Rationally Designed Semisynthetic Natural Product Analogues for Stabilization of 14‐3‐3 Protein–Protein Interactions

The natural product family of fusicoccanes are stabilizers of 14‐3‐3 mediated protein–protein interactions (PPIs), some of which possess antitumor activity. In this study, the first use of molecular dynamics (MD) to rationally design PPI stabilizers with increased potency is presented. Synthesis of a focused library, with subsequent characterization by fluorescence polarization, mutational studies, and X‐ray crystallography confirmed the power of the MD‐based design approach, revealing the potential for an additional hydrogen bond with the 14‐3‐3 protein to lead to significantly increased potency. Additionally, these compounds exert their action in a cellular environment with increased potency. The newly found polar interaction could provide an anchoring point for new small‐molecule PPI stabilizers. These results facilitate the development of fusicoccanes towards drugs or tool compounds, as well as allowing the study of the fundamental principles behind PPI stabilization.     

Homo‐molecular Fluorescence Complementation for Direct Visualization of Receptor Oligomerization in Living Cells

Cell surface receptor oligomerization is an attractive target process for drug screening. However, simple but reliable (and thus high‐throughput) visualization methods for receptor oligomerization are still lacking. Herein, we report on a new single‐construct homo‐molecular fluorescence complementation (Homo‐FC) probe, which shows strong fluorescence signals by oligomerization of fused receptors in living cells with unexpectedly low background signals. Importantly, this high signal‐to‐noise ratio was not affected by expression level variations of fused receptors. The Homo‐FC probe was developed by optimized flopped fusion of split fragments of superfolder green fluorescence protein and subsequent surface charge engineering. Homo‐FC reliably visualized the oligomerization of diverse natural receptors such as GPCR, EGFR, and even cytosolic DAI.     

Graphene Oxide as an Enhancer of Fluorescence

Solvent‐dependent switching of graphene oxide (GO) as fluorescence quencher or enhancer was observed. In some solvents, GO increases the fluorescence yield of a hydrophilic molecule 7‐(diethylamino)‐coumarin‐3‐carboxylic acid (7‐DCA), and in some solvents GO act as a quencher of fluorescence.     

Differential Laser‐Induced Perturbation Spectroscopy for Analysis of Mixtures of the Fluorophores l‐Phenylalanine,l‐Tyrosine and l‐Tryptophan Using a Fluorescence Probe

Quantitative detection of common endogenous fluorophores is accomplished using differential laser‐induced perturbation spectroscopy (DLIPS) with a 193‐nm UV fluorescence probe and various UV perturbation wavelengths. In this study, DLIPS is explored as an alternative to traditional fluorescence spectroscopy alone, with a goal of exploring natural fluorophores pursuant to biological samples and tissue analysis. To this end, aromatic amino acids, namely, l ‐phenylalanine, l ‐tyrosine and l ‐tryptophan are mixed with differing mass ratios and then classified with various DLIPS schemes. Classification with a traditional fluorescence probe is used as a benchmark. The results show a 20% improvement in classification performance of the DLIPS method over the traditional fluorescence method using partial least squares (PLS) analysis. Additional multivariate analyses are explored, and the relevant photochemistry is elucidated in the context of perturbation wavelengths. We conclude that DLIPS is a promising biosensing approach with potential for in vivo analysis given the current findings with fluorophores relevant to biological tissues.     

Quadracyclic Adenine: A Non‐Perturbing Fluorescent Adenine Analogue

Fluorescent‐base analogues (FBAs) comprise a group of increasingly important molecules for the investigation of nucleic acid structure and dynamics as well as of interactions between nucleic acids and other molecules. Here, we report on the synthesis, detailed spectroscopic characterisation and base‐pairing properties of a new environment‐sensitive fluorescent adenine analogue, quadracyclic adenine (qA). After developing an efficient route of synthesis for the phosphoramidite of qA it was incorporated into DNA in high yield by using standard solid‐phase synthesis procedures. In DNA qA serves as an adenine analogue that preserves the B‐form and, in contrast to most currently available FBAs, maintains or even increases the stability of the duplex. We demonstrate that, unlike fluorescent adenine analogues, such as the most commonly used one, 2‐aminopurine, and the recently developed triazole adenine, qA shows highly specific base‐pairing with thymine. Moreover, qA has an absorption band outside the absorption of the natural nucleobases (>300 nm) and can thus be selectively excited. Upon excitation the qA monomer displays a fluorescence quantum yield of 6.8 % with an emission maximum at 456 nm. More importantly, upon incorporation into DNA the fluorescence of qA is significantly less quenched than most FBAs. This results in quantum yields that in some sequences reach values that are up to fourfold higher than maximum values reported for 2‐aminopurine. To facilitate future utilisation of qA in biochemical and biophysical studies we investigated its fluorescence properties in greater detail and resolved its absorption band outside the DNA absorption region into distinct transition dipole moments. In conclusion, the unique combination of properties of qA make it a promising alternative to current fluorescent adenine analogues for future detailed studies of nucleic acid‐containing systems.     

