Z‐DNA Recognition in B‐Z‐B Sequences by a Cationic Zinc Porphyrin

For the first time it has been shown by spectroscopic studies such as circular dichroism and UV/Vis that cationic zinc porphyrin serves as a selective spectroscopic sensor that is able to recognize short left‐handed Z‐DNA tracts embedded in the B‐Z‐B sequences.     

Achieving High Affinity towards a Bacterial Lectin through Multivalent Topological Isomers of Calix[4]arene Glycoconjugates

A family of seven topologically isomeric calix[4]arene glycoconjugates was prepared through the synthesis of a series of alkyne‐derivatised calix[4]arene precursors that are suitable for the attachment of sugar moieties by microwave‐assisted copper(I)‐catalysed azide–alkyne cycloaddition (CuAAC). The glycoconjugates thus synthesised comprised one mono‐functionalised derivative, two 1,2‐ or 1,3‐divalent regioisomers, one trivalent and three tetravalent topoisomers in the cone, partial cone or 1,3‐alternate conformations. The designed glycoconjugates were evaluated as ligands for the galactose‐binding lectin PA‐IL from the opportunistic bacterium Pseudomonas aeruginosa, a major causative agent of lung infections in cystic fibrosis patients. Binding affinities were determined by isothermal titration calorimetry (ITC), and the interaction with the lectin was shown to be strongly dependant on both the valence and the topology. Whereas the trivalent conjugate displayed enhanced affinity when compared to a monosaccharide model, the tetravalent conjugates are to‐date the highest‐affinity ligands measured by ITC. The topologies presenting carbohydrates on both faces of calixarene are the most potent ones with dissociation constants of approximately 200 nM . Molecular modelling suggests that such a multivalent molecule can efficiently chelate two of the binding sites of the tetrameric lectin; this explains the 800‐fold increase of affinity achieved by the tetravalent molecule. Surface plasmon resonance (SPR) experiments confirmed that this glycoconjugate is the strongest inhibitor for binding of PA‐IL to galactosylated surfaces for potential applications as an anti‐adhesive agent.     

The chemical composition and bonding structure of B–C–N–H thin films deposited by reactive magnetron sputtering

The chemical composition and bonding structures of B–C–N–H films fabricated by medium frequency magnetron sputtering, with N₂+CH₄+Ar gas mixture sputtering the boron target, were investigated. XPS and FTIR spectrometric analyses show that the increase of CH₄ flow rate during deposition causes an increase of the C content in the films. The increase in the CH₄ flow rate promotes an increase in the B–C, C–N single and C?N double bonds which are the components of the hybridized B–C–N bonding structure. From the results of Raman spectroscopy analysis, it is seen that the intensity of the D band of the films' Raman spectrum decreases with increasing CH₄ flow rate, indicating a decrease of the sp²‐phase content or the sp² C cluster size. The decreases of I_D/I_G also reflect the formation of more boron‐ or nitrogen‐ bound sp³‐coordinated carbons in the films. Copyright © 2009 John Wiley & Sons, Ltd.     

Honeycomb‐like Ordered Assembly of DNA Induced by Flexible Binuclear Ruthenium(II)–Polypyridyl Complexes

A series of binuclear ruthenium(II)–polypyridyl complexes of the type [Ru₂(N‐N)₄(BPIMBp)]⁴⁺, in which N‐N is 2,2′‐bipyridine (bpy; 1 ), 1,10‐phenanthroline (phen; 2 ), dipyrido[3,2‐d:2′,3‐f] quinoxaline (dpq; 3 ), dipyrido[3,2‐a:2′,3′‐c] phenanzine (dppz; 4 ), and 1,4′‐bis[(2‐pyridin‐2‐yl)‐1H‐imidazol‐1‐yl)methyl]‐1,1′‐biphenyl (BPIMBp) is a bridging ligand, have been synthesized and characterized. These complexes are charged (4+) cations and flexible due to the ?CH₂ group of the bridging ligand and possess terminal ligands with variable intercalative abilities. The interaction of complexes 1 – 4 with calf thymus DNA (CT‐DNA) was explored by using UV/Vis absorption spectroscopy, steady‐state emission, emission quenching with K₄[Fe(CN)₆], ethidium bromide displacement assay, Hoechst displacement assay, and viscosity measurements and revealed a groove‐binding mode for all the complexes through a spacer and an intercalative mode for complexes 3 and 4 . A decrease in the viscosity of DNA revealed bending and coiling of DNA, an initial step toward aggregation. Interestingly, a distinctive honeycomb‐like ordered assembly of the DNA–complex species was visualized by fluorescence microscopy in the solution state. The use of SEM and AFM confirmed the disordered self‐organization of the DNA–complex adduct on evaporation of the solvent. The small orderly nanosized DNA aggregates were confirmed by means of circular dichroism, dynamic light scattering (DLS), and TEM. These complexes are moderately cytotoxic against three different cell lines, namely, MCF‐7, HeLa, and HL‐60.     

