Conformational Variability in Modified Nucleosides. Crystal and Molecular Structure of 2',3'-O-Isopropylidene Inosine

The crystal structure of 2',3'-O-isopropylidene inosine shows a number of interesting features. The four independent molecules in the asymmetric unit exhibit significant conformational variations. Ribose puckers fall in the O(4')-exo region, unfavourable in unsubstituted nucleosides. Hypoxanthine bases show base-pairing (I.I) in a manner analogous to the guanine self pairs (G.G) in 2',3'-O-isopropylidene guanosine but with a C(2)-H…O(6) hydrogen bond instead of N(2)-H…O(6).

Cyclopentaannulation of allyl alcohols via a radical cyclisation reaction. Total synthesis of 4-epibakkenolide-A

A four step cyclopentaannulation methodology starting from allyl alcohols using 5-exo-trig radical cyclisation as the key reaction, and its application to the total synthesis of 4-epibakkenolide is described.

Synthetic approaches to homogynolides A and B

A four step, efficient and general methodology for the conversion of a cyclic ketone into the corresponding alpha-spiro-beta-methylene-gamma-butyrolactone, the key structural feature present in tricyclic sesquiterpenes bakkanes, has been developed employing a regiospecific 5-exo dig radical cyclisation reaction as the key step. The methodology has been extended to the total synthesis of bakkanes including homogynolide-B and chiral homogynolide-A.

Radical Cyclization Methodology to Lignans: Synthesis of (.+-.)- Enterolactone

Synthesis of enterolactone, the first lignan of human origin, starting from 3-methoxycinnamyl alcohol employing a 5-exo-trig radical cyclisation reaction of mixed bromoacetal as the key step is described.

Unusual ribose conformation in a ternary copper(II) 2?deoxyribonucleotide complex

The ternary metal deoxyribonucleotide complex [Cu(bzim)(5?-dGMP)(H2O)3](bzim = benzimidazole, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate) has been prepared and the structure analysed by X-ray diffraction. The compound crystallizes in the space group P1 with a= 7.069(6), b= 13.959(10), c= 14.204(12)Å, ?= 75.12(6), ?= 94.15(6), ?= 97.98(6)° and Z= 2. The structure was solved by the heavy-atom method and refined by full-matrix least-squares procedures on the basis of 2813 observed [I[gt-or-equal] 3?(I)] reflections to final R and R? values of 0.050 and 0.052 respectively. There are two independent molecules in the asymmetric unit and both copper(II) centres have square-pyramidal co-ordination geometry. An unusual feature of the structure is the co-ordination of the metal by N(7) of the base, in the presence of a ?-aromatic amine, bzim. The structure is stabilized by intermolecular base�bzim stacking. The nucleotides of both the molecules have an anti conformation about the glycosyl bond, and a gauche-gauche conformation about the C(4?)�C(5?) bond. A feature of particular interest is the unusual sugar conformation. The base furanose rings of the two nucleotide molecules adopt C(3?)-exo/C(2?)-endo pucker and C(3?)-exo pucker respectively.

A formal total synthesis of (+/-)-enterolactone

A radical cyclization based methodology has been applied for the formal total synthesis of (+/-)-enterolactone (1), the first lignan isolated from human source. Bromoacetalization reaction of the cinnamyl alcohols 7 and 13 using ethyl vinyl ether and NBS, generated the bromoacetals 8 and 15. The 5-exo-trig radical cyclization reaction of the bromoacetals 8 and 15 with in situ generated catalytic tri-a-butyltin hydride and AIBN furnished a 3 : 2 diastereomeric mixture of the cyclic acetals 9 and 16. Sonochemically accelerated Jones oxidation of the cyclic acetals 9 and 16 yielded the gamma-butyrolactones 10 and 12 completing the formal total synthesis of (+/-)-enterolactone. Alternatively radical cyclization of the bromoacetate 17 furnished a 1 : 2 mixture of the lactone 10 and the reduced product 18.

