Studies on transfer ribonucleic acids and related compounds. VI. Synthesis of yeast alanine transfer ribonucleic acid 3'-terminal nonanucleotides and 5'-terminal hexanucleotides

Mousy off-flavor of wine: precursors and biosynthesis of the causative N-heterocycles 2-ethyltetrahydropyridine, 2-acetyltetrahydropyridine, and 2-acetyl-1-pyrroline by Lactobacillus hilgardii DSM 20176

The N-heterocyclic bases, 2-ethyltetrahydropyridine (1), 2-acetyl-1-pyrroline (2), and 2-acetyltetrahydropyridine (3) are associated with the occurrence of mousy off-flavor in wine. The biosynthesis of these N-heterocycles by the wine lactic acid bacterium, Lactobacillus hilgardii DSM 20176, was studied by high-cell-density incubation in combination with a minimal chemically defined N-heterocycle assay medium. The key components of the defined N-heterocycle assay medium included D-fructose, ethanol, L-lysine, L-ornithine, and mineral salts. N-heterocycle formation was quantitatively determined by gas chromatography-mass spectrometry. The formation of 2 and 3 required the concomitant availability of a fermentable carbohydrate (D-fructose), ethanol, and iron (Fe(2+)). In addition, L-ornithine stimulated the formation of 2 and repressed 3 formation, whereas L-lysine stimulated the formation of 3 and repressed 2 formation. Incorporation of d(6)-ethanol into the acetyl side chain of 2 and 3, and of d(4)-acetaldehyde into the acetyl side chain of 3, confirmed that ethanol and acetaldehyde could serve as major side chain precursors. A pathway for the formation of 2 and 3 by heterofermentative lactic acid bacteria is proposed involving the interaction of accumulated C-2 intermediates from the heterolactic pathway and N-heterocyclic intermediates derived from the metabolism of L-ornithine and L-lysine.

Chromatography on Sephadex LH20 as an efficient purification step after removal of internucleotide 2,2,2-trichloroethyl protective groups from oligoribonucleotide phosphotriesters

Chromatography on Sephadex LH20, in a linear gradient of methanol in 0.02M TEAB buffer pH 7.5, is proposed as a fast and efficient method for the isolation and purification of protected oligoribonucleotide phosphodiesters obtained by deprotection of internucleotide phosphotriesters, and for the monitoring of the deprotection step itself. Its utility is shown on the example of removal of 2,2,2-trichloroethyl groups from oligoribonucleotide phosphotriester I of sequence CCCAUAA by two methods: /1/ reductive elimination with zinc in the presence of acetylacetone modified as presented here, and /2/ hydrogenolytic dehalogenation over palladium in pyridine. This method of chromatography on Sephadex LH20 is used as a key purification step during the removal of 2,2,2-trichloroethyl groups from I by method /1/ and allows to raise the yield of III during fianl deprotection step from 5 to 65%.

Studies on transfer ribonucleic acids and related compounds. XXXII. Synthesis of ribonucleotides corresponding to residues 1-5 and 6-10 of tRNAfMet from E. coli and their base conversion analogs

E. Coli tRNAfMet fragments, C-G-C-G-Gp (bases 1-5), U-G-C-G-Gp (base 1 transition, analog) pG-G-C-G-Gp (base 1 transversion analog) and pG-G-s4U-G-Gp (bases 6-10) were synthesized by triester methods using 2'-O-(o-nitrobenzyl) nucleotides including a 3',5'-bisphosphorylated guanosine derivative. The s4U containing pentanucleotide was derived from the pG-G-C-G-Gp by treatment with liquid hydrogen sulfide.

Joining of 3'-modified oligonucleotides by T4 RNA ligase. Synthesis of a heptadecanucleotide corresponding to the bases 61--77 from Escherichia coli tRNAfMet

Chemically synthesized fragments corresponding to the 3' end of tRNAfMet from Escherichia coli were joined by T4-induced RNA ligase to yield a heptadecanucleotide (bases 61--77). The 3' terminus of C-C-A was modified by introduction of the ethoxymethylidene group to prevent intra- and intermolecular self-joining reactions at the 3' end. The terminal trimer was phosphorylated using polynucleotide kinase and joined to C-A-A with RNA ligase. The hexamer [C-A-A-C-C-A(ethoxymethylidene)] corresponding to bases 72--77 was obtained in a yield of 60%. An undecanucleotide (bases 61--71) which had been synthesized in a yield of 34% by similar enzymatic joining of U-C-C-G-G to pC-C-C-C-C-G was allowed to react with the 5'-phosphorylated hexamer (bases 72--77) using an excess of RNA ligase to yield the heptadecanucleotide U-C-C-G-G-C-C-C-C-C-G-C-A-A-C-C-A (bases 61--77). The product was identified by homochromatography and nearest neighbor analysis.

