Efficient synthesis of 3'-amino-3'-deoxythymidine derivatives

An efficient method of reduction of 3'-azido-3'-deoxythymidine and its 5'-protected derivatives to 3'-aminothymidine derivatives on a palladium catalyst using ammonium formate as a source of hydrogen was suggested.     

Inhibition of ribonucleases by ribonucleotides and transition state analogs in cell-free extracts from Ehrlich ascites tumor cells.

We investigated the ribonucleolytic breakdown of poly(U), poly(A), RNA trascribed from calf thymus DNA with E. coli RNA polymerase, ribosomal RNA, tRNA and mengovirus RNA by an enzyme fraction obrained from a postribosomal supernatant of Ehrlich ascites tumor cells. The single-stranded homopolyribonucleotides are preferentially degraded by the enzyme fraction with the production of ribonucleoside 5'-monophosphates. The RNase activity is completely dependent on the presence of Mg2+ ions and is highest at Mg2+ and K+ concentrations optimal for cell-free protein synthesis. Ribonucleoside 5'-monophosphates, ribonucleoside 2'(3')-monophosphates, ribonucleoside 2'(3'),5'-bisphosphates and transition state analogs consisting of vanadyl sulfate and either ribonucleosides or ribonucleoside 5'-monophosphates in a molar ratio 1:1 inhibit the ribonucleolytic activity of the enzyme fraction. The ribonucleoside 2'(3'),5'-bisphosphates and the transition state analogs are the most effective inhibitors. However, only in the presence of ribonucleoside 2'(3'),5'-bisphosphates a concomitant stimulation by 50 to 60% of poly(U)-directed polyphenylalanine synthesis is observed; all the other RNase inhibitors tested also inhibit polypeptide synthesis. The results of preliminary experiments show that poly(U) and ribonucleoside 2'(3'),5'-bisphosphates are well suited as ligands for affinity chromatography of ribonucleases from Ehrlich ascites tumor cells.     

3'-(N-hydroxyimino)-2',3-dideoxynucleosides and their derivatives: synthesis, broad spectrum antiviral properties and synthetical application for the preparation of other nucleoside analogues.

A series of 3'-(N-hydroxyimino)-2',3'-dideoxynucleosides bearing different nucleic bases has been prepared. In vitro antiviral activity studies showed that among these compounds the thymine derivative possesses significant activity against HIV, HSV, EBV and HBV. Conveniently 5'-protected 3'-(N-hydroxyimino)-2',3'-dideoxythymidine was further used as a synthon for the preparation of other nucleoside analogues.     

Absence of detectable RNA ligase activity in eukaryotic cells.

Reports of the existence of eukaryotic RNA ligases may be incorrect. Evidence for this activity has been based upon the conversion of [5′-32p]-terminated oligoribonucleotides to an alkaline phosphatase resistant form and upon the detection of radioactive ribonucleoside monophosphates after alkaline hydrolysis of the reaction products. Although we have in part confirmed these observations, we find the labeled ribonucleoside monophosphate to be the 5′-isomer, and not the expected 2′ (3′)-isomer. In addition, roughly equivalent amounts of ribonucleoside monophosphate were observed whether or not alkaline hydrolysis was performed. We conclude that the existence of RNA ligase activity in eukaryotic cells is suspect.     

Attempted stereoselective synthesis of P-chiral analogues of oligodeoxyribonucleotides

Reaction of diastereomeric 5'MMT-nucleoside 3'-O-(4-nitrophenylmethanephosphate) or 3'-O-[O-(4-nitrophenyl)-S-(2-nitrobenzyl)phosphorothioate] with tBuMgCl-activated, 3'-protected nucleoside is stereospecific and leads, after appropriate work-up, to dinucleoside-3',5'-methanephosphonate or dinucleoside-3',5'-phosphorothioate, respectively. This procedure extended to 5'-activated nucleotides, allows to prepare short, stereoregular oligonucleotide analogues bearing at internucleotide positions methanephosphonate or phosphorothioate function of predetermined sense of chirality at P-centers.     

Membrane-bound nucleotidase of Bacillus cereus.

A membrane-bound nucleotidase of Bacillus cereus T was solubilized by digestion with trypsin and subsequently purified more than 300-fold. The purified nucleotidase was most active on ribonucleoside 5'-monophosphates and was slightly less active (40 to 60%) on deoxyribonucleoside 5'-monophosphates and ribonucleoside 3'-monophosphates. In addition to hydrolytic activity, the nucleotidase preparation possessed phosphotransferase activity by which phosphate is transferred from a phosphate donor to the 5' position of nucleosides.     