Long‐Wavelength Fluorescence from 2‐Aminopurine‐Nucleobase Dimers in DNA

When 2‐aminopurine (2AP) is substituted for adenine in DNA, it is widely accepted that its fluorescence spectrum is essentially unchanged from that of the free fluorophore. We show that 2AP in DNA exhibits long‐wavelength emission and excitation bands, in addition to the familiar short‐wavelength spectra, as a result of formation of a ground‐state heterodimer with an adjacent, π‐stacked, natural base. The observation of dual emission from 2AP in a variety of oligodeoxynucleotide duplexes and single strands demonstrates the generality of this phenomenon. The photophysical and conformational properties of the long‐wavelength‐emitting 2AP‐nucleobase dimer are examined. Analogous long‐wavelength fluorescence is seen when 2AP π‐stacks with aromatic amino acid sidechains in the active sites of methyltransferase enzymes during DNA nucleotide flipping.     

A Novel Pyrene‐Based Fluorescing Amphiphile with Unusual Bulk and Interfacial Properties

We have synthesised a new, pyrene‐based, low‐molecular‐mass, amphiphilic molecule that displays a wealth of properties of potential interest for aggregation and interfacial applications. In order to elucidate some of the key properties of this molecule, which consists of a pyrene‐containing hydrophobic head and a short PEG‐based hydrophilic tail, we investigate herein some aspects of its concentration‐dependent behaviour in aqueous solutions. We show that the inclusion of the hydrophobic pyrene group not only provides the molecule with intriguing bulk and interfacial properties down to low concentrations, but also with various means of assessing its aggregation behaviour by means of its well‐characterised fluorescence properties. Combining a range of fluorescence techniques with microscopic imaging (optical and Cryo‐TEM), interfacial tension measurements and foaming studies, we have been able to identify and characterise three concentration‐dependant regimes. At low concentrations, the molecule is dissolved in monomeric form. At intermediate concentrations, labile aggregates are formed, which, at higher concentrations, give way to aggregates containing pre‐associated pyrenes. Our measurements strongly imply that the latter aggregates are hexagonally close‐packed tubular micelles. In this latter regime we also find a range of micron‐sized precipitates. Additionally, the molecule displays strong interfacial activity, yet a surprisingly slow dynamics of interfacial adsorption. Finally, we demonstrate the possibility of using it to visualize interfaces and also create reasonably stable (1 hour) and fluorescing foams.     

Environment‐sensitive Fluorescent Turn‐on Chemical Probe for the Specific Detection of O‐Methylguanine‐DNA Methyltransferase (MGMT) in Living Cells

MGMT protein, which has been associated with resistance to antitumor alkylation drugs for many patients, is a very useful prognostic marker to provide a guide for therapeutic decisions. Considering the large number of cellular samples that have to be handled daily at the hospitals, it is thus important to develop a rapid and simple analytical method to distinguish MGMT activity in different types of cells. In this paper, we describe a MGMT‐activated fluorescence turn‐on probe for the rapid no‐wash imaging of MGMT in living cells. The probe consists of a specific MGMT suicide pseudosubstrate, O⁶‐benzyl‐guanine and an environment‐sensitive fluorophore, SBD. In the presence of MGMT, the enzyme transfers SBD to the protein active site where the hydrophobic surrounding causes the fluorophore to exhibit more than 50‐fold fluorescence enhancement. With this probe, bright fluorescence was observed for MGMT‐positive, Hela S3 and MCF‐7 cells, while MGMT‐deficient CHO cells displayed no fluorescence. We believe that this fluorescence activation probe design can also be extended to detect other transferases, for which there are still no effective methods to image them in living cells.     

