Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

Metabolite-sensing mRNAs, or "riboswitches," specifically interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, capable of ligand-induced structural changes, and downstream regions, harboring expression-controlling elements. We report the crystal structures of the add A-riboswitch and xpt G-riboswitch aptamer modules that distinguish between bound adenine and guanine with exquisite specificity and modulate expression of two different sets of genes. The riboswitches form tuning fork-like architectures, in which the prongs are held in parallel through hairpin loop interactions, and the internal bubble zippers up to form the purine binding pocket. The bound purines are held by hydrogen bonding interactions involving conserved nucleotides along their entire periphery. Recognition specificity is associated with Watson-Crick pairing of the encapsulated adenine and guanine ligands with uridine and cytosine, respectively.     

Chiral amplification in macromolecular helicity assisted by noncovalent interaction with achiral amines and memory of the helical chirality

Poly[(4-carboxyphenyl)acetylene] (poly-1) exhibits an intense induced circular dichroism (ICD) in the UV-visible region upon complexation with excess (R)-1-(1-naphthyl)ethylamine ((R)-2), owing to the formation of a predominantly single-handed helical conformation of the polymer backbone. In the presence of a small amount of (R)-2, poly-1 showed a very weak ICD due to the lack of a single-handed helical conformation. However, we have found that the co-addition of the excess bulky, achiral 1-naphthylmethylamine (5) with a small amount of (R)-2 caused a dramatic increase in the ICD magnitude, comparable to the full ICD induced by excess (R)-2. This indicates that an almost single-handed helix can be induced on poly-1 upon complexation with a small amount of (R)-2 assisted by achiral 5. Furthermore, the induced single-handed helical poly-1 could be successfully memorized by the replacement of (R)-2 and 5 with achiral 2-aminoethanol or n-butylamine.     

Cyclic PNA-based compound directed against HIV-1 TAR RNA: modelling, liquid-phase synthesis and TAR binding

A cyclic molecule including a hexameric PNA sequence has been designed and synthesized in order to target the TAR RNA loop of HIV-1 through the formation of a "kissing complex". For comparison, its linear analogue has also been investigated. The synthesis of the cyclic and linear PNA has been accomplished following a liquid-phase strategy using mixed PNA and fully N-protected (aminoethylglycinamide) fragments. The interactions of this cyclic PNA and its linear analogue with TAR RNA have been studied and the results indicate clearly that no interaction occurs between the cyclic antisense PNA and TAR RNA, whereas a tenuous interaction has been detected with its linear PNA analogue.     

Conversion of Allylic Alcohols into Allylic Nitromethyl Compounds via a Palladium-Catalyzed Solvolysis: An Enantioselective Synthesis of an Advanced Carbocyclic Nucleoside Precursor(1)

A two-step reaction sequence to homoallylic nitro compounds from allylic alcohols is presented. Ethoxy carbonylation of the alcohols with ethyl chloroformate provides the corresponding allylic ethyl carbonates in high yields. Exposure of these substrates to catalytic palladium(0) in CH(3)NO(2) initiates a reaction sequence, ionization-decarboxylation-nitromethylation, that culminates with the formation of nitroalkenes. The regio- and stereochemical outcomes of the nitromethyl allylation reaction can be explained by the behavior of the transient pi-allylpalladium complexes. This methodology serves as a centerpiece for the synthesis of an important carbocyclic nucleoside intermediate.     

First asymmetric total synthesis of tetrodotoxin

Tetrodotoxin, a toxic principle of puffer fish poisoning, is one of the most famous marine natural products because of the complex structure having many functional groups and its potent biological activity leading to death. Since the structure elucidation in 1964, this toxin has been recognized as a formidable target molecule for total synthesis. We have recently achieved the first asymmetric total synthesis from 2-acetoxy-tri-O-acetyl-d-glucal as a chiral starting material. The highly hydroxylated cyclohexane ring was constructed by Claisen rearrangement and regioselective hydroxylations of an acetone moiety and an intramolecular directed aldol condensation of the precursor having methyl ketone with dihydroxyacetone, which was synthesized through Sonogashira coupling. Installation of nitrogen functionality was unsuccessful through an attempted Overman rearrangement. We, therefore, employed a new intramolecular conjugate addition strategy between the carbamate and unsaturated ester groups. The alpha-hydroxyl lactone moiety was synthesized through an intramolecular epoxide opening by the Z-enolate of aldehyde, which was followed by oxidation-reduction of the resulting cyclic vinyl ether. The lactone was then converted to a protected ortho ester, and then gunanidinylation was followed by cleavage of the 1,2-glycol to give the fully protected tetrodotoxin. Selection of the protective groups has finally led us to accomplish the total synthesis of tetrodotoxin in an enantiomerically pure form. All the stereogenic centers were controlled with high selectivity, and the hydroxyl groups were differently protected to discriminate for the future analogue synthesis of a bioorganic program. The synthetic tetrodotoxin was purified by ion exchange chromatography and characterized to be identical with the natural compound.     