Novel approach to nucleoside-5'-(1-hydroxymethylene-1, 1-bisphosphonates): synthesis of new AZT analogues

An efficient synthetic method of nucleoside-5'-(1-hydroxymethylene-1,1-bisphosphonates) is reported here. The procedure was optimized with 3'-protected thymidine and then applied to synthesis of new AZT analogues.     

Synthesis of oligoribonucleotides by the N-phosphonate method using alkali-labile 2'-o-protective groups. II. Various aspects of using 2'-o-benzoyl and anisole protective groups

The N-acyl, 5'-O-trityl (MeOTr, (MeO)2Tr, Me3Tr), 2'-O-benzoyl (and anisole) nucleosides were prepared by selective aroylation of N,5'-protected nucleosides. By means of the reverse-phase microcolumn liquid chromatography it was shown that the rate of the aryl 2'----3'-isomerisation is lower in case of 2'-anisoylnucleosides and depends on structure of the 5'-O-protecting group. The prepared synthons were used for the manual H-phosphonate solid-phase synthesis of oligoribonucleotides (6-10-mers).     

Synthesis of phosphono-pyrimidine and -purine ribonucleosides

The reaction of the lithiated species of 2', 3', 5'-tri-O-protected uridines and 6-chloropurine ribonucleoside with diethyl chlorophosphate provided the corresponding diethyl phosphonate derivatives (III, IV and VIII). The Arbuzov-reaction of 2', 3', 5'-tri-O-protected 4-chloro-2(1H)-pyrimidinone ribonucleoside with triethyl phosphite afforded the diethyl phosphonate derivative (VI).     

Studies on deoxyribonucleic acids and related compounds. V. Synthesis of pentadecanucleotide duplex containing the ideal Pribnow sequence of promoter by the phosphotriester method using a new phosphorylating reagent.

A phosphorylating reagent o-chlorophenyl phosphoro-p-anisi-dochloridate was synthesized to phosphorylate the 3'-hydroxyl group of N, 5'-protected deoxynucleosides. These nucleotides served as 3'-terminal units for the synthesis of oligonucleotide blocks. By condensation of these oligonucleotide blocks the partially complementary deoxypentadecanucleotides dAGCTTATAATGC-TCG and dAGCTCGAGCATTATA, which contained the ideal Pribnow sequence TATAATG, were synthesized.     

Chemoselective deprotection of alpha-indole and imidazole ribonucleosides

A series of 2 ',3 '-isopropylidene and 5 '-trityl-protected alpha-indole and alpha/beta-benzimidazole and imidazole ribonucleosides were deprotected with different acids. Selectivity was achieved for 5 '-versus 2 ',3 '- deprotection by using formic acid in the alpha-indole ribonucleoside series. Treatment of alpha-indole ribonucleosides with a mixture of formic acid and ether at room temperature afforded 2 ',3 '-deprotected alpha-ribonucleosides, whereas treatment of the alpha-benzimidazole ribonucleosides with the same acid afforded the 5 '-deprotected ribonucleoside without any 2 ', 3 '-deprotected products. The structures of these ribonucleosides were elucidated with 2D (NOESY, COSY, and HMQC) NMR spectroscopy.     

Difficulties in the deprotection of 1,2-ketals in nucleosides containing alkylidencarbazoyl groups

The synthesis of unprotected alkylidencarbazoyl nucleoside derivatives 8a-8d is shown. A direct deprotection route from readily available 2',3'-isopropylidene protected nucleosides 5a-5d. prepared from a chemoenzymatic procedure, did not give the selective cleavage of the ketal function without affecting the C=N bond. The next option tried was to look at the previous compound in the retrosynthetic route: 2',3'-protected carbazoyl nucleoside 4. However, in all cases we obtained unsatisfactory results. Stepping further back, the hydrolysis of compound 3a led us to unprotected carbonate nucleoside 9 in quantitative yield. With this compound available, the synthesis towards derivatives 8 was accomplished through a known procedure.     

Ribonucleoside 3'-di- and -triphosphates. Synthesis of guanosine tetraphosphate (ppGpp).

