Bleaching-resistant,Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding

Photobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions. Using two orthogonal sequences, we show that our method is adaptable to Förster Resonance Energy Transfer (FRET) and that can be used to study the conformational dynamics of dynamic structures, such as DNA Holliday junctions, for extended periods. By adjusting the temporal resolution and observation span, our approach enables capturing the conformational dynamics of proteins and nucleic acids over a wide range of timescales.     

A comparative physicochemical study of unsymmetrical indium phthalocyanines in the presence of magnetic nanoparticles or quantum dots

Asymmetric indium phthalocyanine (3, containing an NH₂ group) was conjugated (via an amide bond) to magnetic nanoparticle (MNP) functionalized with carboxylic acid or glutathione-capped CdTe/ZnSe/ZnO quantum dots to form 3-MNPs or 3-QDs. Techniques such as time-resolved fluorescence measurements, transmission electron microscopy, XPS, elemental analysis, FTIR, NMR (¹H, ¹³C, and cozy), electronic spectroscopy, as well as mass spectroscopy were employed to characterize 3 and its nanoconjugates. The phthalocyanine conjugated to quantum dot (3-QDs) possesses the lowest Ф_pd higher Ф_? and Ф_T as well as longer triplet lifetimes compares to 3-MNPs and free phthalocyanine.     

Multienzyme detection and in-situ monitoring of enzyme activity by bending CE using quantum dots-based polypeptide substrate

Multienzyme detection and monitoring enzyme activity in situ are significant for the disease to diagnose. This study aims to develop a quantum dots (QDs)-based nanoprobe Cyanine5-DDDLEVLFQFPGLVPRGSGGHHHHHH-QDs (Cy5-LEVLVP-QD), which is able to detect two enzymes inside a bent capillary using CE. Cy5-LEVLVP and QDs were allowed to bind with each other through metal affinity interaction and then injected the Cy5-LEVLVP-QD complex into a capillary with different bends, followed by related enzyme that can cleave the Cy5-LEVLVP peptide. The fluorescence of Cy5 was excited by QDs due to Förster resonance energy transfer. By monitoring the peaks produced by the original Cy5-LEVLVP-QD complex and a significant fluorescence change, sensitive analysis of two different enzymes was conducted. Therefore, the novel approach of using capillaries with semicircular bends could prove particularly useful for enzyme investigating in disease.     

Characterization of the Biological Activities of Human Luteinizing Hormone and Chorionic Gonadotropin by a Förster Resonance Energy Transfer-Based Biosensor Assay

A Förster resonance energy transfer (FRET)-based cyclic adenosine monophosphate (cAMP) biosensor was used to study the activation of the mutual receptor for human luteinizing hormone (hLH) and human chorionic gonadotropin (hCG) in living cells stably expressing the shared recombinant receptor for these hormones. This work demonstrates the applicability of a cAMP biosensor-based assay for the study of receptor-mediated signal transduction and the characterization of the biological activities of gonadotropins and their isoforms. The importance of this approach lies in the fact that only the active portion of the total hormone concentration elicits a measurable response. No significant differences in early receptor activation profiles were detected for either of the tested recombinant gonadotropins. However, the subsequent physiological regulations mediated by these hormones may be more complex. The ability to detect biologically active hormones at low concentrations forms the basis for the future quantification of human chorionic gonadotropin in embryo culture medium and the use of this information for unbiased embryo selection during in vitro fertilization. Herein, a novel method for describing the biological activities of gonadotropins in various samples and preparations is reported.     

Synthesis of Symmetrical Multichromophoric Bodipy Dyes and Their Facile Transformation into Energy Transfer Cassettes

Multichromophoric boron‐dipyrromethene (Bodipy) dyes synthesized on phenylene‐ethynylene platforms have been be converted to energy transfer cassettes in a one‐step chemical transformation. Excitation energy transfer processes in these highly symmetrical derivatives were studied in detail, including time‐resolved fluorescence spectroscopy techniques. Excitation spectra and the emission lifetimes suggest efficient energy transfer between the donor and acceptor chromophore. These novel energy transfer cassettes, while highlighting a short‐cut approach to similar energy transfer systems, could be useful as large pseudo‐Stokes shift multichromophoric dyes with potential applications in diverse applications.     

