Pyrrole studies part 41. Reactivity of 3,4-diformyl-2,5-dimethylpyrrole with diaminoalkanes. An unusual formation of 2-azafulvenes

3,4-Diformyl-2,5-dimethylpyrrole (1) reacts with ,ω-diamino-alkanes, NH₂(CH₂)_nNH₂t' to form either the potentially tautomeric 2:2 macrocyclic adduct (7a) (8), when N = 2, or the potentially tautomeric 1:1 bicyclic adduct (18) (19), when N = 4, 5, 6, and 12. ¹H and ¹³C N.m.r. spectral data indicate that the 2-azafulvene structures predominate for both types of cycloadducts. Only polymeric material was obtained when N = 3.     

The protection of uracil and guanine residues in oligonucleotide synthesis

The protection of uracil and 2-$\text{N}$-acyl guanine residues with 4-$\text{O}$-phenyl [or 4-$\text{O}$-(2,4-dimethylphenyl)] and 6-$\text{O}$-(2-nitrophenyl) groups as in $\text{7a}$ [or $\text{7b}$] and $\text{9}$, respectively, is described. These $\text{O}$-aryl protecting groups, which appear to withstand the usual conditions of oligonucleotide synthesis, may readily be removed by treatment with 2-nitrobenzaldoximate ions.     

Univalent cation-exchange in organic solvent water and organic solvent-water-phenol mixtures

Selectivity coefficients, K(H)(M), for the exchange of alkali metal ions and ammonium ions with the hydrogen form of ZeoKarb 225 cation-exchange resin have been determined in various organic solvent-water and organic solvent-water-phenol mixtures. There is an increase in K(H)(M) in passing from purely aqueous conditions to media of increasing organic solvent content, frequently with the effect of producing magnified differences and selectivity reversals between one ion and another. The results are discussed in terms of the relationship between K(H)(M) and the reciprocal of the dielectric constant of the medium and also in the light of free energies of transfer of cations between methanol-water systems. The effect of phenol giving a lowering of K(H)(Cs) in methanol-water, of K(H)(K) and K(H)(Na) in ethanol-water and of K(H)(Na) and K(H)(L1) in acetone-water systems cannot be fully reconciled with the mechanism involving bonding proposed by earlier workers.     

Anodic stripping voltammetry of sulphide at a nickel film: towards the development of a reagentless sensor

The determination of sulphide at an electrochemically generated nickel oxide layer at glassy carbon and screen-printed electrodes in acidic media has been examined and appraised. The NiO layer was found to produce a stripping-like signal to sulphide and gave a linear peak current response from 20 to 90 μM. The response was further enhanced by repetitive cycling allowing accumulation of nickel sulphide at the electrode surface such that lower micromolar levels of sulphide (i.e. 5 μM) can be determined. The response at the NiO layer to sulphide is shown to be reproducible over a period of 24 h, thereby offering the development of a disposable amperometric sensor for sulphide.     

The influence of the purine 2-amino group on DNA conformation and stability-II: Synthesis and physical characterization of d[CGT(2-NH2)ACG], d[CGU(2-NH2)ACG], and d[CGT(2-NH2)AT(2-NH2)ACG]

Synthesis of an N-protected derivative of 2-amino-2'-deoxyadenosine (dA') from 2'-deoxyguanosine is reported. The syntheses of several oligodeoxynucleotides containing this modified nucleoside are described, together with physical characterization via melting studies and CD conformational analysis. As expected, the 2-amino group is seen to add to the duplex stability. Although the sequence d(TA')₃ was found to undergo a salt-induced conformational transition, mixed sequences such as d(CGTA'CG) did not display this behavior. All guanine residues present in these sequences were O⁶ protected, either with the cyanoethyl group or the 4-nitrophenylethyl group, to eliminate guanine degradation during phosphorylation and condensation reactions. Procedures for the introduction and removal of these O⁶ protecting groups are described.     