Synthesis based on cyclohexadienes .23. Total synthesis of 5-epi-pupukean-2-one

A new strategy for the construction of the isotwistane skeleton is reported from easily available cyclohexadienes which involves stereoselective alkylation of a bicyclooctenone derivative and a decarboxylative 5-exo-trig radical cyclisation as the key steps in the total synthesis of 5-epi-pupukean-2-one.

Synthesis based on cyclohexadienes .24. A new total synthesis of pupukean-2-one and a facile entry to copa and ylanga type sesquiterpene skeletons

A novel tandem 5-exo-trig allyl and 3-exo-trig radical cyclisation and rearrangement to copa and ylanga type sesquiterpene skeletons from easily prepared cyclohexadienes is reported, A new total synthesis of pupukean-2-one 8, which belongs to a novel class of sesquiterpenes, involving a 5-exo-trig allyl radical cyclisation as the key step is also reported.

N-4-anisoylcytidine dihydrate

The title compound, C17H19N3O7. 2H(2)O, has C2'-endo, C3'-exo puckering, The orientation of the base with respect to the sugar is anti and the geometry about C4'-C5' is gauche,trans. The angle between the cytidine base and the phenyl ring of the anisoyl group is 15.5(2)degrees.

N-6-anisoyladenosine monohydrate

The title compound, C18H19N5O6. H2O, has a syn conformation about the glycosidic bond. Its furanose ring shows a C2'-endo-C3'-exo twist conformation and trans-gauche geometry about the C4'-C5' bond. The angle between the adenine base and the phenyl ring of the anisoyl group is 22.9 degrees. Adenine and anisoyl groups stack along the b axis at a separation of 3.4 Angstrom.

Biopolymers in nanopores: challenges and opportunities

We review the current status of various aspects of biopolymer translocation through nanopores and the challenges and opportunities it offers. Much of the interest generated by nanopores arises from their potential application to third-generation cheap and fast genome sequencing. Although the ultimate goal of single-nucleotide identification has not yet been reached, great advances have been made both from a fundamental and an applied point of view, particularly in controlling the translocation time, fabricating various kinds of synthetic pores or genetically engineering protein nanopores with tailored properties, and in devising methods (used separately or in combination) aimed at discriminating nucleotides based either on ionic or transverse electron currents, optical readout signatures, or on the capabilities of the cellular machinery. Recently, exciting new applications have emerged, for the detection of specific proteins and toxins (stochastic biosensors), and for the study of protein folding pathways and binding constants of protein-protein and protein-DNA complexes. The combined use of nanopores and advanced micromanipulation techniques involving optical/magnetic tweezers with high spatial resolution offers unique opportunities for improving the basic understanding of the physical behavior of biomolecules in confined geometries, with implications for the control of crucial biological processes such as protein import and protein denaturation. We highlight the key works in these areas along with future prospects. Finally, we review theoretical and simulation studies aimed at improving fundamental understanding of the complex microscopic mechanisms involved in the translocation process. Such understanding is a pre-requisite to fruitful application of nanopore technology in high-throughput devices for molecular biomedical diagnostics.

A stereospecific approach to cis-anti-cis triquinanes

A methodology for the synthesis of compounds containing the cis-anti-cis fused triquinane system has been developed starting from tricyclo[5.2. 1.0(2.6)]deca-4,8-dien-3-(exo)ol 6 involving Ireland ester Claisen rearrangement and intramolecular diazo ketone cyclopropanation reactions as key steps.

