1965 Heidelberg vs Otterbein Football Program

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Investigation of the DNA-dependent cyclohexenyl nucleic acid polymerization and the cyclohexenyl nucleic acid-dependent DNA polymerization

DNA polymerases from different evolutionary families [Vent (exo−) DNA polymerase from the B-family polymerases, Taq DNA polymerase from the A-family polymerases and HIV reverse transcriptase from the reverse transcriptase family] were examined for their ability to incorporate the sugar-modified cyclohexenyl nucleoside triphosphates. All enzymes were able to use the cyclohexenyl nucleotides as a substrate. Using Vent (exo−) DNA polymerase and HIV reverse transcriptase, we were even able to incorporate seven consecutive cyclohexenyl nucleotides. Using a cyclohexenyl nucleic acid (CeNA) template, all enzymes tested were also able to synthesize a short DNA fragment. Since the DNA-dependent CeNA polymerization and the CeNA-dependent DNA polymerization is possible to a limited extend, we suggest CeNA as an ideal candidate to use in directed evolution methods for the development of a polymerase capable of replicating CeNA

Asymmetric Synthesis of New β-Lactam Lipopeptides as Bacterial Signal Peptidase I Inhibitors

International audienceThe transmembrane bacterial enzyme, signal peptidase I, is recognized as being a promising target for reducing the emergence of drug resistance. The asymmetric synthesis and the biological evaluation of original β-lactam lipopeptides have been performed to discover potent signal peptidase inhibitors. The importance of the azetidinone motif of these lipopeptides has been demonstrated and can serve as a starting point to exploit and improve the reactivity of the β-lactam in peptidomimetics

Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides

Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties. In order to study the conformation of cyclohexenyl nucleosides by NMR, the HexRot program was developed to calculate conformations from scalar coupling constants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the thermodynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between (2)H(3) (N-type) and (2)H(3) (S-type) is 1.8 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleoside (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 4–20 kJ/mol). The flexibility of the cyclohexenyl nucleoside was demonstrated by the fast equilibrium between two conformational states that was observed in a CeNA-U monomer, combined with the (2)H(3) conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the (2)H(3) conformation when incorporated in a d(5′-GCGT*GCG-3′)/d(5′-CGCACGC-3′) duplex, as determined by the NMR spectroscopy. This represents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences

Synthesis and conformational analysis of 1-[2,4-dideoxy-4-C-hydroxymethyl-alpha-L-lyxopyranosyl]thymine

Previously different types of nucleosides with a six-membered carbohydrate moiety have been evaluated for their potential antiviral and antibiotic properties and as building blocks in nucleic acid synthesis. However, a pyranose nucleoside with a 1,4-substitution pattern like 1-[2,4-dideoxy-4-C-hydroxymethyl-alpha-L-lyxopyranosyl]thymine (4) has not been studied yet. Modeling suggested that this nucleoside would show the (4)C(1) conformation in contrast to anhydrohexitol nucleosides (1) whose most stable conformation is (1)C(4). The key to the synthesis of 4 involves the stereoselective introduction of the hydroxymethyl group onto the C-4 carbon of the pyranose sugar. Attempts to achieve this via hydroboration/oxidation of a C-4'-exocyclic vinylic intermediate selectively yielded the undesired a-directed hydroxymethyl group. Therefore, we envisaged another approach in which the C-4 substituent was introduced upon treatment of 2,3-O-isopropylidene-1-O-methyl-4-O-phenoxythiocarbonyl-alpha-L-lyxopyranose with beta-tributylstannyl styrene. This allowed stereoselective beta-directed introduction of a 2-phenylethenyl group at C-4, which was converted via oxidation/reduction (OsO(4), NaIO(4)/NaBH(4)) into the desired 4-hydroxymethyl group (20). The resulting 1-O-methyl-2,3,6-tri-O-acetyl-protected sugar was coupled with silylated thymine, using SnCl(2) as Lewis acid (22). After suitable protection, Barton deoxygenation of the 2'-hydroxyl function of the obtained ribo-nucleoside yielded the desired 2'-deoxynucleoside 4, indeed showing the expected equatorial orientation of the thymine ring ((4)C(1))