A procedure has been outlined for the synthesis of ribonucleoside 3'-di- and -triphosphates. The synthetic scheme involves the conversion of a ribonucleoside 3'-monophosphate to its 2'-(5'-di)-O-(1-methoxyethyl) derivative, followed by successive treatments of the blocked ribonucleotide with 1,1'-carbonyldiimidazole and mono(tri-n-butylammonium) phosphate or pyrophosphate. The resulting ribonucleoside 3'-di- and -triphosphate derivatives are then deblocked by treatment with dilute aqueous acetic acid, pH 3.0. The use of this procedure is illustrated for adenosine 3'-monophosphate, which has been converted to its corresponding 3'-di- and -triphosphates in 61% overall yield. The decomposition of adenosine 3'-di- and -triphosphates to adenosine 2'-monophosphate, adenosine 3'-monophosphate, and adenosine cyclic 2',3'-monophosphate as a function of pH at 100 degrees has been studied as has the attempted polymerization of adenosine 3'-diphosphate with polynucleotide phosphorylase. Also prepared was guanosine 5'-diphosphate 3'-diphosphate (guanosine tetraphosphate; ppGpp), which was accessible via treatment of 2'-O-(1-methoxyethyl)guanosine 5'-monophosphate 3'-monophosphate with the phosphorimidazolidate of mono(tri-n-butyl ammonium) phosphate. The resulting blocked tetraphosphate was deblocked in dilute aqueous acetic acid to afford ppGpp in an overall yield of 18%.     

Synthesis of isotopically labeled D-[1'-13C]ribonucleoside phosphoramidites

The preparation of fully protected labeled diisopropylamino-beta-cyanoethyl-[1'-13C]ribonucleoside phosphoramidites with regioisomeric purity is described. We demonstrated in this paper that a regioselective 2'-O-silylation, through a 3',5'-O-di-tert-butylsilanediyl protection, has been applied for the synthesis of [1'-13C]ribonucleoside phosphoramidite units. This method allowed us to obtain only the desired 2'-O-silyl-3'-O-phosphoramidites avoiding the undesired 3'-O-silyl-2'-O-phosphoramidite nucleosides isolated by standard procedures. This is a suitable procedure to RNA precursors with respect to the isotope-containing precursors.     

Flexibility in RNA priming of Okazaki pieces at the E. coli replication fork

We present results which suggest considerable flexibility in the RNA priming of Okazaki pieces at the E. coli replication fork. Using film lysates on cellophane discs, we have identified RNA at the 5' ends of Okazaki pieces. All four ribonucleotides are found to be present at the RNA-DNA junction if all four ribonucleoside triphosphates are used. However, if only ATP, or ATP and GTP are used, then only 2' (3')AMP, or 2' (3')AMP and 2' (3')GMP are found at the RNA-DNA junction. A nearest neighbor analysis of RNA associated with Okazaki pieces using alpha 32P-CTP as a probe shows a similar dependence of nearest neighbor composition on the ribonucleoside triphosphate composition of the incubation mixture. Thus, the nucleotide composition of the RNA primers at the ends of Okazaki pieces varies as a function of the ribonucleoside triphosphates available.     

Transition-state stabilization by adenosine deaminase: 1,6-addition of water to purine ribonucleoside, the enzyme's affinity for 6-hydroxy-1,6-dihydropurine ribonucleoside, and the effective concentration of substrate water at the active site

Positions of equilibria of highly unfavorable addition reactions, whose products are present at concentrations below the limits of detection, can be determined from equilibria of combination of anionic nucleophiles with quaternized enamines. Applied to the newly prepared 1-methylpurinium ribonucleoside cation, this method yields approximate equilibrium constants of 2 X 10(-9) M-1 for addition of water and 4 X 10(-5) M-1 for addition of N-acetylcysteine to neutral purine ribonucleoside, in dilute aqueous solution. Positions of 13C magnetic resonances and UV absorption maxima of the above complexes and comparison with those of adenosine deaminase complexes strongly suggest that purine ribonucleoside is bound by adenosine deaminase as the 1,6 covalent hydrate, not as a covalently bonded complex formed by addition of a thiol group at the active site. The favorable position of equilibrium of the hydration reaction on the enzyme, together with its extremely unfavorable position in free solution, indicates that the effective activity of substrate water at the active site is in the neighborhood of 10(10) M. The Ki value of the active diastereomer of 6-hydroxy-1,6-dihydropurine ribonucleoside is estimated as 1.6 X 10(-13) M, more than 8 orders of magnitude lower than the apparent dissociation constants of enzyme complexes with the substrate adenosine or the product inosine. The enzyme's remarkable affinity for this hydrated species, which is vanishingly rare in free solution, seems understandable in terms of the hydrate's close resemblance to a hydrated intermediate approaching the transition state in direct water attack on adenosine.     

