Kinetic analysis of an efficient DNA-dependent TNA polymerase

alpha-l-Threofuranosyl nucleoside triphosphates (tNTPs) are tetrafuranose nucleoside derivatives and potential progenitors of present-day beta-d-2'-deoxyribofuranosyl nucleoside triphosphates (dNTPs). Therminator DNA polymerase, a variant of the 9 degrees N DNA polymerase, is an efficient DNA-directed threosyl nucleic acid (TNA) polymerase. Here we report a detailed kinetic comparison of Therminator-catalyzed TNA and DNA syntheses. We examined the rate of single-nucleotide incorporation for all four tNTPs and dNTPs from a DNA primer-template complex and carried out parallel experiments with a chimeric DNA-TNA primer-DNA template containing five TNA residues at the primer 3'-terminus. Remarkably, no drop in the rate of TNA incorporation was observed in comparing the DNA-TNA primer to the all-DNA primer, suggesting that few primer-enzyme contacts are lost with a TNA primer. Moreover, comparison of the catalytic efficiency of TNA synthesis relative to DNA synthesis at the downstream positions reveals a difference of no greater than 5-fold in favor of the natural DNA substrate. This disparity becomes negligible when the TNA synthesis reaction mixture is supplemented with 1.25 mM MnCl(2). These results indicate that Therminator DNA polymerase can recognize both a TNA primer and tNTP substrates and is an effective catalyst of TNA polymerization despite changes in the geometry of the reactants.     

Frontispiece: BIAN-NHC Ligands in Transition-Metal-Catalysis: A Perfect Union of Sterically Encumbered,Electronically Tunable N-Heterocyclic Carbenes?

The discovery of NHCs (NHC = N-heterocyclic carbenes) as ancillary ligands in transition-metal-catalysis ranks as one of the most important developments in synthesis and catalysis. It is now well-recognized that the strong σ-donating properties of NHCs along with the ease of scaffold modification and a steric shielding of the N-wingtip substituents around the metal center enable dramatic improvements in catalytic processes, including the discovery of reactions that are not possible using other ancillary ligands. In this context, although the classical NHCs based on imidazolylidene and imidazolinylidene ring systems are now well-established, recently tremendous progress has been made in the development and catalytic applications of BIAN-NHC (BIAN = bis(imino)acenaphthene) class of ligands. The enhanced reactivity of BIAN-NHCs is a direct result of the combination of electronic and steric properties that collectively allow for a major expansion of the scope of catalytic processes that can be accomplished using NHCs. BIAN-NHC ligands take advantage of (1) the stronger σ-donation, (2) lower lying LUMO orbitals, (3) the presence of an extended π-system, (4) the rigid backbone that pushes the N-wingtip substituents closer to the metal center by buttressing effect, thus resulting in a significantly improved control of the catalytic center and enhanced air-stability of BIAN-NHC-metal complexes at low oxidation state. Acenaphthoquinone as a precursor enables facile scaffold modification, including for the first time the high yielding synthesis of unsymmetrical NHCs with unique catalytic properties. Overall, this results in a highly attractive, easily accessible class of ligands that bring major advances and emerge as a leading practical alternative to classical NHCs in various aspects of catalysis, cross-coupling and C−H activation endeavors.     

Structural Characterization of N‐Alkylated Twisted Amides: Consequences for Amide Bond Resonance and N−C Cleavage

Herein, we describe the first structural characterization of N‐alkylated twisted amides prepared directly by N‐alkylation of the corresponding non‐planar lactams. This study provides the first experimental evidence that N‐alkylation results in a dramatic increase of non‐planarity around the amide N?C(O) bond. Moreover, we report a rare example of a molecular wire supported by the same amide C=O‐Ag bonds. Reactivity studies demonstrate rapid nucleophilic addition to the N?C(O) moiety of N‐alkylated amides, indicating the lack of n_N to π^*_C=O conjugation. Most crucially, we demonstrate that N‐alkylation activates the otherwise unreactive amide bond towards σ N?C cleavage by switchable coordination.     

Phase polymorphism and thermal decomposition of hexadimethylsulphoxidemagnesium(II) chlorate(VII)

Differential scanning calorimetry (DSC) measurements were performed over the temperature range 93–480 K and three enantiotropic (at 323, 409, and 461 K) and one monotropic (at 271 K) phase transitions were detected. Thus, four solid phases (three of them stable and one metastable) and one liquid phase were found. It was concluded, from the entropy change (ΔS) values of these phase transitions that two of them are stable rotational phases and two are crystalline phases (one stable and one metastable). The thermal decomposition of [Mg((CH₃)₂SO)₆](ClO₄)₂, which was studied using thermogravimetry (TG) with simultaneous differential thermal analysis (SDTA), takes place in two main stages. The gaseous products of the decomposition were identified on-line by a quadruple mass spectrometer (QMS). In the first stage, which starts just above ca. 432 K, the compound loses two dimethylsulphoxide (DMSO) molecules per one formula unit. In the second stage (502–673 K) [Mg(DMSO)₄](ClO₄)₂ decomposes explosively and Cl₂, O₂, H₂, and MgSO₄ are finally produced.     

