A new family of sequence-specific DNA-cleaving agents directed by triple-helical structures: benzopyridoindole-EDTA conjugates

Sequence-specific DNA recognition can be achieved by oligonucleotides that bind to the major groove of oligopyrimidine x oligopurine sequences. These intermolecular structures could be used to modulate gene expression and to create new tools for molecular biology. Here we report the synthesis and biochemical characterization of triple helix-specific DNA cleaving reagents. It is based on the previously reported triplex-specific ligands, benzo[e]pyridoindole (BePI) and benzo[g]pyridoindole (BgPI), covalently attached to ethylenediaminotetraacetic acid (EDTA). In the presence of iron, a reducing agent and molecular oxygen, BgPI-EDTA x FeII but not BePI-EDTA x FeII induced a double-stranded cut in a plasmid DNA at the single site where a triplex-forming oligonucleotide binds. At single nucleotide resolution, it was found that upon triplex formation BePI-EDTA x FeII led to cleavage of the pyrimidine strand and protection of the purine strand. BgPI-EDTA x FeII cleaved both strands with similar efficiency. The difference in cleavage efficiency between the two conjugates was rationalized by the location of the EDTA x FeII moiety with respect to the grooves of DNA (major groove: BePI-EDTA x FeII, minor groove: BgPI-EDTA x FeII). This work paves the way to the development of a new class of triple helix directed DNA cleaving reagents. Such molecules will be of interest for sequence-specific DNA cleavage and for investigating triple-helical structures, such as H-DNA, which could play an important role in the control of gene expression in vivo.     

Production of hybrid 16-membered macrolides by expressing combinations of polyketide synthase genes in engineered Streptomyces fradiae hosts

Combinations of the five polyketide synthase (PKS) genes for biosynthesis of tylosin in Streptomyces fradiae (tylG), spiramycin in Streptomyces ambofaciens (srmG), or chalcomycin in Streptomyces bikiniensis (chmG) were expressed in engineered hosts derived from a tylosin-producing strain of S. fradiae. Surprisingly efficient synthesis of compounds predicted from the expressed hybrid PKS was obtained. The post-PKS tailoring enzymes of tylosin biosynthesis acted efficiently on the hybrid intermediates with the exception of TylH-catalyzed hydroxylation of the methyl group at C14, which was efficient if C4 bore a methyl group, but inefficient if a methoxyl was present. Moreover, for some compounds, oxidation of the C6 ethyl side chain to an unprecedented carboxylic acid was observed. By also expressing chmH, a homolog of tylH from the chalcomycin gene cluster, efficient hydroxylation of the 14-methyl group was restored.     

Diastereoselective formation of cyanohydrins from alpha-alkoxy aldehydes

[reaction: see text] The reaction of alpha-alkoxy aldehydes with Et4NAg(CN)2 or Me3SiCN in the presence of MgBr2 x OEt2 in CH2Cl2 at 0 degrees C gives the corresponding syn cyanohydrins in good yield with high diastereoselectivity. Excess MgBr2 x OEt2 (typically 5 equiv) is required for high diastereoselectivity. Et4NAg(CN)2 (but not Me3SiCN) is sufficiently reactive to give cyanohydrins at -78 degrees C, and higher diastereoselectivity is obtained at this temperature.     

Artificial metalloenzymes for enantioselective catalysis based on biotin-avidin

Homogeneous and enzymatic catalysis offer complementary means to generate enantiomerically pure compounds. Incorporation of achiral biotinylated rhodium-diphosphine complexes into (strept)avidin yields artificial metalloenzymes for the hydrogenation of N-protected dehydroamino acids. A chemogenetic optimization procedure allows one to produce (R)-acetamidoalanine with 96% enantioselectivity. These hybrid catalysts display features reminiscent both of enzymatic and of homogeneous systems.     