Chain extension of ribonucleic acid by enzymes from rat liver cytoplasm

1. The 105000g supernatant fraction of rat liver catalyses the incorporation of ribonucleotides from ribonucleoside triphosphates into polyribonucleotide material. The reaction requires Mg²⁺ ions and is enhanced by the addition of an ATP-generating system and RNA, ATP, UTP and CTP but not GTP are utilized in this reaction. In the case of UTP, the product is predominantly a homopolymer containing 2–3 uridine residues, and there is evidence that these may be added to the 3′-hydroxyl ends of RNA or oligoribonucleotide primers. 2. The microsome fraction of rat liver incorporates ribonucleotides from ATP, GTP, CTP and UTP into polyribonucleotide material. This reaction requires Mg²⁺ ions and is enhanced slightly by the addition of an ATP-generating system, and by RNA but not DNA. Supplementation of the reaction mixture with the three complementary ribonucleoside 5′-triphosphates greatly increases the utilization of a single labelled ribonucleoside 5′-triphosphate. The optimum pH is in the range 7·0–8·5, and the reaction is strongly inhibited by inorganic pyrophosphate and to a much smaller degree by inorganic orthophosphate. It is not inhibited by actinomycin D or by deoxyribonuclease. In experiments with [³²P]UTP in the absence of ATP, GTP and CTP, 80–90% of ³²P was recovered in UMP-2′ or -3′ after alkaline hydrolysis of the reaction product. When the reaction mixture was supplemented with ATP, GTP and CTP, however, about 40% of the ³²P was recovered in nucleotides other than UMP-2′ or -3′. Although the reactions seem to lead predominantly to the synthesis of homopolymers, the possibility of some formation of some heteropolymer is not completely excluded.     

S1 nuclease of Aspergillus oryzae: characterization of the associated phosphomonoesterase activity

S₁ nuclease (EC 3.1.30.1) of Aspergillus oryzae was found to catalyze the hydrolysis of 2′- or 3′-phosphomonoester groups from several mono- and oligonucleotides. The specificity of the enzyme for mononucleotide substrates was determined by steady-state kinetic measurements at pH 4.5. The values of V were similar for all ribonucleoside 3′-phosphates tested, and they were 50–400 times greater than those for the corresponding deoxyribonucleotides or ribonucleoside 2′-phosphates. Purine nucleotides had lower apparent K_m values than pyrimidine nucleotides. Apparent K_m values of mononucleotides were also strongly dependent on the type of sugar and the positions of phosphoryl groups. Substrate specificity, as expressed by $\text{V}\text{K}{}_{\mathrm{m}}$, occurred in the following order: ribonucleoside 3′,5′-bisphosphate > ribonucleoside 3′-phosphate > deoxyribonucleoside 3′,5'-bisphosphate > deoxyribonucleoside 3′-phosphate ≈ ribonucleoside 2′-phosphate. S₁ nuclease also catalyzed the dephosphorylation of the dinucleotide ApAp at a high rate and the release of PP_i from adenosine 3′-diphosphate 5′-phosphate at a low rate. The phosphomonoesterase activity of the enzyme was competitively inhibited by single-stranded DNA and 5′-nucleotides. Apparent K_i values for adenosine compounds occurred in the order ATP < ADP < AMP ? adenosine. Tests of S₁ nuclease for phosphotransferase activity at pH 4.5 and 7.0 were negative.     

Synthesis and crystal structures of some 8,5'-carbamoyloxy-bridged purine nucleosides

The X-ray analysis of 8,5'-(N-carbamoyloxy)-2-dimethylamino- methylene-9-(2',3'-0-isopropylidene-beta-D-ribofuranosyl)guanine (2a) has disclosed that some bond angles are significantly larger or smaller than the corresponding angles of normal ribonucleosides. Abnormally longer or shorter bond lengths have also been found. The base-sugar torsion angle of 2a has proved to reside between the C1'-C2' and C1'-C3' lines, and quite near the latter line. Some new 8,5'-carbamoyloxy bridged adenosines were also synthesized as 2',3'-protected forms.     

Purine nucleotide production in normal and HPRT- cells

1. Both normal cells and cells deficient in hypoxanthine-guanine phosphoribosyltransferase (HPRT) are able to produce adenine and guanine nucleotides from aminoimidazole carboxamide (AICA) or its ribonucleoside (AICAR), but not from formaminoimidazole carboxamide ribonucleoside (FAICAR). 2. The level of purine nucleotide production from AICA in HPRT- cells is at least equal to the production of purine nucleotides from hypoxanthine in normal cells. 3. The concentration of AICA or AICAR at which nucleotide production was half-maximal was between 30 and 100 microM in various cell lines. 4. Adenosine kinase is required to convert AICAR to its nucleotide; adenine phosphoribosyltransferase is required to convert AICA to its nucleotide. Cells lacking either of these enzymes are unable to produce purine nucleotides from the respective precursor. 5. Purine production from AICAR in HPRT- cells is not greatly increased by the addition of formate, folate or leucovorin.