellar aggregates. From the anisotropy measurement it is found that the rotational motion of C153 is more hindered in the [C₁₆mim]Cl/BHDC-NaCh mixed micelles compared to that inside the individual vesicles. The fluorescence correlation spectroscopic (FCS) study also confirms that the mixed micelles have a more compact structure than that of the [C₁₆mim]Cl-vitamin E and BHDC-vitamin E vesicles. Altogether, the micelle to vesicle transition involving any vitamin and their disruption by bile salt would be an interesting investigation both from the view point of basic colloidal chemistry and towards the generation of new drug delivery vehicle due to their unique microenvironment. Therefore, in future, these systems can be utilised as vehicle for the transport and as well as delivery of drugs and as probable reactor in nanomaterial synthesis.

Kinetic modelling: an integrated approach to analyze enzyme activity assays

BACKGROUND

In general, enzyme activity is estimated from spectrophotometric data, by taking the slope of the linear part of the progress curve describing the rate of change in the substrate or product monitored. As long as the substrate concentrations are sufficiently high to saturate the enzyme and, the velocity of the catalyzed reaction is directly proportional to the enzyme concentration. Under these premises, this velocity can be taken as a measure of the amount of active enzyme present. Estimation of the enzyme activity through linear regression of the data should only be applied when linearity is true, which is often not the case or has not been checked.

RESULTS

In this paper, we propose a more elaborate method, based on a kinetic modelling approach, to estimate the in vitro specific enzyme activity from spectrophotometric assay data. As a case study, kinetic models were developed to estimate the activity of the enzymes pyruvate decarboxylase and alcohol dehydrogenase extracted from 'Jonagold' apple (Malus x domestica Borkh. cv. 'Jonagold'). The models are based on Michaelis-Menten and first order kinetics, which describe the reaction mechanism catalyzed by the enzymes.

CONCLUSIONS

In contrast to the linear regression approach, the models can be used to estimate the enzyme activity regardless of whether linearity is achieved since they integrally take into account the complete progress curve. The use of kinetic models to estimate the enzyme activity can be applied to all other enzymes as long as the underlying reaction mechanism is known. The kinetic models can also be used as a tool to optimize the enzyme assays by systematically studying the effect of the various design parameters.

Thin-Film Transistor-Based Biosensors for Determining Stoichiometry of Biochemical Reactions

The enzyme kinetic in a biochemical reaction is critical to scientific research and drug discovery but can hardly be determined experimentally from enzyme assays. In this work, a charge-current transducer (a transistor) is proposed to evaluate the status of biochemical reaction by monitoring the electrical charge changes. Using the malate-aspartate shuttle as an example, a thin-film transistor (TFT)-based biosensor with an extended gold pad is demonstrated to detect the biochemical reaction between NADH and NAD⁺. The drain current change indicates the status of chemical equilibrium and stoichiometry.

Optimized Detection of Plasmodium falciparum Topoisomerase I Enzyme Activity in a Complex Biological Sample by the Use of Molecular Beacons

The so-called Rolling Circle Amplification allows for amplification of circular DNA structures in a manner that can be detected in real-time using nucleotide-based molecular beacons that unfold upon recognition of the DNA product, which is being produced during the amplification process. The unfolding of the molecular beacons results in a fluorescence increase as the Rolling Circle Amplification proceeds. This can be measured in a fluorometer. In the current study, we have investigated the possibility of using two different molecular beacons to detect two distinct Rolling Circle Amplification reactions proceeding simultaneously and in the same reaction tube by measurement of fluorescence over time. We demonstrate the application of this fluorometric readout method, for automated and specific detection of the activity of the type IB topoisomerase from the malaria parasite Plasmodium falciparum in the presence of human cell extract containing the related topoisomerase I from humans. The obtained results point towards a future use of the presented assay setup for malaria diagnostics or drug screening purposes. In longer terms the method may be applied more broadly for real-time sensing of various Rolling Circle Amplification reactions.

5-Methyl Salicylic Acid-Induced Thermo Responsive Reversible Transition in Surface Active Ionic Liquid Assemblies: A Spectroscopic Approach

This article describes the formation of stable unilamellar vesicles involving surface active ionic liquid (SAIL), 1-hexadecyl-3-methylimidazolium chloride (C16mimCl), and 5-methyl salicylic acid (5mS). Turbidity, dynamic light scattering (DLS), transmission electron microscopy (TEM), and viscosity measurements suggest that C16mimCl containing micellar aggregates are transformed to elongated micelle and finally into vesicular aggregates with the addition of 5mS. Besides, we have also investigated the photophysical aspects of a hydrophobic (coumarin 153, C153) and a hydrophilic molecule (rhodamine 6G (R6G) perchlorate) during 5mS-induced micelle to vesicle transition. The rotational motion of C153 becomes slower, whereas faster motion is observed for R6G during micelle to vesicle transition. Moreover, the fluorescence correlation spectroscopy (FCS) measurements suggest that the translational diffusion of hydrophobic probe becomes slower in C16mimCl-5mS aggregates in comparison to C16mimCl micelle. However, a reverse trend in translational diffusion motion of hydrophilic molecule has been observed in C16mimCl-5mS aggregates. Moreover, we have also found that the C16mimCl-5mS containing vesicles are transformed into micelles upon enhanced temperature, and it is further confirmed by turbidity, DLS measurements that this transition is a reversible one. Finally, temperature-induced rotational motion of C153 and R6G has been monitored in C16mimCl-5mS aggregates to get a complete scenario regarding the temperature-induced vesicle to micelle transition.

