Phosphotriester Approach In Solution Research Articles

Preparation of an Octadeoxyribonucleoside Heptaphosphorothioate by the Phosphotriester Approach in Solution†

The synthesis of the octadeoxyribonucleoside heptaphosphorothioate, d[Tp(s)Tp(s)Gp(s)Gp(s)Gp(s)Gp(s)Tp(s)T] by the phosphotriester approach in solution is described. The phosphorothioate internucleotide linkages are protected by the S-(2-cyanoethyl) group and 1-(mesitylene-2-sulfonyl)-3-nitro-1,2,4-1H-triazole (MSNT) is used as the coupling agent. A block synthesis strategy (2 + 2 → 4 and 4 + 4 → 8) is followed. This article is dedicated to the memory of Professor Tsujiaki Hata

The Chemical Synthesis of E. coli tRNALys Anticodon Loop Fragment and Its Analogues

E. coli tRNALys anticodon loop fragment (Umnm5sUUUt6A) 1 and its analogues 2–6 were synthesized by the classical phosphotriester approach in solution. The preparation of suitably protected derivatives of N6-threonylcarbamoyladenosine 18 is also described.

ChemInform Abstract: Synthesis of S‐Alkyl Esters of Protected 2′‐Deoxyribonucleoside 3′‐ Phosphorothioates. Building Blocks for the Large‐Scale Synthesis of Phosphorothioate Analogues of Oligodeoxyribonucleotides by the Phosphotriester Approach in Solution.

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Synthesis of S-alkyl esters of protected 2′-deoxyribonucleoside 3′-phosphorothioates. Building blocks for the large-scale synthesis of phosphorothioate analogues of oligodeoxyribonucleotides by the phosphotriester approach in solution

Triethylammonium salts of 5′-O-(9-phenylxanthen-9-yl)-2′-deoxyribonucleoside 3′-(H-phosphonates)23, 33a, 33b and 33c, derived from thymidine, 6-N-pivaloyl-2′-deoxyadenosine, 4-N-benzoyl-2′-deoxycytidine and 2-N-phenylacetyl-2′-deoxyguanosine, react with N-(2-cyanoethylsulfanyl)phthalimide 21 in the presence of chlorotrimethylsilane and 4-methylmorpholine to give the corresponding 3′-phosphorothioate S-(2-cyanoethyl) esters 24c, 34a, 34b and 34c, respectively, in good yield. The S-(2-cyanoethyl) group appears to be suitable for the protection of internucleotide linkages in the synthesis of oligonucleotide phosphorothioates by the phosphotriester approach in solution.

Spectroscopic and enzymatic characterization of 2′–5′ and 3′–5′ RNA hexamers AACCUU synthesised by phosphotriester approach in solution using 2′-t-butyldimethylsilyl protection

Comparative 1H, 31P NMR and CD spectroscopic results and enzymatic cleavage of single stranded RNA hexamers which have identical base sequence (AACCUU) but are regioisomeric at the internucleotide phosphate linkages (2′–t′, 3′–5′ and their covalent hybrid) are presented. The 31P NMR results revealed significant differences in local phosphate backbone conformation among these isomers, with 2′–5′ isomer exhibiting maximum heterogeneity as compared to the 3′–5′ isomer, the analogous DNA hexamer and the covalent hybrid hexamer. In contrast to this, there are no appreciable differences in the overall base-base stacking as seen in the CD spectra of 2′–5′ and 3′–5′ isomers. All RNA hexamers were synthesised by solution phase phosphotriester chemistry with t-butyldimethylsilyl (TBDMS) as 2′-O-protecting group. The fully protected oligorobomers were deprotected in two steps: (i) saturated anhydrous MeOHNH 3 for phosphate and amino deprotections and (ii) TBAF for removal of 2′-O-TBDMS group. Use of sat. MeOHNH 3 (instead of aq. NH 3) prevents 2′–3′ internucleotide phosphate migrations, chain fragmentations and 5′-terminal modifications by neighbouring group participation (NGP). The retention of isomeric integrity and absence of 5′-terminal modification in the final products was established by digestion with several nucleases.

