Nonenzymatic oligomerization reactions on templates containing inosinic acid or diaminopurine nucleotide residues.

The template-directed oligomerization of nucleoside-5'-phosphoro-2-methyl imidazolides on standard oligonucleotide templates has been studied extensively. Here, we describe experiments with templates in which inosinic acid (I) is substituted for guanylic acid, or 2,6-diaminopurine nucleotide (D) for adenylic acid. We find that the substitution of I for G in a template is strongly inhibitory and prevents any incorporation of C into internal positions in the oligomeric products of the reaction. The substitution of D for A, on the contrary, leads to increased incorporation of U into the products. We found no evidence for the template-directed facilitation of oligomerization of A or I through A-I base pairing. The significance of these results for prebiotic chemistry is discussed.     

Nonenzymatic recombination of RNA by means of transesterification

Coupled nonenzymatic cleavage/ligation of oligoribonucleotides catalyzed by magnesium ions afforded longer RNA molecules with a new sequence. The efficiency of formation of ligation products reaches 6%. The possible role of this reaction in the evolution of the RNA world is discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2413–2419, December, 2007.     

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure.

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine. Comparison of the oligomerization efficiencies on HNA, RNA, and DNA decacytidylate templates under various conditions suggests strongly that only nucleic acid double helices with the A structure support efficient template-directed synthesis when 5'-phosphoroimidazolides of nucleosides are used as substrates.     

TNA synthesis by DNA polymerases

Threose nucleic acid (TNA), which has a repeat unit one atom shorter than that of DNA, is capable of Watson-Crick base pairing with DNA, RNA, and TNA. Because of its chemical simplicity, TNA is considered to be a possible progenitor of RNA. As an initial step toward developing the molecular tools necessary to investigate the functional capabilities of TNA by in vitro selection, we have screened a variety of DNA polymerases for TNA synthesis activity on a DNA template. We wish to report that several polymerases show surprisingly good ability to synthesize TNA using alpha-l-threofuranosyl thymidine-3'-triphosphate as a substrate.     

Pyrene aromatic arrays on RNA duplexes as helical templates

RNA oligomers having multiple (2 to 4) pyrenylmethyl substituents at the 2'-O-sugar residues were synthesized. UV-melting studies showed that the pyrene-modified RNAs could form duplexes with complementary RNA sequences without loss of thermal stability. Absorption, fluorescence, and circular dichroism (CD) spectra revealed that the incorporated pyrenes projected toward the outside of A-form RNA duplexes and assembled in helical aromatic arrays along the minor grooves of the RNA duplexes. Results of computer simulations agreed with the assembled structures of the pyrenes. The helical pyrene arrays exhibited remarkably strong excimer fluorescence, which was dependent on the sequence contexts of RNA duplexes.     

Detection of Potential TNA and RNA Nucleoside Precursors in a Prebiotic Mixture by Pure Shift Diffusion‐Ordered NMR Spectroscopy

In the context of prebiotic chemistry, one of the characteristics of mixed nitrogenous‐oxygenous chemistry is its propensity to give rise to highly complex reaction mixtures. There is therefore an urgent need to develop improved spectroscopic techniques if onerous chromatographic separations are to be avoided. One potential avenue is the combination of pure shift methodology, in which NMR spectra are measured with greatly improved resolution by suppressing multiplet structure, with diffusion‐ordered spectroscopy, in which NMR signals from different species are distinguished through their different rates of diffusion. Such a combination has the added advantage of working with intact mixtures, allowing analyses to be carried out without perturbing mixtures in which chemical entities are part of a network of reactions in equilibrium. As part of a systems chemistry approach towards investigating the self‐assembly of potentially prebiotic small molecules, we have analysed the complex mixture arising from mixing glycolaldehyde and cyanamide, in a first application of pure shift DOSY NMR to the characterisation of a partially unknown reaction composition. The work presented illustrates the potential of pure shift DOSY to be applied to chemistries that give rise to mixtures of compounds in which the NMR signal resolution is poor. The direct formation of potential RNA and TNA nucleoside precursors, amongst other adducts, was observed. These preliminary observations may have implications for the potentially prebiotic assembly chemistry of pyrimidine threonucleotides, and therefore of TNA, by using recently reported chemistries that yield the activated pyridimidine ribonucleotides.     

Thermal oligomerization of isophthalonitrile catalyzed by o-carborane

The thermal reaction of equimolar quantities of isophthalonitrile and o-carborane has been shown to produce an adduct oligomer of isophthalonitrile. The structure was determined to involve condensation of three to five isophthalonitrile molecules to form a triazine-type system. This type of bonding gave rise to a trimer and pentamer. Further, the reaction was a homogeneous liquid phase reaction in which o-carborane is involved in a catalytic manner in the oligomerization. The overall reaction has first-order kinetics with an activation energy of 32.2 kcal/mole.     