Photophysical studies on binding of curcumin to bovine serum albumins

The excited-state photophysical properties of curcumin in the presence of bovine serum albumin (BSA) have been studied. The absorption and fluorescence changes in curcumin on binding to BSA have been followed at varying concentrations of either curcumin or BSA to determine the binding constant, which has been found to be approximately 10(4) to 10(5) M(-1). Stopped-flow kinetics studies suggested at least two distinct kinetic steps for the binding of curcumin to BSA. The photophysical properties of the singlet-excited state of the curcumin-BSA complex have also been studied. Whereas the absorption spectrum of curcumin is redshifted, the fluorescence spectrum of curcumin was blueshifted in the presence of BSA. The fluorescence quantum yield of curcumin on complexing with BSA was approximately 0.05. Steady-state fluorescence anisotropy studies showed a significant increase in the anisotropy value of 0.37 in BSA-bound curcumin. The fluorescence decay of the curcumin-BSA complex followed a biexponential decay with fluorescence lifetimes of 413 ps (33%) and 120 ps (67%). On the basis of these complementary results, it has been concluded that curcumin shows very high binding to BSA, probably at the hydrophobic cavities inside the protein.     

Can the pi-facial selectivity of solvation be predicted by atomistic simulation?

This work is concerned with the rationalization and prediction of solvent and temperature effects in nucleophilic addition to alpha-chiral carbonyl compounds leading to facial diastereoselectivity. We study, using molecular dynamics simulations, the facial solvation of (R)-2-phenyl-propionaldehyde in n-pentane and n-octane at a number of temperatures and compare it with experimental selectivity data for the nBuLi addition leading to syn- and anti-(2R)-2-phenyl-3-heptanol, which give nonlinear Eyring plots with the presence of inversion temperatures. We have found from simulations that the facial solvation changes with temperature and alkane. Moreover, by introducing a suitable molecular chirality index we have been able to predict break temperatures (T(CI)) for the two solvents within less than 20 degrees of the inversion temperatures experimentally observed in the diastereoselective nBuLi addition. We believe this could lead to a viable approach for predicting inversion temperatures and other subtle solvent effects in a number of stereoselective reactions.     

Upward temperature shift of the intrinsic phase lag of the magnetization of Bis(phthalocyaninato)terbium by ligand oxidation creating an S = 1/2 spin

An alternating-current (ac) magnetic susceptibility measurement for the [(Pc)(2)Tb(III)](0) complex (Pc = phthalocyaninato) has shown that ligand oxidation of the anionic [(Pc)(2)Tb(III)](-) complex gives rise to a significant upward shift of the temperature range where the magnetization response shows a phase lag behind the time-varying external magnetic field. The peaks of the out-of-phase component of the ac susceptibility of the pi-radical [(Pc)(2)Tb(III)](0) were observed at 50, 43, and 36 K with ac magnetic fields of 10(3), 10(2), and 10 Hz, respectively, which were more than 10 K higher than the corresponding values of the anionic complex with a closed-shell pi-system. The ac susceptibility measurements on the complex with octa(dodecoxy)-substituted Pc ligand, which is readily dilutable in diamagnetic media, proved that the significant rise of the temperatures occurs as an intrinsic single-molecular property of the complex possessing both J = 6 and S = (1)/(2) systems, and is not due to long-range magnetic order or interactions between adjacent unpaired pi-electrons.     

Transparent conducting oxides: texture and microstructure effects on charge carrier mobility in MOCVD-derived CdO thin films grown with a thermally stable, low-melting precursor

A series of low-melting, thermally stable cadmium metal-organic chemical vapor deposition (MOCVD) precursors have been synthesized, structurally and spectroscopically characterized, and implemented in growth of highly conductive and transparent CdO thin films. One member of the series, bis(1,1,1,5,5,5-hexafluoro-2,4-pentanedionato)(N,N-diethyl-N',N'-dimethyl-ethylenediamine)cadmium(II), Cd(hfa)(2)()(N,N-DE-N',N'-DMEDA), represents a particularly significant improvement over previously available Cd precursors, owing to the low melting point and robust thermal stability. High-quality CdO films were grown by MOCVD on glass and single-crystal MgO(100) between 300 and 412 degrees C. Film growth parameters and substrate surface have large effects on microstructure and electron carrier transport properties. Enhanced mobilities observed for highly biaxially textured films grown on MgO(100) vs glass are attributed, on the basis of DC charge transport and microstructure analysis, to a reduction in neutral impurity scattering and/or to a more densely packed grain microstructure. Although single-grained films grown on MgO(100) exhibit greater mobilities than analogues with discrete approximately 100 nm grains and similar texture, this effect is attributed, on the basis of charge transport and Hall effect measurements as well as optical reflectivity analysis, to differences in carrier concentration rather than to reduced grain boundary scattering. Unprecedented conductivities and mobilities as high as 11,000 S/cm and 307 cm(2)/V.s, respectively, are obtained for epitaxial single-grained films (X-ray diffraction parameters: fwhm(omega) = 0.30 degrees, fwhm(phi) = 0.27 degrees ) grown in situ on MgO(100) at a relatively low temperature (400 degrees C).     

High-dimensional quantum dynamical study of the dissociation of H2 on Pd110

We report the first six-dimensional quantum dynamical study of the dissociative adsorption of H(2) on a (110) surface. We have performed quantum coupled-channel calculations for the system H(2)/Pd(110) based on a potential energy surface (PES) that was derived from ab initio electronic structure calculations. In particular, we have focused on the effects of the corrugation and anisotropy of the PES on the H(2) dissociation probability. Our results agree well with the available experimental data for the sticking probability as a function of the initial kinetic energy and the angle of incidence. Because of the coupling between the anisotropy and corrugation of the potential energy surface our calculations predict an unusual rotational heating and a rather small rotational alignment in desorption.