Synthese und Molekülstruktur neuer Ringsysteme aus 1,1,3,3-Tetrachlor-1,3-diphosphapropan

Synthesis and Molecular Structure of new Ring Systems from 1,1,3,3-Tetrachloro-1,3-diphosphapropane 1,1,3,3-Tetrachloro-1,3-diphosphapropane 1 reacts in two different ways to form new heterocycles. Partial oxidation of 1 with tetrachloroorthobenzoquinone furnishes the methylene-bridged λ³P, λ⁵P species 3 . Subsequent reactions with di- and triethylamine lead to the condensed ring system 6 with the P?C bonds connected to a central four-membered ring. Compound 6 displays crystallographic inversion symmetry, a short transannular P? P distance and an extremely distorted tetrahedral coordination geometry at the four-membered ring phosphorus atoms. 1 reacts with 7 to give the heterocycle 8 with a central eight-membered ring involving four phosphorus atoms. The eight – membered ring shows a ?bent”? crown conformation, the condensed five – membered rings display envelope conformation.     

Oxidation reactions of an anionic gallium(I) N-heterocyclic carbene analogue with group 16 compounds

The reactivity of an anionic gallium(I) heterocycle, [K(tmeda)][:Ga([N(Ar)C(H)]2)], Ar = C6H3Pr(i)2-2,6, towards sources of elemental chalcogens and diorgano-dichalcogenides has been investigated and comparisons drawn with the reactivity of the valence isoelectronic N-heterocyclic carbene class of ligand. The reactions of the heterocycle with N2O or (Te)PEt3 yielded the dimeric, dianionic gallium(III) complexes, [K(L)]2[(mu-E)Ga([N(Ar)C(H)]2)]2, E = O, L = tmeda; E = Te, L = THF. Treatment of [K(tmeda)][:Ga([N(Ar)C(H)]2)] with the diphenyl dichalcogenides, PhEEPh, E = Se or Te, gave the one dimensional polymer, [K[(PhSe)2Ga([N(Ar)C(H)]2)]]infinity and the monomeric complex, [K(OEt2)3][(PhTe)2Ga([N(Ar)C(H)]2)], respectively. The X-ray crystal structures of the four complexes are reported.     

S1P1-selective in vivo-active agonists from high-throughput screening: off-the-shelf chemical probes of receptor interactions, signaling, and fate

The essential role of the sphingosine 1-phosphate (S1P) receptor S1P(1) in regulating lymphocyte trafficking was demonstrated with the S1P(1)-selective nanomolar agonist, SEW2871. Despite its lack of charged headgroup, the tetraaromatic compound SEW2871 binds and activates S1P(1) through a combination of hydrophobic and ion-dipole interactions. Both S1P and SEW2871 activated ERK, Akt, and Rac signaling pathways and induced S1P(1) internalization and recycling, unlike FTY720-phosphate, which induces receptor degradation. Agonism with receptor recycling is sufficient for alteration of lymphocyte trafficking by S1P and SEW2871. S1P(1) modeling and mutagenesis studies revealed that residues binding the S1P headgroup are required for kinase activation by both S1P and SEW2871. Therefore, SEW2871 recapitulates the action of S1P in all the signaling pathways examined and overlaps in interactions with key headgroup binding receptor residues, presumably replacing salt-bridge interactions with ion-dipole interactions.     

Plasma total homocysteine measurement by ion-paired reversed-phase HPLC with electrochemical detection

Homocysteine is thought to be a risk factor for vascular disease and this has led to an increase in demand for its assay in clinical laboratories. An HPLC method, incorporating electrochemical detection, for measurement of plasma total homocysteine is presented. The method is simple to perform, precise and suitable for clinical applications.     

Protein fold recognition

Summary An important, yet seemingly unattainable, goal in structural molecular biology is to be able to predict the native three-dimensional structure of a protein entirely from its amino acid sequence. Prediction methods based on rigorous energy calculations have not yet been successful, and best results have been obtained from homology modelling and statistical secondary structure prediction. Homology modelling is limited to cases where significant sequence similarity is shared between a protein of known structure and the unknown. Secondary structure prediction methods are not only unreliable, but also do not offer any obvious route to the full tertiary structure. Recently, methods have been developed whereby entire protein folds are recognized from sequence, even where little or no sequence similarity is shared between the proteins under consideration. In this paper we review the current methods, including our own, and in particular offer a historical background to their development. In addition, we also discuss the future of these methods and outline the developments under investigation in our laboratory.