Single‐Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA–Protein Interactions

Genomic DNA in bacteria exists in a condensed state, which exhibits different biochemical and biophysical properties from a dilute solution. DNA was concentrated on streptavidin‐covered single‐walled carbon nanotubes (Strep ? SWNTs) through biotin–streptavidin interactions. We reasoned that confining DNA within a defined space through mechanical constraints, rather than by manipulating buffer conditions, would more closely resemble physiological conditions. By ensuring a high streptavidin loading on SWNTs of about 1 streptavidin tetramer per 4 nm of SWNT, we were able to achieve dense DNA binding. DNA is bound to Strep ? SWNTs at a tunable density and up to as high as 0.5 mg mL^?1 in solution and 29 mg mL^?1 on a 2D surface. This platform allows us to observe the aggregation behavior of DNA at high concentrations and the counteracting effects of HU protein (a histone‐like protein from Escherichia coli strain U93) on the DNA aggregates. This provides an in vitro model for studying DNA–DNA and DNA–protein interactions at a high DNA concentration.     

Systematic Dissection of an Aminopyrrolic Cage Receptor for β‐Glucopyranosides Reveals the Essentials for Effective Recognition

A set of structures designed for the recognition of glucosides has been obtained by systematically destructuring a tripodal aminopyrrolic cage receptor that selectively recognizes octyl‐β‐D ‐glucopyranoside (OctβGlc). NMR spectroscopy and isothermal titration calorimetry binding measurements showed that cleavage of one pillar of the cage was beneficial to the binding properties of the receptor, as long as two residual amino groups of the cleaved pillar were present. Removal of these two residual amino groups produced a dramatic loss of affinity for OctβGlc of the resulting monocyclic analogue of the parent cage receptor. A significant improvement in the binding ability was achieved by replacing one pillar with two aminopyrrolic hydrogen‐bonding arms, despite the loss of a preorganized structure. In contrast to the cage receptor, recognition of OctβGlc was observed, even in a competitive medium (30 % DMF in chloroform). Structural studies in solution, carried out through NMR spectroscopy and molecular modeling calculations, led to the elucidation of the 3D binding modes of the side‐armed monocyclic receptors; this highlighted the key role of the amino groups and demonstrated the occurrence of a rotaxane‐like complex, which featured the octyl chain of the glucoside threaded through the macrocyclic ring.     

Transition‐State Stabilization by a Secondary Substrate–Ligand Interaction: A New Design Principle for Highly Efficient Transition‐Metal Catalysis

A library of monodentate phosphane ligands, each bearing a guanidine receptor unit for carboxylates, was designed. Screening of the library gave some excellent catalysts for regioselective hydroformylation of β,γ‐unsaturated carboxylic acids. A terminal alkene, but‐3‐enoic acid, was hydroformylated with a linear/branched (l/b) regioselectivity up to 41. An internal alkene, pent‐3‐enoic acid was hydroformylated with regioselectivity up to 18:1. Further substrate selectivity (e.g., acid vs. methyl ester) and reaction site selectivity (monofunctionalization of 2‐vinylhept‐2‐enoic acid) were also achieved. Exploration of the structure–activity relationship and a practical and theoretical mechanistic study gave us an insight into the nature of the supramolecular guanidinium–carboxylate interaction within the catalytic system. This allowed us to identify a selective transition‐state stabilization by a secondary substrate–ligand interaction as the basis for catalyst activity and selectivity.     

Design and Construction of a Smart Targeting Drug Delivery System Based on Phototriggered Competition of Host–Guest Interaction

A smart targeting drug delivery nanocarrier is successfully constructed based on phototriggered competition of host–guest interaction. The targeting motif, i.e., biotin is first concealed by β‐cyclodextrin (β‐CD) via host–guest interaction. When the nanoparticles are exposed to UV light, the cleavage of photosensitive groups results in the exposure of adamantane (Ad) groups initially located in the interior of nanoassemblies, and β‐CDs capped on biotin ligands can be replaced by Ad because of the higher binding constant between Ad and β‐CD than that between biotin and β‐CD. The competition of host–guest interaction leads to the recovery of targeting capacity of biotin ligands on the nanocarriers. By virtue of photoregulation, the nanocarriers exhibit controllable ligand‐receptor recognition, which is proved by flow cytometry, laser confocal microscopy, and cytotoxicity assay. This strategy has a potential to improve the selectivity and safety of targeting drug delivery systems.     