ChemInform Abstract: Synthesis of the 3′‐Terminal Half of Yeast Alanine Transfer Ribonucleic Acid (tRNAAla) by the Phosphotriester Approach in Solution. Part 2.

ChemInformVolume 21, Issue 4 Natural Products ChemInform Abstract: Synthesis of the 3′-Terminal Half of Yeast Alanine Transfer Ribonucleic Acid (tRNAAla) by the Phosphotriester Approach in Solution. Part 2. J. M. BROWN, J. M. BROWN Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorC. CHRISTODOULOU, C. CHRISTODOULOU Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorA. S. MODAK, A. S. MODAK Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorC. B. REESE, C. B. REESE Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorH. T. SERAFINOWSKA, H. T. SERAFINOWSKA Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this author J. M. BROWN, J. M. BROWN Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorC. CHRISTODOULOU, C. CHRISTODOULOU Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorA. S. MODAK, A. S. MODAK Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorC. B. REESE, C. B. REESE Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this authorH. T. SERAFINOWSKA, H. T. SERAFINOWSKA Dep. Chem., King's Coll., London WC2R 2LS, UKSearch for more papers by this author First published: January 23, 1990 https://doi.org/10.1002/chin.199004295Citations: 1AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume21, Issue4January 23, 1990 RelatedInformation

ChemInform Abstract: Synthesis of the 3′‐Terminal Half of Yeast Alanine Transfer Ribonucleic Acid (tRNAAla) by the Phosphotriester Approach in Solution. Part 1. Preparation of the Nucleoside Building Blocks.

Adenosine and cytidine are converted into their 6-N- and 4-N-(4-t-butylbenzoyl) derivatives [(12) and (13b), respectively] which are then converted into the corresponding 2′-O-(4-methoxytetrahydropyran-4-yl)[(21; B =5b) and (21; B =6b), respectively] and 5′-O-[2-(dibromomethyl)benzoyl]2′-O-(4-methoxytetrahydropyran-4-yl) derivatives [(35; B =5b) and (35; B =6b), respectively]. The conversion of (12) into its 2′,3′-O-methoxymethylene derivative (24) is also described. Guanosine is converted, by two routes, into its 6-O-(3-chlorophenyl)-2-N-phenylacetyl derivative (16a), and the latter compound is converted into its 5′-O-[2-(dibromomethyl)benzoyl]-2′-O-(4-methoxytetrahydropyran-4-yl) and 5′-O-(9-phenylxanthen-9-yl)-2′-O-(4-methoxytetrahydropyran-4-yl) derivatives [(35; B =9b) and (26), respectively]. The preparation of 2′-O-(4-methoxytetrahydropyran-4-yl)-4-O-(2,4-dimethylphenyl)uridine (18) from 2′-O-(4-methoxytetrahydropyran-4-yl)uridine (17a) and its conversion to its 5′-O-[2-(dibromomethyl)benzoyl]derivative (35; B =10) are described. 5-Methyluridine (19; B =27), pseudouridine (19; B =28a) and inosine (19; B =29) are converted into their 2′-O-(4-methoxytetrahydropyran-4-yl) derivatives (21; B =27, 28a, and 29, respectively); (21; B =27) is further converted into its 4-O-phenyl derivative (30), (21; B =28a) is further converted into its 1-N-(4-bromobenzenesulphonyl) and 5′-O-[2-(dibromomethyl)benzoyl]-1-N-(4-bromobenzenesulphonyl) derivatives [(32) and (35; B =28b), respectively], and (21; B =29) is further converted into its 1-N-pivaloyloxymethyl- and 1-N-methyl derivatives [(33a) and (33b), respectively]. The N1,N1,N3,N3-tetramethylguanidinium E-2-nitrobenzaldoximate-promoted removal of O-aryl protecting groups from the 2′-O-(4-methoxytetrahydropyran-4-yl) derivatives of 6-O-(3-chlorophenyl)-2-N-phenylacetylguanosine, 4-O-(2,4-dimethylphenyl)uridine, 5-methyl-4-O-phenyluridine and 1-N-(4-bromobenzenesulphonyl)-5-β-D-ribofuranosyluracil [(21; B =9b), (18), (30), and (32), respectively], and the ammonia-promoted removal of the 1-N-pivaloyloxymethyl group from (33a) are described. Finally, the synthesis of 2-(isopropylthiomethoxymethyl)benzoic acid [Ptmt acid, (40)], the conversion of (18) and (21; B =5b) into their 5′-O-Ptmt derivatives [(41a) and (41b)], and the two-step procedure for the removal of the Ptmt protecting group are described.