Liposomal FRET Assay Identifies Potent Drug-Like Inhibitors of the Ceramide Transport Protein (CERT)

Ceramide transfer protein (CERT) mediates non-vesicular transfer of ceramide from endoplasmic reticulum to Golgi apparatus and thus catalyzes the rate-limiting step of sphingomyelin biosynthesis. Usually, CERT ligands are evaluated in tedious binding assays or non-homogenous transfer assays using radiolabeled ceramides. Herein, a facile and sensitive assay for CERT, based on Förster resonance energy transfer (FRET), is presented. To this end, we mixed donor and acceptor vesicles, each containing a different fluorescent ceramide species. By CERT-mediated transfer of fluorescent ceramide, a FRET system was established, which allows readout in 96-well plate format, despite the high hydrophobicity of the components. Screening of a 2 000 compound library resulted in two new potent CERT inhibitors. One is approved for use in humans and one is approved for use in animals. Evaluation of cellular activity by quantitative mass spectrometry and confocal microscopy showed inhibition of ceramide trafficking and sphingomyelin biosynthesis.     

Synthesis and Spectroscopic Characterization of Fluorophore‐Labeled Oligospiroketal Rods

Fluorescence probes consisting of well‐established fluorophores in combination with rigid molecular rods based on spirane‐type structures were investigated with respect to their fluorescence properties under different solvent conditions. The attachment of the dyes was accomplished by 1,3‐dipolar cycloaddition between alkynes and azides (‘click’ reaction) and is a prime example for a novel class of sensor constructs. Especially, the attachment of two (different) fluorophores on opposite sides of the molecular rods paves the way to new sensor systems with less bulky (compared to the conventional DNA‐ or protein‐based concepts), nevertheless rigid spacer constructs, e.g., for FRET‐based sensing applications. A detailed photophysical characterization was performed in MeOH (and in basic H₂O/MeOH mixtures) for i) rod constructs containing carboxyfluorescein, ii) rod constructs containing carboxyrhodamine, iii) rod constructs containing both carboxyfluorescein and carboxyrhodamine, and iv) rod constructs containing both pyrene and perylene parts. For each dye (pair), two rod lengths with different numbers of spirane units were synthesized and investigated. The rod constructs were characterized in ensemble as well as single‐molecule fluorescence experiments with respect to i) specific rod? dye and ii) dye? dye interactions. In addition to MeOH and MeOH/NaOH, the rod constructs were also investigated in micellar systems, which were chosen as a simplified model for membranes.     

Synthesis of Site‐Specific Dye‐Labeled Polymer via Atom Transfer Radical Polymerization (ATRP) for Quantitative Characterization of the Well‐Defined Interchain Distance

Novel difunctional initiators that incorporate Förster/fluorescence resonance energy transfer (FRET) pairs are generated to carry out atom transfer radical polymerization of styrene, methyl methacrylate, and n‐butyl methacrylate monomers by an efficient manner. Based on the chemical structures of the initiators, the locations of the fluorophore moiety are dictated to be in the center of the chain with accurately quantified chain functionality (>90% labeling ratio). The site‐specific integration of FRET dyes into separate polymer chain centers allows for characterization of the well‐defined interchain distance quantitatively based on the response between these fluorescent probes. The reliability of this technique is verified in bulk state, which is in well agreement with the theoretical ones. This well‐defined FRET system is expected to be a promising candidate to provide a distinct physical image at a microscopic level regarding scaling chain dimension, chain interpenetration, and polymer compatibility.