New Insight into Metal Ion-Driven Catalysis of Nucleic Acids by Influenza PA-Nter

PA subunit of influenza RNA-dependent RNA polymerase deserves constantly increasing attention due to its essential role in influenza life cycle. N-terminal domain of PA (PA-Nter) harbors endonuclease activity, which is indispensable in viral transcription and replication. Interestingly, existing literature reports on in vitro ion preferences of the enzyme are contradictory. Some show PA-Nter activity exclusively with Mn²⁺, whereas others report Mg²⁺ as a natural cofactor. To clarify it, we performed a series of experiments with varied ion concentrations and substrate type. We observed cleavage in the presence of both ions, with a slight preference for manganese, however PA-Nter activity highly depended on the amount of residual, co-purified ions. Furthermore, to quantify cleavage reaction rate, we applied fluorescence cross-correlation spectroscopy (FCCS), providing highly sensitive and real-time monitoring of single molecules. Using nanomolar ssDNA in the regime of enzyme excess, we estimated the maximum reaction rate at 0.81± 0.38 and 1.38± 0.34 nM/min for Mg²⁺ and Mn²⁺, respectively. However, our calculations of PA-Nter ion occupancy, based on thermodynamic data, suggest Mg²⁺ to be a canonical metal in PA-Nter processing of RNA in vivo. Presented studies constitute a step toward better understanding of PA-Nter ion-dependent activity, which will possibly contribute to new successful inhibitor design in the future.

Dense transcript profiling in single cells by image correlation decoding

Sequential barcoded fluorescent in situ hybridization (seqFISH) allows large numbers of molecular species to be accurately detected in single cells, but multiplexing is limited by the density of barcoded objects. We present correlation FISH (corrFISH), a method to resolve dense temporal barcodes in sequential hybridization experiments. Using corrFISH, we quantified highly expressed ribosomal protein genes in single cultured cells and mouse thymus sections, revealing cell-type-specific gene expression.

Scanning fluorescence correlation spectroscopy as a versatile tool to measure static and dynamic properties of soft matter systems

We present the formalism and experimental implementation of scanning fluorescence correlation spectroscopy (SFCS) for the measurements of soft matter system structure and dynamics. We relate the SFCS function Fourier transform to the system intermediate scattering function and demonstrate how SFCS can be combined with specific labelling to measure the desired statistical and kinetic features of the system. Using DNA as a model polymer, we demonstrate the application of SFCS to measure (1) the static structure factor of the system, (2) polymer end-to-end distance distribution, and (3) polymer segmental dynamics in dilute and in dense solutions. The measured DNA end-to-end distance distributions are close to Gaussian. Implementing SFCS we obtain reliable data on segmental mean-square displacement kinetics in dense solutions, where the static FCS approach fails because of dye photobleaching. For moderate concentrations in the semidilute regime (at ∼7 overlap concentrations) segmental dynamics exhibit only weak entanglements. Both of these experimental findings are consistent with theoretical predictions of the weakness of excluded interactions in semiflexible polymers.

Real-time investigation of human topoisomerase I reaction kinetics using an optical sensor: a fast method for drug screening and determination of active enzyme concentrations

Human DNA topoisomerase I (hTopI) is a nuclear enzyme that catalyzes relaxation of super helical tension that arises in the genome during essential DNA metabolic processes. This is accomplished through a common reaction mechanism shared among the type IB topoisomerase enzymes, including eukaryotic and poxvirus topoisomerase I. The mechanism of hTopI is specifically targeted in cancer treatment using camptothecin derivatives. These drugs convert the hTopI activity into a cellular poison, and hence the cytotoxic effects of camptothecin derivatives correlate with the hTopI activity. Therefore, fast and reliable techniques for high throughput measurements of hTopI activity are of high clinical interest. Here we demonstrate potential applications of a fluorophore-quencher based DNA sensor designed for measurement of hTopI cleavage-ligation activities, which are the catalytic steps affected by camptothecin. The kinetic analysis of the hTopI reaction with the DNA sensor exhibits a characteristic burst profile. This is the result of a two-step ping-pong reaction mechanism, where a fast first reaction, the one creating the signal, is followed by a slower second reaction necessary for completion of the catalytic cycle. Hence, the burst profile holds information about two reactions in the enzymatic mechanism. Moreover, it allows the amount of active enzyme in the reaction to be determined. The presented results pave the way for future high throughput drug screening and the potential of measuring active hTopI concentrations in clinical samples for individualized treatment.