Boronate‐Affinity Glycan‐Oriented Surface Imprinting: A New Strategy to Mimic Lectins for the Recognition of an Intact Glycoprotein and Its Characteristic Fragments

Lectins possess unique binding properties and are of particular value in molecular recognition. However, lectins suffer from several disadvantages, such as being hard to prepare and showing poor storage stability. Boronate‐affinity glycan‐oriented surface imprinting was developed as a new strategy for the preparation of lectin‐like molecularly imprinted polymers (MIPs). The prepared MIPs could specifically recognize an intact glycoprotein and its characteristic fragments, even within a complex sample matrix. Glycan‐imprinted MIPs could thus prove to be powerful tools for important applications such as proteomics, glycomics, and diagnostics.     

Carbohydrate–Arene Interactions Direct Conformational Equilibrium of a Flexible Glycophane in Water

Water, the flexibility of the maltose molecule , and sugar/arene interactions are responsible for the equilibrium between a folded ( I ) and nonfolded ( II ) conformation in a glycophane ( III is an intermediate). Glycophanes are cyclodextrin–cyclophane hybrids, which are of interest as models of receptors.     

Highly Sensitive and Selective Spectroscopic Detection of Mercury(II) in Water by Using Pyridylporphyrin–DNA Conjugates

Single‐labeled pyridylporphyrin–DNA conjugates are reported as highly sensitive and selective spectroscopic sensors for mercury(II) ions in water. The effects of chemical structure (thymine versus adenine), number of nucleotides (monomer versus octamer), and porphyrin metalation (Zn versus free base) on the sensitivity and selectivity of mercury(II) detection are explored. The results indicated that pyridylporphyrin rather than the nucleobase plays a crucial role in mercury(II) sensing, because porphyrin conjugates with both adenosine and thymidine exhibited excellent mercury(II) detection. Mercury(II) recognition was shown in emission quenching, as well as in a redshift of the porphyrin Soret band absorption. The limit of detection (LOD, 3σ/slope) of zinc(II) pyridylporphyrin‐5′‐oligodeoxythymidine ( ZnPorT8 ) obtained by fluorescence quenching was calculated to be 21.14 nM . Other metal cations (Zn²⁺, Cd²⁺, Pb²⁺, Mn²⁺, Ca²⁺, Ni²⁺, Mg²⁺, Fe²⁺, Cu²⁺, and Na⁺) did not interfere with the emission and absorption sensing of mercury(II). Free‐base porphyrin–oligothymine conjugate 2HPorT8 displayed similar sensitivity to ZnPorT8 but different selectivity. The results also implied that the sensing properties of porphyrin–deoxythymidine conjugates could potentially be tuned by porphyrin metalation.     

On the Role of Flexibility in Protein–Ligand Interactions: the Example of p53 Tetramerization Domain

The recognition of protein surfaces by designed ligands has become an attractive approach in drug discovery. However, the variable nature and irregular behavior of protein surfaces defy this new area of research. The easy to understand “lock‐and‐key” model is far from being the ideal paradigm in biomolecular interactions and, hence, any new finding on how proteins and ligands behave in recognition events paves a step of the way. Herein, we illustrate a clear example on how an increase in flexibility of both protein and ligand can result in an increase in the stability of the macromolecular complex. The biophysical study of the interaction between a designed flexible tetraguanidinium‐calix[4]arene and the tetramerization domain of protein p53 (p53TD) and its natural mutant p53TD‐R337H shows how the floppy mutant domain interacts more tightly with the ligand than the well‐packed wild‐type protein. Moreover, the flexible calixarene ligand interacts with higher affinity to both wild‐type and mutated protein domains than a conformationally rigid calixarene analog previously reported. These findings underscore the crucial role of flexibility in molecular recognition processes, for both small ligands and large biomolecular surfaces.     