Creation of Chiral Thixotropic Gels through a Crown–Ammonium Interaction and their Application to a Memory‐Erasing Recycle System

A unique class of oligothiophene‐based organogelator bearing two crown ethers at both ends was synthesized. This compound could gelatinize several organic solvents, forming one‐dimensional fibrous aggregates. From the observation of circular dichroism, it was confirmed that the helical handedness of the fibrous assembly is controllable by the chirality of 1,2bisammonium guests, thus suggesting that one guest molecule bridges two gelator molecules through the crown–ammonium interaction. Interestingly, we have found that such chirality is created by thermal gelation, whereas it disappears by thixotropic gelation. The new finding implies that the present organogel system is applicable as a reversible switching memory device, featuring memory creation by a heat mode and memory erasing by a mechanical mode.     

Oriented Circular Dichroism Analysis of Chiral Surface‐Anchored Metal–Organic Frameworks Grown by Liquid‐Phase Epitaxy and upon Loading with Chiral Guest Compounds

Oriented circular dichroism (OCD) is explored and successfully applied to investigate chiral surface‐anchored metal–organic frameworks (SURMOFs) based on camphoric acid (D‐ and Lcam) with the composition [Cu₂(Dcam)_2x(Lcam)_2?2x(dabco)]_n (dabco=1,4‐diazabicyclo‐[2.2.2]‐octane). The three‐dimensional chiral SURMOFs with high‐quality orientation were grown on quartz glass plates by using a layer‐by‐layer liquid‐phase epitaxy method. The growth orientation, as determined by X‐ray diffraction (XRD), could be switched between the [001] and [110] direction by using either OH‐ or COOH‐terminated substrates. These SURMOFs were characterized by using OCD, which confirmed the ratio as well as the orientation of the enantiomeric linker molecules. Theoretical computations demonstrate that the OCD band intensities of the enantiopure [Cu₂(Dcam)₂(dabco)]_n grown in different orientations are a direct result of the anisotropic nature of the chiral SURMOFs. Finally, the enantiopure [Cu₂(Dcam)₂(dabco)]_n and [Cu₂(Lcam)₂(dabco)]_n SURMOFs were loaded with the two chiral forms of ethyl lactate [(+)‐ethyl‐D ‐lactate and (?)‐ethyl‐L ‐lactate)]. An enantioselective enrichment of >60 % was observed by OCD when the chiral host scaffold was loaded from the racemic mixture.     

A Pyrimidopyrimidine Janus‐AT Nucleoside with Improved Base‐Pairing Properties to both A and T within a DNA Duplex: The Stabilizing Effect of a Second Endocyclic Ring Nitrogen

Janus bases are heterocyclic nucleic acid base analogs that present two different faces able to simultaneously hydrogen bond to nucleosides that form Watson–Crick base pairs. The synthesis of a Janus‐AT nucleotide analogue, ^N J_AT , that has an additional endocyclic ring nitrogen and is thus more capable of efficiently discriminating T/A over G/C bases when base‐pairing in a standard duplex‐DNA context is described. Conversion to a phosphoramidite ultimately afforded incorporation into an oligonucleotide. In contrast to the first generation of carbocyclic Janus heterocycles, it remains in its unprotonated state at physiological pH and, therefore, forms very stable Watson–Crick base pairs with either A or T bases. Biophysical and computational methods indicate that ^N J_AT is an improved candidate for sequence‐specific genome targeting.     

Reciprocal Self‐Assembly of Peptide–DNA Conjugates into a Programmable Sub‐10‐nm Supramolecular Deoxyribonucleoprotein

To overcome the limitations of molecular assemblies, the development of novel supramolecular building blocks and self‐assembly modes is essential to create more sophisticated, complex, and controllable aggregates. The self‐assembly of peptide–DNA conjugates (PDCs), in which two orthogonal self‐assembly modes, that is, β‐sheet formation and Watson–Crick base pairing, are covalently combined in one supramolecular system, is reported. Despite extensive research, most self‐assembly studies have focused on using only one type of building block, which restricts structural and functional diversity compared to multicomponent systems. Multicomponent systems, however, suffer from poor control of self‐assembly behaviors. Covalently conjugated PDC building blocks are shown to assemble into well‐defined and controllable nanostructures. This controllability likely results from the decrease in entropy associated with the restriction of the molecular degrees of freedom by the covalent constraints. Using this strategy, the possibility to thermodynamically program nano‐assemblies to exert gene regulation activity with low cytotoxicity is demonstrated.     

Determination of phenamacril residues in flour and rice based on Z‐Sep+ using ultra‐high‐performance liquid chromatography–tandem mass spectrometry

Phenamacril is a new broad‐spectrum fungicide that is commonly used for the control of fungal diseases in wheat and rice. In this study, ultra‐high‐performance liquid chromatography–tandem mass spectrometry was used to establish a method for analyzing the residual phenamacril in flour and rice based on the improved QuEChERS (quick, easy, cheap, effective, rugged and safe) method using Z‐Sep+ as the adsorbent in the pre‐treatment process. The average recovery of phenamacril in flour and rice was 82.2–96.0%, the relative standard deviation was 2.1–5.6% and the limit of quantification was 0.5 μg/kg. The accuracy and sensitivity of this method meet the requirements for residue analysis. The method was applied to commercially available flour and rice samples, and the detected concentrations of phenamacril were 0.005–0.033 mg/kg. This method provides technical support for the safety evaluation of phenamacril.     