Synthesis of the 3′-terminal half of yeast alanine transfer ribonucleic acid (tRNAAla) by the phosphotriester approach in solution. Part 2

The preparation, by the phosphotriester approach in solution, of the 3′-terminal decaribonucleoside nonaphosphate [UpCpGpUpCpCpApCpCpA (48)], nonadecaribonucleoside octadecaphosphate [ApUpUpCpCpGpGpApCpUpCpGpUpCpCpApCpCpA (49)], and heptatriacontaribonucleoside hexatriacontaphosphate [GpGpApGpApGpGpUpCpUpCpCpGpGpTpψpCpGpApUpUpCpCpGpGpApCpUpCpGpUpCpCpApCpCpA (50)] sequences of yeast alanine transfer ribonucleic acid are described. With the exception of the 3′-terminal adenosine residue which was protected as its 2′,3′-O-methoxymethylene [Mm] derivative, the 2′-hydroxy functions were protected with 4-methoxytetrahydropyran-4-yl [Mthp] groups. The 5′-hydroxy functions of intermediate building blocks were protected with 2-(dibromomethyl)benzoyl [Dbmb (2)], 2-(isopropylthiomethoxymethyl)benzoyl [Ptmt (3)] or 9-phenylxanthen-9-yl [Px (4)] groups. The base residue of the adenosine, cytidine, guanosine, uridine, pseudouridine and 5-methyluridine building blocks were protected as in (5), (6), (7), (8), (9), and (10), respectively. Internucleotide linkages were protected with the 2-chlorophenyl group, and the 2,4-dinitrobenzyl (Dnb) group was used for the temporary protection of 3′-phosphodiester functions. The first phosphorylation step (leading to 3′-phosphodiester intermediates) was carried out by treatment with 2-chlorophenyl bis(1,2,4-triazoyl)phosphate (11) in the presence of 1-methylimidazole in tetrahydrofuran followed by triethylamine and water. 1-(Mesitylene-2-sulphonyl)-3-nitro-1,2,4-triazole [MSNT (15)] was used as the condensing agent in the second phosphorylation step. The final unblocking procedure involved treatment with (i)N1,N1,N3,N3-tetramethylguanidinium E-2-nitrobenzaldehyde oximate in dioxane–acetonitrile–water, (ii) concentrated aqueous ammonia, and (iii) 0.01 M hydrochloric acid.

Synthesis of the 3′-terminal half of yeast alanine transfer ribonucleic acid (tRNAAla) by the phosphotriester approach in solution. Part 1. Preparation of the nucleoside building blocks