Atomic charge distribution in 4-isopropylphenol molecule derived from atomic polar tensors

On the basis of the calculated atomic polar tensors the generalized atomic polar tensor charges have been calculated for 4-isopropylphenol (4-IP) and related compounds: benzene, quinone, phenol and p-nitroaniline (p-NA). The second order Möller–Plesset perturbation method and Huzinaga–Dunning's double valence ζ basis set supplemented by d polarisation function on heavy atoms and p on hydrogen atoms (D95V^**) have been used. Analysis of the atomic charges has been done. It is found that the phenyl rings of the 4-IP and p-NA molecules have an intermediate structure between the aromatic ring and the quinoid one.     

Directed evolution of ATP binding proteins from a zinc finger domain by using mRNA display

Antibodies have traditionally been used for isolating affinity reagents to new molecular targets, but alternative protein scaffolds are increasingly being used for the directed evolution of proteins with novel molecular recognition properties. We have designed a combinatorial library based on the DNA binding domain of the human retinoid-X-receptor (hRXRalpha). We chose this domain because of its small size, stable fold, and two closely juxtaposed recognition loops. We replaced the two loops with segments of random amino acids, and used mRNA display to isolate variants that specifically recognize adenosine triphosphate (ATP), demonstrating a significant alteration of the function of this protein domain from DNA binding to ATP recognition. Many novel independent sequences were recovered with moderate affinity and high specificity for ATP, validating this scaffold for the generation of functional molecules.     

Luminescence efficiency of aromatic carboxylates of europium and terbium when methylene bridges and nitro groups are present in the ligands

We discuss the possibility of optimizing the brightness of luminescence for phenylcarboxylates, naphthylcarboxylates, and indolylcarboxylates of europium and terbium and their adducts with 1,10-phenanthroline and 2,2′-bipyridine by modifying the ligands. We have studied the efficiency of luminescence and luminescence excitation. We consider the effect of blocking energy transfer from the ligands to the Eu³⁺ and Tb³⁺ ions by methylene (-CH₂-) bridges dividing the π-electron system of the ligands into two parts and by the electronacceptor nitro group (-NO₂). We have analyzed the pathways for transfer and degradation of the excitation energy at 77 K and 300 K. From the phosphorescence spectra of gadolinium salts, we have determined the energies of the lowest excited triplet states of the ligands. We consider the effect of the relative positions of the triplet levels of the ligands and the excited levels of the Eu³⁺ and Tb³⁺ ions on the luminescence efficiency. We found channels for dissipation of the excitation energy via the ππ* and nπ* states of the aromatic system of the carboxylate and the NO₂ group. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 74, No. 1, pp. 48–54, January–February, 2007.     

Artificial lantipeptides from in vitro translations

We have devised a protocol for enzyme-free insertion of dehydroalanine, dehydrobutyrine and thioether crosslinks into translated peptides. In vitro translation using 4-selenalysine and 4-selenoisoleucine as substitutes for lysine and isoleucine yields peptides that can be converted to polycyclic structures using mild chemistry in water. This methodology presents a gateway for exploring the potential of artificial lantipeptides as scaffolds for drug development.     

Synthesis of alpha-L-threofuranosyl nucleoside triphosphates (tNTPs)

[structure: see text] The alpha-l-threofuranosyl nucleoside triphosphates of T, G, and D (tTTP, tGTP, and tDTP) were synthesized from the described 2'-O-DMT-protected derivatives using the Eckstein method, while the corresponding C derivative (tCTP) was prepared from the 2'-O-acetyl derivative. The prepared alpha-l-threofuranosyl nucleoside triphosphates, despite being one carbon shorter than the native 2'-deoxyfuranosyl nucleoside triphosphates, are effective substrates for selected DNA polymerases.     

In Vitro Selection of Specific Ligand-binding Nucleic Acids

In vitro selection is a method that allows the simultaneous screening of very large numbers of nucleic acid molecules for a wide range of properties from binding characteristics to catalytic properties; moreover, the isolation of the very rare functional molecules becomes possible. Binding sites between proteins and nucleic acids, for example, have been evaluated by this methodology in order to gain information about protein/nucleic acid interactions. Structure and function of catalytic RNA (“ribozymes”) has been studied by in vitro selection and has led to new ribozymes with improved catalytic function. Substrate specificity of catalytic RNA has been changed and has led to a ribozyme that cleaves DNA. Other applications include the isolation of nucleic acids that bind specifically to small organic molecules and of RNA molecules that form triple helices with double-stranded DNA. In this article we discuss the background, design, and results of in vitro genetic experiments, which bridge biochemical/molecular biological and organic chemical approaches to molecular recognition.