Synthesis of 1,5‐Anhydrohexitol Building Blocks for Oligonucleotide Synthesis

This unit describes in detail, the optimized preparations of 1,5‐anhydrohexitol and the 1,5‐anhydrohexitol building blocks for oligonucleotide synthesis (hG, hA, hC, hT).Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143593/1/cpnc0109.pd

Post-transcriptional modification mapping in the Clostridium acetobutylicum 16S rRNA by mass spectrometry and reverse transcriptase assays

Post-transcriptional modifications in ribosomal RNA are believed to fine-tune the RNA functions. The present study describes the characterization of the post-transcriptional modifications in Clostridium acetobutylicum 16S rRNA, using high-pressure liquid chromatography (HPLC) coupled to electrospray ionization mass spectrometry and reverse transcriptase assays. The combination of these techniques allowed the identification of eleven modified nucleosides, which were mapped onto the rRNA sequence. The C. acetobutylicum modification map is similar to that of Escherichia coli, with the majority of the modifications near functionally important sites in the rRNA. Although, in general, the number of modifications in rRNA is smaller than in tRNA, the conservation of the modification sites seems to indicate that the post-transcriptional modifications in 16S rRNA provide a necessary prerequisite for the ribosomal function

The naturally occurring N6-threonyl adenine in anticodon loop of Schizosaccharomyces pombe tRNA(i) causes formation of a unique U-turn motif

Modified nucleosides play an important role in structure and function of tRNA. We have determined the solution structure of the anticodon stem–loop (ASL) of initiator tRNA of Schizosaccharomyces pombe. The incorporation of N6-threonylcarbamoyladenosine at the position 3′ to the anticodon triplet (t(6)A37) results in the formation of a U-turn motif and enhances stacking interactions within the loop and stem regions (i.e. between A35 and t(6)A37) by bulging out U36. This conformation was not observed in a crystal structure of tRNAi including the same modification in its anticodon loop, nor in the solution structure of the unmodified ASL. A t(6)A modification also occurs in the well studied anti-stem–loop of lys-tRNA(UUU). A comparison of this stem–loop with our structure demonstrates different effects of the modification depending on the loop sequence

Synthesis of Modified Peptidoglycan Precursor Analogues for the Inhibition of Glycosyltransferase.

The peptidoglycan glycosyltransferases (GTs) are essential enzymes that catalyze the polymerization of glycan chains of the bacterial cell wall from lipid II and thus constitute a validated antibacterial target. Their enzymatic cavity is composed of a donor site for the growing glycan chain (where the inhibitor moenomycin binds) and an acceptor site for lipid II substrate. In order to find lead inhibitors able to fill this large active site, we have synthesized a series of substrate analogues of lipid I and lipid II with variations in the lipid, the pyrophosphate, and the peptide moieties and evaluated their biological effect on the GT activity of E. coli PBP1b and their antibacterial potential. We found several compounds able to inhibit the GT activity in vitro and cause growth defect in Bacillus subtilis . The more active was C16-phosphoglycerate-MurNAc-(l-Ala-d-Glu)-GlcNAc, which also showed antibacterial activity. These molecules are promising leads for the design of new antibacterial GT inhibitors

Ontological simulation for educational process organisation in a higher educational institution

Following the new-generation standards is needed to form a task list connected with planning and organizing of an academic process, structure and content formation of degree programmes. Even when planning the structure and content of an academic process, one meets some problems concerning the necessity to assess the correlation between degree programmes and demands of educational and professional standards and to consider today's job-market and students demands. The paper presents examples of ontological simulations for solutions of organizing educational process problems in a higher educational institution and gives descriptions of model development. The article presents two examples: ontological simulation when planning an educational process in a higher educational institution and ontological simulation for describing competences of an IT-specialist. The paper sets a conclusion about ontology application perceptiveness for formalization of educational process organization in a higher educational institution