Adenosine and cytidine are converted into their 6-N- and 4-N-(4-t-butylbenzoyl) derivatives [(12) and (13b), respectively] which are then converted into the corresponding 2′-O-(4-methoxytetrahydropyran-4-yl)[(21; B =5b) and (21; B =6b), respectively] and 5′-O-[2-(dibromomethyl)benzoyl]2′-O-(4-methoxytetrahydropyran-4-yl) derivatives [(35; B =5b) and (35; B =6b), respectively]. The conversion of (12) into its 2′,3′-O-methoxymethylene derivative (24) is also described. Guanosine is converted, by two routes, into its 6-O-(3-chlorophenyl)-2-N-phenylacetyl derivative (16a), and the latter compound is converted into its 5′-O-[2-(dibromomethyl)benzoyl]-2′-O-(4-methoxytetrahydropyran-4-yl) and 5′-O-(9-phenylxanthen-9-yl)-2′-O-(4-methoxytetrahydropyran-4-yl) derivatives [(35; B =9b) and (26), respectively]. The preparation of 2′-O-(4-methoxytetrahydropyran-4-yl)-4-O-(2,4-dimethylphenyl)uridine (18) from 2′-O-(4-methoxytetrahydropyran-4-yl)uridine (17a) and its conversion to its 5′-O-[2-(dibromomethyl)benzoyl]derivative (35; B =10) are described. 5-Methyluridine (19; B =27), pseudouridine (19; B =28a) and inosine (19; B =29) are converted into their 2′-O-(4-methoxytetrahydropyran-4-yl) derivatives (21; B =27, 28a, and 29, respectively); (21; B =27) is further converted into its 4-O-phenyl derivative (30), (21; B =28a) is further converted into its 1-N-(4-bromobenzenesulphonyl) and 5′-O-[2-(dibromomethyl)benzoyl]-1-N-(4-bromobenzenesulphonyl) derivatives [(32) and (35; B =28b), respectively], and (21; B =29) is further converted into its 1-N-pivaloyloxymethyl- and 1-N-methyl derivatives [(33a) and (33b), respectively]. The N1,N1,N3,N3-tetramethylguanidinium E-2-nitrobenzaldoximate-promoted removal of O-aryl protecting groups from the 2′-O-(4-methoxytetrahydropyran-4-yl) derivatives of 6-O-(3-chlorophenyl)-2-N-phenylacetylguanosine, 4-O-(2,4-dimethylphenyl)uridine, 5-methyl-4-O-phenyluridine and 1-N-(4-bromobenzenesulphonyl)-5-β-D-ribofuranosyluracil [(21; B =9b), (18), (30), and (32), respectively], and the ammonia-promoted removal of the 1-N-pivaloyloxymethyl group from (33a) are described. Finally, the synthesis of 2-(isopropylthiomethoxymethyl)benzoic acid [Ptmt acid, (40)], the conversion of (18) and (21; B =5b) into their 5′-O-Ptmt derivatives [(41a) and (41b)], and the two-step procedure for the removal of the Ptmt protecting group are described.

Synthesis and characterization of oligodeoxynucleotides containing 4-O-methylthymine.

The carcinogenicity of N-nitroso compounds is believed to result from the alkylation of DNA, particularly on O-6 of the guanine and O-4 of the thymine residues. In order to study the base-pairing properties of 4-O-methylthymidine (T*) residues and the structural changes produced in DNA by the presence of this alkylated nucleoside, the oligodeoxyribonucleotides T*GCG, CGCAAGCTT*GCG, CGCGAGCTT*GCG, and CGCAAGCTTGCG were synthesized by the phosphotriester approach in solution. The 4-O-methylthymidine required for oligonucleotide synthesis was prepared by treating the 4-(3-nitro-1,2,4-triazolo) derivative of 3',5'-bis-O-(methoxyacetyl)thymidine with 1,8-diazabicyclo[5.4.0]-undec-7-ene (DBU) in methanol solution. The susceptibility of the 4-O-methyl group of T* toward nucleophiles enables this group of 4-O-methylthymidine-containing oligomers to be labeled by a direct exchange reaction with [13C]- or [14C]methanol in the presence of DBU. Although it has been previously suggested that 4-O-methylthymine forms stable base pairs with guanine, the thermal melting profiles of the double helices formed by these dodecamers suggest that the presence of 4-O-methylthymine paired to either adenine or guanine destablizes the helix. The melting curve of the sequence containing a 4-O-methylthymine residue base paired to guanine was biphasic and similar to that of an analogous sequence containing 6-O-methylguanine paired to thymine.

Solid phase synthesis of the 3′-terminal nonadecaribonucleoside octadecaphosphate sequence of yeast alanine transfer ribonucleic acid

The rapid synthesis of the 3′-terminal decaribonucleoside nonaphosphate and nonadecaribonucleoside octadecaphosphate sequences of yeast tRNA Ala by the phosphoramidite approach on controlled pore glass is described; the synthetic products were found to be identical to the authentic oligoribonucleotides, prepared by the phosphotriester approach in solution.

Rapid oligodeoxyribonucleotide synthesis by the “filtration” method

A rapid method for the synthesis of oligodeoxyribonucleotides by the phosphotriester approach in solution is described; the method is suitable for the preparation of relatively large quantities of pure compounds.

Sur l'Obtention d'Oligonucleotides en Serie Ara-A

Abstract The synthesis of dimer, trimer and tetramer of Ara A was described by phosphotriester approach in solution. All of these compounds and building blocks are identified and described unambiguously.