Quantifying the Effect of Surface Ligands on Dendron–DNA Interactions: Insights into Multivalency through a Combined Experimental and Theoretical Approach

We report the synthesis, DNA binding ability and preliminary gene delivery profiles of dendrons with different amine surface groups, 1,3‐diaminopropane (DAP), N,N‐di‐(3‐aminopropyl)‐N‐(methyl)amine (DAPMA) and spermine (SPM). By using a combination of ethidium bromide displacement, gel electrophoresis and transfection assays, it is shown that the dendrons with SPM groups are the most effective DNA binders, while the DAPMA‐functionalised dendrons were the most effective systems for gene delivery (although the gene delivery profiles were still modest). In order to provide deeper insight into the experimental data, we performed a molecular dynamics simulation of the interactions between the dendrons and DNA. The results of these simulations demonstrated that, in general terms, the enthalpic contribution to binding was roughly proportional to the dendron surface charge, but that dendrons with DAP (and DAPMA) surface amines had significant entropic costs of binding to DNA. In the case of DAP, this is a consequence of the fact that the entire dendron structure has to be organised in order for each individual monoamine charge to make effective contact with DNA. For SPM, however, each surface ligand is already a multivalent triamine, therefore, each individual charge has a much lower entropic cost of binding. For DAPMA, we observed that strong binding of the hindered tertiary amine to the DNA double helix led to ligand back‐folding and significant geometric distortion of DNA. Although this weakens the overall binding, we suggest that this distortion might be an explanation for the experimentally observed enhanced gene delivery, in which DNA compaction is an important step. Overall, this paper demonstrates how structure–activity relationships can be developed for multivalent dendritic ligands and provides insights into the thermodynamics of multivalent interactions.     

Stable Cyclohexyl–Phenyl Recognition in the Center of a DNA Duplex

Even saturated carbocycles are compatible with Watson–Crick pairing, as shown by the incorporation of phenylcyclohexyl‐C‐nucleoside pairs into the center of a DNA double helix (see picture). The increase in duplex stability arises from cyclohexyl/phenyl CH/π interactions. This makes the system an interesting scaffold for studying hydrophobic interactions and allows for the incorporation of additional molecular entities into the double helix.

     

Triazine‐Carbon Nanotubes: New Platforms for the Design of Flavin Receptors

The synthesis of functionalised carbon nanotubes as receptors for riboflavin (RBF) is reported. Carbon nanotubes, both single‐walled and multi‐walled, have been functionalised with 1,3,5‐triazines and p‐tolyl chains by aryl radical addition under microwave irradiation and the derivatives have been fully characterised by using a range of techniques. The interactions between riboflavin and the hybrids were analysed by using fluorescence and UV/Vis spectroscopic techniques. The results show that the attached functional groups minimise the π‐π stacking interactions between riboflavin and the nanotube walls. Comparison of p‐tolyl groups with the triazine groups shows that the latter have stronger interactions with riboflavin because of the presence of hydrogen bonds. Moreover, the triazine derivatives follow the Stern–Volmer relationship and show a high association constant with riboflavin. In this way, artificial receptors in catalytic processes could be designed through specific control of the interaction between functionalised carbon nanotubes and riboflavin.     

Coumarin‐3‐Aldehyde as a Scaffold for the Design of Tunable PET‐Modulated Fluorescent Sensors for Neurotransmitters

NeuroSensor 521 (NS521) is a fluorescent sensor for primary‐amine neurotransmitters based on a platform that consists of an aryl moiety appended to position C4 of the coumarin‐3‐aldehyde scaffold. We demonstrate that sensors based on this platform behave as a directly linked donor–acceptor system that operates through an intramolecular acceptor‐excited photoinduced electron transfer (a‐PET) mechanism. To evaluate the PET process, a series of benzene‐ and thiophene‐substituted derivatives were prepared and the photophysical properties, binding affinities, and fluorescence responses toward glutamate, norepinephrine, and dopamine were determined. The calculated energy of the highest occupied molecular orbital (E_HOMO) of the pendant aryl substituents, along with oxidation and reduction potential values derived from the calculated molecular orbital energy values of the platform components, allowed for calculation of the fluorescence properties of the benzene sensor series. Interestingly, the thiophene derivatives did not fit the typical PET model, highlighting the limitations of the method. A new sensor, NeuroSensor 539, displayed enhanced photophysical properties aptly suited for biological imaging. NeuroSensor 539 was validated by selectively labeling and imaging norepinephrine in secretory vesicles of live chromaffin cells.