High‐Throughput Approaches in Carbohydrate‐Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors,Evolution, and Discovery

Carbohydrates are attached and removed in living systems through the action of carbohydrate‐active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high‐throughput approaches look at many enzymes at once. Similarly, high‐throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. In this review, we provide an overview of how these enzymes and inhibitors can be sought using techniques such as high‐throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence‐activated cell sorting, and metagenomics.     

High‐Throughput Approaches in Carbohydrate‐Active Enzymology: Glycosidase and Glycosyl Transferase Inhibitors,Evolution, and Discovery

Carbohydrates are attached and removed in living systems through the action of carbohydrate‐active enzymes such as glycosyl transferases and glycoside hydrolases. The molecules resulting from these enzymes have many important roles in organisms, such as cellular communication, structural support, and energy metabolism. In general, each carbohydrate transformation requires a separate catalyst, and so these enzyme families are extremely diverse. To make this diversity manageable, high‐throughput approaches look at many enzymes at once. Similarly, high‐throughput approaches can be a powerful way of finding inhibitors that can be used to tune the reactivity of these enzymes, either in an industrial, a laboratory, or a medicinal setting. In this review, we provide an overview of how these enzymes and inhibitors can be sought using techniques such as high‐throughput natural product and combinatorial library screening, phage and mRNA display of (glyco)peptides, fluorescence‐activated cell sorting, and metagenomics.     

Artificial β‐Double Helices from Achiral γ‐Peptides

Double helices are not common in polypeptides and proteins except in the peptide antibiotic gramicidin A and analogous l,d ‐peptides. In contrast to natural polypeptides, remarkable β‐double‐helical structures from achiral γ‐peptides built from α,β‐unsaturated γ‐amino acids have been observed. The crystal structures suggest that they adopted parallel β‐double helical structures and these structures are stabilized by the interstrand backbone amide H‐bonds. Furthermore, both NMR spectroscopy and fluorescence studies support the existence of double‐helical conformations in solution. Although a variety of folded architectures featuring distinct H‐bonds have been discovered from the β‐ and γ‐peptide foldamers, this is the first report to show that achiral γ‐peptides can spontaneously intertwine into β‐double helical structures.     

Discrimination of G‐Quadruplexes from Duplex and Single‐Stranded DNAs with Fluorescence and Energy‐Transfer Fluorescence Spectra of Crystal Violet

G‐rich nucleic acid sequences with the potential to form G‐quadruplex structures are common in biologically important regions. Most of these sequences are present with their complementary strands, so the development of a sensitive biosensor to distinguish G‐quadruplex and duplex structures and to determine the competitive ability of quadruplex to duplex structures has received a great deal of attention. In this work, the interactions between two triphenylmethane dyes (malachite green (MG) and crystal violet (CV)) and G‐quadruplex, duplex, or single‐stranded DNAs were studied by fluorescence spectroscopy and energy‐transfer fluorescence spectroscopy. Good discrimination between quadruplexes and duplex or single‐stranded DNAs can be achieved by using the fluorescence spectrum of CV or the energy‐transfer fluorescence spectra of CV and MG. In addition, by using energy‐transfer fluorescence titrations of CV with G‐quadruplexes, the binding‐stoichiometry ratios of CV to G‐quadruplexes can be determined. By using the fluorescence titrations of G‐quadruplex–CV complexes with C‐rich complementary strands, the fraction of G‐rich oligonucleotide that engages in G‐quadruplex structures in the presence of the complementary sequence can be measured. This study may provide a simple method for discrimination between quadruplexes and duplex or single‐stranded DNAs and for measuring G‐quadruplex percentages in the presence of the complementary C‐rich sequences.     

Spectrofluorimetric Study on the Weak Interaction between ATP and Na-4-Tosyl-L-arginine Methyl Ester Hydrochloride

In this paper, some new results on the selective weak interaction between Na-4-tosyl-L-arginine methyl ester hydrochloride （TAME） and adenosine-5＇-triphosphate （ATP） have been reported. Fluorescence spectrophotometry and Fourier transform infrared （FT-IR） spectroscopy were used to investigate this kind of weak interaction. In fluorescence experiments, obvious fluorescence quenching phenomena were observed when TAME was added, which indicated the weak interactions between TAME and ATP. It has been identified by fluorescence titration experiments that TAME exhibited high selectivity to ATP over ADP and AMP. FT-IR spectral results showed that an ATP-TAME adduct was formed. The experimental results indicated that the interaction sites were the guanidinium group of TAME main-chain and the γ-phosphate group of ATP, and the interaction took place through hydrogen bonding and electrostatic force. In addition, the effects of metal ions on the weak interaction between ATP and TAME, or between ATP and analogues of L-arginine were studied.     