Facile One‐Pot Synthesis of Functional Gold Nanoparticle–Polymer Hybrids Using Ionic Block Copolymers as a Nanoreactor

A highly versatile approach to fabricate functional gold nanoparticle (AuNP)‐polymer hybrids is demonstrated by employing sulfonated block copolymers. The 3–5 nm sized ionic domain of the sulfonated poly(styrene‐block‐methylbutylene) (S_nMB_m) copolymers can be utilized as a nanoreactor where the Au ions can be selectively sequestered and reduced to AuNPs using a simple photochemical method. The size of the AuNPs can be adjusted in fine‐steps from 2.0 ± 0.3 to 3.9 ± 0.5 nm by changing the sulfonation levels of the S_nMB_m copolymers. Remarkably, significantly improved methanol oxidation properties are achieved with the hybrid materials owing to the ion conducting–SO₃H groups and the interconnected network of AuNPs confined within the self‐assembled microstructures, which provides electronic conductivity.     

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.     

The Effect of DNA Sequence Directionality on G‐Quadruplex Folding

Sequence inversion in G‐rich DNA from 5′→3′ to 3′→5′ exerts a substantial effect on the number of structures formed, while the type of G‐quadruplex fold is in fact determined by the presence of K⁺ or Na⁺ ions. The melting temperatures of G‐quadruplexes adopted by oligonucleotides with sequences in the 5′→3′ direction are higher than those of their 3′→5′ counterparts with both KCl and NaCl. CD, UV, and NMR spectroscopy demonstrates the importance of primary sequence for the structural diversity of G‐quadruplexes. The changes introduced by mere sequence reversal of the G‐rich DNA segment have a substantial impact on the polymorphic nature of the resulting G‐quadruplexes and their potential physiological roles. The insights resulting from this study should enable extension of the empirical rules for the prediction of G‐quadruplex topology.     

Metal‐induced B–H Activation. Addition of Methyl Acetylene Carboxylates to Cp*Rh‐ and Cp*Ir 16 e Halfsandwich Complexes containing a Chelating 1,2‐Dicarba‐closo‐dodecaborane‐1,2‐diselenolato Ligand

Reactions of the 16e halfsandwich complexes Cp*M[Se₂C₂(B₁₀H₁₀)] ( 5 M = Rh, 6 M = Ir) with both methyl acetylene monocarboxylate and dimethyl acetylene dicarboxylate were studied in order to obtain information on the influence of the chalcogen (selenium versus sulfur), as well as further evidence for B–H activation, ortho‐metalation and substitution of the carborane. In the case of the rhodium‐selenium complex 5 , the reaction with methyl acetylene monocarboxylate gave products which were all structurally different compared to those of the sulfur analogue of 5 : a polycyclic derivative 12 with a B(6)‐substituted carborane cage was obtained as one of the final products; in addition, both geometrical isomers containing a Rh–B bond ( 10 , 11 ) and isomers without a Rh–B bond ( 8 , 9 ) were isolated, the latter being the result of twofold insertion into one of the Rh–Se bonds. In the case of the iridium‐selenium complex 6 , the reaction with methyl acetylene monocarboxylate led to the geometrical isomers 13 and 14 (similar to 10 and 11 ) with structures possessing an Ir–B bond. Both 5 and 6 reacted with dimethyl acetylene dicarboxylate at room temperature to give the complexes 15 and 16 which are formed by addition of the C≡C unit to the metal center and insertion into one of the metal‐selenium bonds. The proposed structures in solution were deduced from NMR data (¹H, ¹¹B, ¹³C, ⁷⁷Se, ¹⁰³Rh NMR), and an X‐ray structural analysis was carried out for the rhodium complex 12 .     

Substrate‐induced formation of a recognition structure in a four‐polypeptide–lipid monolayer system

Poly(γ‐methyl L ‐glutamate)s with Ser, His, Asp, and Glu residues at the amino terminal as the serine protease catalytic site were prepared. The number‐average degree of polymerization of the polypeptides was 51. A dipalmitoylphosphatidylcholine monolayer containing the polypeptides was formed at the air–water interface and was transferred onto gold‐deposited glass plates. The binding of N‐acetyltyrosine ethyl ester, a typical substrate of the serine protease, to the monolayer was characterized by surface plasmon resonance measurements. The four‐polypeptide–lipid monolayer system conditioned on an aqueous solution containing the substrate N‐acetyltyrosine ethyl ester exhibited Langmuir‐type binding of the substrate. Its binding constant of 6.1 × 10⁴ M⁻¹ was about 20 times larger than that observed for a monolayer prepared on pure water. The behavior may have arisen from a substrate‐induced rearrangement of the four kinds of polypeptides in the monolayer, forming a substrate‐binding structure similar to that found in serine protease. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 2186–2191, 2000