The chemical synthesis of the anticodon loop of an eukaryotic initiator tRNA containing the hypermodified nucleoside N6-/N-threonylcarbonyl/-adenosine/t6A/1

In this work, the first example of chemical synthesis of oligoribonucleotide containing the hypermodified nucleoside N6-/N-threonylcarbonyl/-adenosine /t6A/ is presented. Synthesis of the heptamer C-C-C-A-U-t6A-A IX, the sequence of which is related to the anticodon loop of the initiator tRNA from yellow lupine, was achieved by: /i/ phosphotriester block synthesis of suitably protected heptamer VI containing an adenosine unit with a free exo-NH2 group, /ii/ highly effective "one-flask" procedure for the transformation of the free exo-NH2 group of adenosine unit of heptamer VI into a N,N'-disubstituted urea system of t6A of heptamer VII /hypermodification/, and /iii/ final deprotection of VIII /32% total yield/ with the use of a new approach for simultaneous hydrogenolysis /PdO-hydrogen-pyridine/ of the p-nitrobenzyl group and 2,2,2-trichloroethyl groups from carboxyl function of t6A and internucleotide phosphates respectively.

Reconstitution of chemically synthesized ribooligonucleotides with naturally occurring tRNA fragments

Chemically synthesized yeast tRNA terminal fragments were reconstituted with natural tRNA fragments which were obtained by partial digestion with RNase T1. The synthetic 3'-nonanucleotide (I) accepted alanine (3% with respect to the intact tRNA) when combined with a 4-fold excess of the natural 5'-quarter and the chemically synthesized hexanucleotide (II) stimulated the aminoacylation of the natural 3'-half molecule.

New phosphoramidates as protecting groups in ribooligonucleotides synthesis

N, N-Dimethyl-p-phenylenediamine, glycine amide and p-methylthioaniline were condensed with uridine 5'-phosphate and the phosphoramidates obtained were tested for their stability in anhydrous pyridine, 50% aqueous pyridine or 80% acetic acid. The p-methylthioanilidate (IIc) was oxidized to give p-methylsulfoxylanilidate of uridine 5'-phosphate (IId) which was found to be 5 times more stable than the p-methylthio compound. The p-methylsulfoxylanilidate of 2'-O-benzoyluridine 3'-phosphate was condensed with the mononucleotide to yield the dinucleotide, MMTrU(OBz)-p-U(OBz)-p in 28% yield.

Stepwise enzymatic oligoribonucleotide synthesis including modified nucleotides

A method has been developed for the routine synthesis of 2'(3')-o-monoacyl ribonucleoside 5'-diphosphates for stepwise synthesis of oligoribonucleotides with Escherichia coli polynucleotide phosphorylase. The use of triethyl orthoisovalerate allows the facile preparation of 2'(3')-o-isovaleryl-UDP, -CDP, -ADP, -GDP, -IDP, -EPLISON-APD, eplison-CDP, and N6-isopentenyl-ADP. The synthesis of N6-isopentenyl-ADP from ADP by N1-alkylation and the Dimroth rearrangement to N6 is reported. The effects of several factors including the nature of the divalent cation, pH, SALT CONCENTRATION, AND TIME ON THE EFFICIENCY OF THE POLYNUCLEOTIDE PHPSPHORYLASE CATALYZED SINGLE ADDITIONS OF THE 2'(3')-O-ISOVALERYL RIBONUCLEOSIDE 5'-DIPHOSPHATES TO AN OLIGORIBONUCLEOTIDE PRIMER ARE REPORTED. The syntheses of many tetranucleoside triphosphates and two pentanucleoside tetraphosphates in yields of 20-75 per cent are reported. The 2'(3')-o-isovaleryl derivatives of IDP, eplison-ADP, eplison-CDP, and N6-isopentenyl-ADP were all accepted by polynucleotide phosphorylase as substrates for the monoaddition reaction. The extension of the method to include the syntheses of oligoribonucleotides containing modified nucleosides offers a means of studying the role s of these modification by the use of relatively simple model compounds.

Studies on transfer ribonucleic acids and related compounds. IX. Ribooligonucleotide synthesis using a photosensitive o-nitrobenzyl protection at the 2'-hydroxyl group

o-Nitrobenzyl group was introduced to the 2'-hydroxyl function of uridine via 2',3'-O-(dibutylstannylene) uridine. The benzylated uridine was protected at the 5'-hydroxyl group with monomethoxytrityl chloride and condensed with 2',3'-O-dibenzoyluridine 5'-phosphate or N,N',2',3'-O-tetrabenzoyladenosine 5'-phosphate using dicyclohexylcarbodiimide (DCC). o-Nitrobenzyl ether linkage of the dinucleotides was removed by UV irradiation with wavelength longer than 320 nm. Deprotected UpU and UpA thus obtained were characterized by RNase A digestion.

Studies on transfer ribonucleic acids and related compounds. 8(1). Further studies on aromatic phosphoramidates as a protecting group for phosphomonoesters

Stability of aromatic phosphoramidates was studied using 2',3'-O-dibenzoyluridine 5'-phosphoramidates and N,2',3'-O-tribenzoylcytidine 5'-phosphate. The effect of dicyclohexylcarbodiimide in this mixture was investigated. Decomposition of the anilidate was slower in the presence of DCC. Substituted anilidates of uridine 5'-phosphate were synthesized and the stability of these amidates in anhydrous pyridine was studied.2'-O-Benzoyluridine 3'-phosphoranilidate and the corresponding beta-naphthylidate were compared in their stabilities in anhydrous pyridine, 50% aqueous pyridine and 80% acetic acid. 2'-O-Benzoyluridine 3'-phosphoro-beta-naphthylidate was used for synthesis of dinucleotides.