Multipronged Biomimetic Approach To Create Optically Tunable Nanoparticles

Current biomimetics for medical applications use a single biomimetic approach to imitate natural structures, which can be insufficient for reconstructing structurally complex natural systems. Multipronged efforts may resolve these complexities. To achieve interesting nanostructure‐driven optical properties, a dual‐biomimetic system contained within a single nanoagent was engineered to recapitulate chlorosomes, efficient light‐harvesting organelles that have unique dye assemblies and tunable photonic properties. A series of chlorin dyes was synthesized, and these hydrophobic assemblies were stabilized inside a high‐density lipoprotein, a second biomimetic that enabled in vivo utility. This system resulted in tunable tumor imaging of intact (photoacoustic) and disrupted (activatable fluorescence) nanostructures. The successful demonstration of this multipronged biomimetic approach opens the door for reconstruction of complex natural systems for biomedical applications.     

Fluorescence imaging and point measurements of tissue: applications to the demarcation of malignant tumors and atherosclerotic lesions from normal tissue

The possibilities of using laser-induced fluorescence for tissue diagnostics are discussed. The tissue types investigated are malignant tumors and atherosclerotic lesions. Studies with natural autofluorescence as well as with fluorescent tumor markers are included in this paper. Fluorescence emission and decay data are presented for some tissue chromophores contributing to tissue autofluorescence. Optical spectroscopic characteristics of fluorescent malignant tumor markers are analyzed and instrumental designs for clinical applications are discussed. Images recorded with a multicolor fluorescence imaging system developed in Lund are presented.     

Temperature‐Responsive Mixed‐Shell Polymeric Micelles for the Refolding of Thermally Denatured Proteins

We have fabricated a mixed‐shell polymeric micelle (MSPM) that closely mimics the natural molecular chaperone GroEL? GroES complex in terms of structure and functionality. This MSPM, which possesses a shared PLA core and a homogeneously mixed PEG and PNIAPM shell, is constructed through the co‐assembly of block copolymers poly(lactide‐b‐poly(ethylene oxide) (PLA‐b‐PEG) and poly(lactide)‐b‐poly(N‐isopropylacryamide) (PLA‐b‐PNIPAM). Above the lower critical solution temperature (LCST) of PNIPAM, the MSPM evolves into a core–shell–corona micelle (CSCM), as a functional state with hydrophobic PNIPAM domains on its surface. Light scattering (LS), TEM, and fluorescence and circular dichroism (CD) spectroscopy were performed to investigate the working mechanism of the chaperone‐like behavior of this system. Unfolded protein intermediates are captured by the hydrophobic PNIPAM domains of the CSCM, which prevent harmful protein aggregation. During cooling, PNIPAM reverts into its hydrophilic state, thereby inducing the release of the bound unfolded proteins. The refolding process of the released proteins is spontaneously accomplished by the presence of PEG in the mixed shell. Carbonic anhydrase B (CAB) was chosen as a model to investigate the refolding efficiency of the released proteins. In the presence of MSPM, almost 93 % CAB activity was recovered during cooling after complete denaturation at 70 °C. Further results reveal that this MSPM also works with a wide spectrum of proteins with more‐complicated structures, including some multimeric proteins. Given the convenience and generality in preventing the thermal aggregation of proteins, this MSPM‐based chaperone might be useful for preventing the toxic aggregation of misfolded proteins in some diseases.     