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.     

Efficient transfer of information from hexitol nucleic acids to RNA during nonenzymatic oligomerization.

Hexitol nucleic acids (HNAs) are DNA analogues that contain the standard nucleoside bases attached to a phosphorylated 1,5-anhydrohexitol backbone. We find that HNAs support efficient information transfer in nonensymatic template-directed reactions. HNA heterosequences appeared to be superior to the corresponding DNA heterosequences in facilitating synthesis of complementary oligonucleotides from nucleoside-5'-phosphoro-2-methyl imidazolides.     

Multistep small-molecule synthesis programmed by DNA templates

The translation of DNA sequences into synthetic products is a key requirement of our approach to evolving synthetic molecules through iterated cycles of translation, selection, and amplification. Here we report general linker and purification strategies for sequence-specific DNA-templated synthesis that collectively enable the product of a DNA-templated reaction to be isolated and to undergo subsequent DNA-templated reactions. Using these strategies, we have achieved the first multistep nucleic acid-templated small-molecule syntheses to generate two different molecules. In addition to representing a method for translating DNA templates sequence-specifically into corresponding multistep synthetic products, our findings also provide experimental support for previously proposed models invoking multistep nucleic acid-templated synthesis as mediating the prebiotic translation of replicable information into the earliest functional molecules.     

Novel macrocyclic templates by ring enlargement of ansa-steroids

Ring enlargement of ansa-steroids leads to a variety of novel templates which are suitable for the preparation of diverse libraries of natural product derivatives. Key steps for the synthesis of these highly functionalized templates were either an ozonolysis-derivatization-ring closing metathesis-sequence or a macrolactonization.     

Template-directed synthesis using the heterogeneous templates produced by montmorillonite catalysis. A possible bridge between the prebiotic and RNA worlds

The synthesis of oligoguanylates [oligo(G)s] is catalyzed by a template of oligocytidylates [oligo(C)s] containing 2',5'- and 3',5'-linked phosphodiester bonds with and without incorporated C5'ppC groupings. An oligo(C) template containing exclusively 2',5'-phosphodiester bonds also serves as a template for the synthesis of complementary oligo(G)s. The oligo(C) template was prepared by the condensation of the 5'-phosphorimidazolide of cytidine on montmorillonite clay. These studies establish that RNA oligomers prepared by mineral catalysis, or other routes on the primitive earth, did not have to be exclusively 3',5'-linked to catalyze template-directed synthesis, since oligo(C)s containing a variety of linkage isomers serve as templates for the formation of complementary oligo(G)s. These findings support the postulate that origin of the RNA world was initiated by the RNA oligomers produced by polymerization of activated monomers formed by prebiotic processes.     

Nickel-based ethylene oligomerization catalysts supported by PNSiP ligands

A series of nickel (II) complexes bearing silicon bridged diphosphines ligands (PNSiP) have been synthesized and characterized. All nickel precatalysts, activated with ethylaluminum dichloride (EtAlCl₂), exhibited moderate to high activities for ethylene dimerization to butylene. The in situ nickel precatalysts formed by mixing N-cyclopentyl-N-((diphenylphosphanyl)dimethylsilyl)-1,1-diphenylphosphanamine (L2) with NiBr₂(DME) showed high catalytic activity (2.40 × 10⁸ g/(mol_Ni·h)) and high product selectivity (88.6%) towards butene using methylcyclohexane as solvent at 1.0 MPa ethylene pressure and 45°C temperature, no polyethylene(PE) was observed. Ligand backbone tuning of PNSiP-based catalytic systems help in precise understanding of steric bulk variation effects on catalytic performance.     

Enzymatic silicone oligomerization catalyzed by a lipid-coated lipase

A lipid (1)-coated lipase can catalyze the oligomerization of diethoxydimethylsilane (DEDMS) in isooctane containing 2wt% water, where the polymerization occurs at the OH group of the coating lipid (1) in the enzyme cavity.     

Self-assembling vanadium oxide nanotubes by organic molecular templates

Vanadium oxide nanotubes were synthesized as the main product by hydrothermal self-assembling from ammonium metavanadate (NH(4)VO(3)) and organic molecules as structure-directing templates. Several kinds of templates including primary amines (C(n)H(2n+1)NH(2)), alpha,omega-diamines (H(2)N[CH(2)](n)NH(2)), and quaternary ammonium salt (CTAB) were demonstrated to be appropriate for the formation of nanotubes. The morphologies and structures of the nanotubes were characterized by X-ray powder diffraction (XRD), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and thermal gravimetric analysis (TGA). The nanotubes were found forming together with the layered structures and the sheetlike structures. On the basis of the growth mechanism of WS(2) nanotubes proposed by our group, a possible rolling mechanism was proposed, which might be a suitable general formation mechanism for types of nanotubes from lamellar structures.