Fluctuation quench and hydrophobic collapse of polymers and biopolymers in water-DMSO binary mixture at low DMSO concentration

Binary mixtures have strong influence on activities of polymers and biopolymers even at low cosolvent concentration. Among the several aqueous binary mixtures studied, water-DMSO especially stands out for its unusual behavior at certain specific concentrations of DMSO. In the present work, we study the effect of water-DMSO binary mixture on polymers and biopolymers by taking a simple linear hydrocarbon chain of intermediate length (n = 30) and the protein lysozyme, respectively. We find that at a mole fraction of 0.05 of DMSO (x(DMSO) = 0.05) in aqueous solution, the hydrocarbon chain adopts the collapsed conformation as the most stable and rigid state. In this case of 0.05 mole fraction of DMSO in bulk, the DMSO concentration in the first hydration layer around the polymer is found to be as large as 17%. Formation of such hydrophobic environment around the polymer is the reason for the collapsed state gaining so much stability. Interestingly, similar quench of conformational fluctuation is also observed for the protein investigated. It is observed that in the case of alkane polymer chains, long wavelength fluctuation gets easily quenched, the polymer being purely hydrophobic. However, in case of the protein, quench of fluctuation is prominent only at the hydrophobic surface, and quench of long wavelength fluctuation becomes insignificant for the full protein. As protein contains both hydrophobic and hydrophilic moieties, the extent of quench of conformational fluctuation with respect to that in pure water is almost half for the biopolymer complex (16.83%) than the same for pure hydrophobic polymer chain (32.43%).

Organophotocatalysis in nanostructured soft gel materials as tunable reaction vessels: comparison with homogeneous and micellar solutions

Riboflavin tetraacetate-catalyzed aerobic photooxidation of 1-(4-methoxyphenyl)ethanol was investigated as a model reaction under blue visible light in different soft gel materials, aiming to establish their potential as reaction vessels for photochemical transformations. Three strategies involving different degrees of organization of the catalyst within the gel network were explored, and the results compared to those obtained in homogeneous and micellar solutions. In general, physical entrapment of both the catalyst and the substrate under optimized concentrations into several hydrogel matrices (including low-molecular-weight and biopolymer-based gels) allowed the photooxidation with conversions between 55 and 100% within 120 min (TOF similar to 0.045-0.08 min(-1); k(obs) similar to 0.011-0.028 min(-1)), albeit with first-order rates ca. 1-3-fold lower than in solution under comparable non-stirred conditions. Remarkably, the organogel made of a cyclohexane-based bisamide gelator in CH3CN not only prevented the photodegradation of the catalyst but also afforded full conversion in less than 60 min (TOF similar to 0.167 min(-1); k(obs) similar to 0.073 min(-1)) without the need of additional proton transfer mediators (e. g., thiourea) as it occurs in CH3CN solutions. In general, the gelators could be recycled without detriment to their gelation ability and reaction rates. Moreover, kinetics could be fine-tuned according to the characteristics of the gel media. For instance, entangled fibrillar networks with relatively high mechanical strength were usually associated with lower reaction rates, whereas wrinkled laminated morphologies seemed to favor the reaction. In addition, the kinetics results showed in most cases a good correlation with the aeration efficiency of the gel media.

Helicobacter pylori DprA alleviates restriction barrier for incoming DNA

Helicobacter pylori is a Gram-negative bacterium that colonizes human stomach and causes gastric inflammation. The species is naturally competent and displays remarkable diversity. The presence of a large number of restriction-modification (R-M) systems in this bacterium creates a barrier against natural transformation by foreign DNA. Yet, mechanisms that protect incoming double-stranded DNA (dsDNA) from restriction enzymes are not well understood. A DNA-binding protein, DNA Processing Protein A (DprA) has been shown to facilitate natural transformation of several Gram-positive and Gram-negative bacteria by protecting incoming single-stranded DNA (ssDNA) and promoting RecA loading on it. However, in this study, we report that H. pylori DprA (HpDprA) binds not only ssDNA but also dsDNA thereby conferring protection to both from various exo-nucleases and Type II restriction enzymes. Here, we observed a stimulatory role of HpDprA in DNA methylation through physical interaction with methyltransferases. Thus, HpDprA displayed dual functional interaction with H. pylori R-M systems by not only inhibiting the restriction enzymes but also stimulating methyltransferases. These results indicate that HpDprA could be one of the factors that modulate the R-M barrier during inter-strain natural transformation in H. pylori.