Fluorescence correlation spectroscopy: principles and applications

Fluorescence correlation spectroscopy (FCS) is used to study the movements and the interactions of biomolecules at extremely dilute concentrations, yielding results with good spatial and temporal resolutions. Using a number of technical developments, FCS has become a versatile technique that can be used to study a variety of sample types and can be advantageously combined with other methods. Unlike other fluorescence-based techniques, the analysis of FCS data is not based on the average intensity of the fluorescence emission but examines the minute intensity fluctuations caused by spontaneous deviations from the mean at thermal equilibrium. These fluctuations can result from variations in local concentrations owing to molecular mobility or from characteristic intermolecular or intramolecular reactions of fluorescently labeled biomolecules present at low concentrations. Here, we provide a basic introduction to FCS, including its technical development and theoretical basis, experimental setup of an FCS system, adjustment of a setup, data acquisition, and analysis of FCS measurements. Finally, the application of FCS to the study of lipid bilayer membranes and to living cells is discussed.

Deep brain optical measurements of cell type-specific neural activity in behaving mice

Recent advances in genetically encoded fluorescent sensors enable the monitoring of cellular events from genetically defined groups of neurons in vivo. In this protocol, we describe how to use a time-correlated single-photon counting (TCSPC)-based fiber optics system to measure the intensity, emission spectra and lifetime of fluorescent biosensors expressed in deep brain structures in freely moving mice. When combined with Cre-dependent selective expression of genetically encoded Ca(2+) indicators (GECIs), this system can be used to measure the average neural activity from a specific population of cells in mice performing complex behavioral tasks. As an example, we used viral expression of GCaMPs in striatal projection neurons (SPNs) and recorded the fluorescence changes associated with calcium spikes from mice performing a lever-pressing operant task. The whole procedure, consisting of virus injection, behavior training and optical recording, takes 3-4 weeks to complete. With minor adaptations, this protocol can also be applied to recording cellular events from other cell types in deep brain regions, such as dopaminergic neurons in the ventral tegmental area. The simultaneously recorded fluorescence signals and behavior events can be used to explore the relationship between the neural activity of specific brain circuits and behavior.

Effect of various intercalators on the fenton-type oxidative cleavage of double-stranded DNA

The intensity of the linear dichroism (LD) in the absorption region of DNA (about 260 nm) decreased with time in the presence of [Fe(EDTA)](2+) (EDTA = ethylenediaminetetraacetic acid), H2O2, and ascorbate. The decrease in the LD signal indicated either an increase in flexibility, a shortening of the DNA stem, or both, owing to oxidative cleavage, and was best described by the difference between the two single-exponential-decay curves, thereby suggesting the involvement of two sequential first-order reactions. The fast reaction was assigned to cleavage of one of two DNA strands, which increased the flexibility of the DNA. The slow reaction corresponded to cleavage at or near the first cleavage site, thereby shortening the DNA stem. The presence of an intercalator, including ethidium, propidium, 9-aminoacridine, and proflavine, inhibited the first step of the cleavage reaction. One of the possible reasons for the observed inhibition might be a change in the DNA conformation near the intercalation site. Intercalation caused an unwinding and elongation of the DNA and resulted in changes in the location of the H atoms of the sugar moiety, which is known to be the main site at which hydroxyl radicals react.

Quantifying intracellular protein binding thermodynamics during mechanotransduction based on FRET spectroscopy

Mechanical force modulates myriad cellular functions including migration, alignment, proliferation, and gene transcription. Mechanotransduction, the transmission of mechanical forces and its translation into biochemical signals, may be mediated by force induced protein conformation changes, subsequently modulating protein signaling. For the paxillin and focal adhesion kinase interaction, we demonstrate that force-induced changes in protein complex conformation, dissociation constant, and binding Gibbs free energy can be quantified by lifetime-resolved fluorescence energy transfer microscopy combined with intensity imaging calibrated by fluorescence correlation spectroscopy. Comparison with in vitro data shows that this interaction is allosteric in vivo. Further, spatially resolved imaging and inhibitor assays show that this protein interaction and its mechano-sensitivity are equal in the cytosol and in the focal adhesions complexes indicating that the mechano-sensitivity of this interaction must be mediated by soluble factors but not based on protein tyrosine phosphorylation.

Dual-color fluorescence cross-correlation spectroscopy on a single plane illumination microscope (SPIM-FCCS)

Single plane illumination microscopy based fluorescence correlation spectroscopy (SPIM-FCS) is a new method for imaging FCS in 3D samples, providing diffusion coefficients, flow velocities and concentrations in an imaging mode. Here we extend this technique to two-color fluorescence cross-correlation spectroscopy (SPIM-FCCS), which allows to measure molecular interactions in an imaging mode. We present a theoretical framework for SPIM-FCCS fitting models, which is subsequently used to evaluate several test measurements of in-vitro (labeled microspheres, several DNAs and small unilamellar vesicles) and in-vivo samples (dimeric and monomeric dual-color fluorescent proteins, as well as membrane bound proteins). Our method yields the same quantitative results as the well-established confocal FCCS, but in addition provides unmatched statistics and true imaging capabilities.