     

Fluorescence resonance energy transfer (FRET) in chemistry and biology: Non-F?rster distance dependence of the FRET rate

Fluorescence resonance energy transfer (FRET) is a popular tool to study equilibrium and dynamical properties of polymers and biopolymers in condensed phases and is now widely used in conjunction with single molecule spectroscopy. In the data analysis, one usually employs the F?rster expression which predicts (l/R ⁶) distance dependence of the energy transfer rate. However, critical analysis shows that this e_xpression can be of rather limited validity in many cases. We demonstrate this by explicitly considering a donor-acceptor system, polyfluorene (PF₆)-tetraphenylporphyrin (TPP), where the size of both donor and acceptor is comparable to the distance separating them. In such cases, one may expect much weaker distance (as l/R ² or even weaker) dependence. We have also considered the case of energy transfer from a dye to a nanoparticle. Here we find l/R ⁴ distance dependence at large separations, completely different from F?rster. We also discuss recent application of FRET to study polymer conformational dynamics. Dedicated to Prof J Gopalakrishnan on his 62nd birthday.     

Chromatographic,Microscopic, and Spectroscopic Characterization of a Wooden Architectural Painting from the Summer Palace,Beijing, China

The wooden construction painting is a type of an ancient decorative art on Chinese ancient structures. Comprehensive reports concerning the composition of these materials are rather limited. Here multiple analytical methods were applied to systematically explore the morphology and materials. Several paintings were characterized using a morphological microscope. Scanning electron microscopy–energy dispersive spectrometry (SEM-EDS), X-ray fluorescence (XRF), and X-ray diffraction (XRD) detected emerald green and ultramarine in the paint layers. Gas chromatography–mass spectrometry (GC-MS) indicated that the binding medium in the first layer was composed of blood. Our study helps to comprehensively understand the preparation of the wooden construction paintings in the renowned Summer Palace and provide a scientific basis for its restoration and related archeology work.     

Natural Compounds against Neurodegenerative Diseases: Molecular Characterization of the Interaction of Catechins from Green Tea with Aβ1–42, PrP106–126, and Ataxin‐3 Oligomers

By combining NMR spectroscopy, transmission electron microscopy, and circular dichroism we have identified the structural determinants involved in the interaction of green tea catechins with Aβ1–42, PrP106–126, and ataxin‐3 oligomers. The data allow the elucidation of their mechanism of action, showing that the flavan‐3‐ol unit of catechins is essential for interaction. At the same time, the gallate moiety, when present, seems to increase the affinity for the target proteins. These results provide important information for the rational design of new compounds with anti‐amyloidogenic activity and/or molecular tools for the specific targeting of amyloid aggregates in vivo.     

Beyond labels: A review of the application of quantum dots as integrated components of assays, bioprobes, and biosensors utilizing optical transduction

A comprehensive review of the development of assays, bioprobes, and biosensors using quantum dots (QDs) as integrated components is presented. In contrast to a QD that is selectively introduced as a label, an integrated QD is one that is present in a system throughout a bioanalysis, and simultaneously has a role in transduction and as a scaffold for biorecognition. Through a diverse array of coatings and bioconjugation strategies, it is possible to use QDs as a scaffold for biorecognition events. The modulation of QD luminescence provides the opportunity for the transduction of these events via fluorescence resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET), charge transfer quenching, and electrochemiluminescence (ECL). An overview of the basic concepts and principles underlying the use of QDs with each of these transduction methods is provided, along with many examples of their application in biological sensing. The latter include: the detection of small molecules using enzyme-linked methods, or using aptamers as affinity probes; the detection of proteins via immunoassays or aptamers; nucleic acid hybridization assays; and assays for protease or nuclease activity. Strategies for multiplexed detection are highlighted among these examples. Although the majority of developments to date have been in vitro, QD-based methods for ex vivo biological sensing are emerging. Some special attention is given to the development of solid-phase assays, which offer certain advantages over their solution-phase counterparts.