Photocontrolled Intramolecular Charge/Energy Transfer and Fluorescence Switching of Tetraphenylethene‐Dithienylethene‐Perylenemonoimide Triad with Donor–Bridge–Acceptor Structure

Photochromic 1,2‐dithienylethene (DTE) derivatives with a high thermal stability and fatigue resistance are appealing for optical switching of fluorescence. Here, we introduce a donor–photochromic bridge–acceptor tetraphenylethene‐dithienylethene‐perylenemonoimide (TPE‐DTE‐PMI) triad, in which TPE acts as the electron donor, PMI as the electron acceptor, and DTE as the photochromic bridge. In this system, the localized and intramolecular charge transfer emission of TPE‐DTE‐PMI with various Stokes shifts have been observed due to the photoinduced intramolecular charge transfer in different solvents. Upon UV irradiation, the fluorescence quenching resulting from photochromic fluorescence resonance energy transfer in TPE‐DTE‐PMI has been demonstrated in solution and in solid films. The fluorescence on/off switching ratio in polymethylacrylate film exceeds 100, a value much higher than in polymethylmethacrylate film, thus indicating that the fluorescence switching is dependent on matrices.     

Absorption and fluorescence emission spectroscopic characters of naphtho‐homologated yy‐DNA bases and effect of methanol solution and base pairing

A comprehensive theoretical study of electronic transitions of naphtho‐homologated base analogs, namely, yy‐T , yy‐C , yy‐A , and yy‐G , was performed. The nature of the low‐lying excited states is discussed, and the results are compared with those from experiment and also with those of y‐bases. Geometrical characteristics of the lowest excited singlet ππ* and nπ* states were explored using the CIS method, and the effects of methanol solution and paring with their complementary natural bases on the relevant absorption and emission spectra of these modified bases were examined. The calculated excitation and emission energies agree well with the measured data, where experimental results are available. In methanol solution, the fluorescence from yy‐A and yy‐G would be expected to occur around 539 and 562 nm, respectively, suggesting that yy‐A is a green‐colored fluorophore, whereas yy‐G is a yellow‐colored fluorophore. The methanol solution was found to red‐shift both the absorption and emission maxima of yy‐A , yy‐T , and yy‐C , but blue‐shift those for yy‐G . Generally, though base pairing has no significant effects on the absorption and fluorescence maxima of yy‐A , yy‐C , and yy‐T , it blue‐shifts those for yy‐G . © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Understanding the Unconventional Effects of Halogenation on the Luminescent Properties of Oligo(Phenylene Vinylene) Molecules

It is commonly known that halogenation tends to decrease the luminescence quantum yield of an organic dye, owing to the high electronegativity and heavy‐atom effect of the halogen atom. However, based on an investigation of the effects of halogenation on the luminescence of the oligo(phenylene vinylene) (OPV) framework, we demonstrate that halogenation can have positive impact on the solid‐state fluorescence and electrochemiluminescence (ECL) properties of OPV derivatives. The chlorinated OPV exhibits a very high solid‐state fluorescence quantum yield (91 %), whilst the brominated analogue gives the highest ECL emission intensity. Time‐dependent density functional theory calculations, natural bond orbital analysis, and natural transition orbital analysis were performed to assist the understanding of the origin of these positive halogenation effects, which provide insight into the rational design of highly luminescent halogenated organic materials for solid‐state devices and ECL applications.     

Tetraphenylethylene Conjugated with a Specific Peptide as a Fluorescence Turn‐On Bioprobe for the Highly Specific Detection and Tracing of Tumor Markers in Live Cancer Cells

Smart molecular probes and flexible methods are attracting remarkable interest for the visualization of cancer‐related biological and chemical events. In this work, a new fluorescence turn‐on probe with dual‐recognition characteristics for the specific imaging of cancer cells is reported. This new bioprobe is rationally designed by linking tetraphenylethylene (TPE), an aggregation‐induced emission (AIE) fluorophore, with the small peptide IHGHHIISVG (referred to as AP2H), a targeting ligand to the broad‐spectrum cancer‐related protein LAPTM4B. The binding of the probe TPE‐AP2H with the target, both in solution and at the cellular level, switches on the fluorescence of TPE because of the inhibition of internal rotations within the TPE framework. Accordingly, this bioprobe allows the real‐time monitoring and subcellular localization of LAPTM4B in cancer cells, with a very high target‐to‐background ratio for the imaging. Furthermore, brighter fluorescence images are detected after incubation of TPE‐AP2H with tumor cells at lower pH values. Thus, this new bioprobe is more advantageous because it can simultaneously target the LAPTM4B protein and sense the characteristic low‐pH environment of tumor cells. In addition, TPE‐AP2H displays high photostability and low cytotoxicity. Therefore, this new bioprobe is promising for the more accurate and reliable imaging of tumor markers in live cancer cells.