The preparation of dimolybdenum(V,V) complexes from molybdenum quadruply bonded metal-metal dimers

Oxidation of quadruply bonded metal-metal dimers in the presence of good π-accepting ligands results in the formation of Mo^V---Mo^V compounds of the type [MO₂(μ-X)₂(Y)(Y′)]²⁺ (X = O or S; Y,Y′ = O,O; S,S; O,S). Reaction of MO₂(O₂CCH₃)₄ with oxygen in the presence of Na₂mnt (mnt = 1,2-dicyanoethylene-2,2-dithiolate) gives [MO₂(μ-S)₂(O)(S)(mnt)₂]²⁻ (1). The compound crystallizes in the monoclinic space group P2₁/c, with cell dimensions a = 19.547(4), b = 15.210(4), c = 18.754(6) Å, β = 101.69(2)°, V= 5460(2) ų, and Z = 4. Similarly, oxidation of o-dichlorobenzene solutions of Mo₂Cl₄(CH₃CN)₄ and 4,4′-dimethyl-2,2′-dipyridyl (dmpby) or, more directly, the reaction of Mo₂Cl₄(dmbpy)₂ with oxygen leads to the formation of a red solid, which was characterized by X-ray crystallography to be Mo₂(μ-O)₂(O)₂(Cl)₂(dmbpy)₂ (2). Red diamond crystals, prepared by slow evaporation of CH₃CN solutions of 2, are trigonal and in the space group P3₁21 with cell dimensions a = 16.135(4), b = 16.135(4), c = 10.709(3) Å, V = 2414.4(13) ų and Z = 3. In both structures, the geometry about each of the molybdenum atoms is a distorted square pyramid with terminal oxygen or sulphur atoms at the apices and in a syn conformation. The molybdenum-molybdenum bond distances of 2.858(1) Å and 2.562(2) Å in structures of 1 and 2, respectively, are typical of other Mo^V---Mo^V dimers and indicative of a single Mo---Mo bond.     

Artificial metalloenzymes: (strept)avidin as host for enantioselective hydrogenation by achiral biotinylated rhodium-diphosphine complexes

We report on the generation of artificial metalloenzymes based on the noncovalent incorporation of biotinylated rhodium-diphosphine complexes in (strept)avidin as host proteins. A chemogenetic optimization procedure allows one to optimize the enantioselectivity for the reduction of acetamidoacrylic acid (up to 96% ee (R) in streptavidin S112G and up to 80% ee (S) in WT avidin). The association constant between a prototypical cationic biotinylated rhodium-diphosphine catalyst precursor and the host proteins was determined at neutral pH: log K(a) = 7.7 for avidin (pI = 10.4) and log K(a) = 7.1 for streptavidin (pI = 6.4). It is shown that the optimal operating conditions for the enantioselective reduction are 5 bar at 30 degrees C with a 1% catalyst loading.     

A priori bounds for approximations of Markov programs

This note determines a priori bounds for B. L. Fox's [J. Math. Anal. Appl., 34 (1971), 665–670] scheme of approximating discounted Markov programs, thus refining bounds recently obtained by D. J. White (Notes in Descision Theory No. 43, University of Manchester, 1977). The approximation scheme focuses careful attention on only a subset of the state space and uses a fixed function to characterize future returns outside the designated subset. The a priori bounds are useful to design the specific approximation, that is, to select the appropriate subset on which the approximation is based.     

Unsupervised cell identification on multidimensional X‐ray fluorescence datasets

A novel approach to locate, identify and refine positions and whole areas of cell structures based on elemental contents measured by X‐ray fluorescence microscopy is introduced. It is shown that, by initializing with only a handful of prototypical cell regions, this approach can obtain consistent identification of whole cells, even when cells are overlapping, without training by explicit annotation. It is robust both to different measurements on the same sample and to different initializations. This effort provides a versatile framework to identify targeted cellular structures from datasets too complex for manual analysis, like most X‐ray fluorescence microscopy data. Possible future extensions are also discussed.