Triester Method Research Articles

The Risk of the Preparation of Artificial DNAs via an Interrupted Automated Solid-Phase Triester Method

In this paper, the risk of the preparation of artificial DNAs via an interrupted automated solid-phase triester procedure is discussed. These results differ completely from the corresponding results obtained by a gradual non-automated synthesis, indicated as solution-phase chemistry. With experimental results focused on model systems under various conditions and molecular–mechanics calculations, it feels as a challenge to offer an explanation for this different behavior. Attention is briefly given to click-linked DNA fragments as a substitute of phosphate linkages.

A facile synthesis of cyclic bis(3′→5′)diguanylic acid

This paper describes a new method for synthesizing biologically important cyclic bis(3′→5′)diguanylic acid (cGpGp) in a higher yield than that of the existing synthetic method. In the new synthesis, the following two means, in place of those used in the existing synthesis are employed as main strategies to cause the increase in product yield. One of these distinctive strategies in the new synthesis is that the phosphoramidite method is used for the preparation of a key synthetic intermediate of a linear guanylyl(3′→5′)guanylic acid derivative. This method allowed higher-yield formation of the intermediate than that by the triester method used in the existing synthesis. The second distinctive strategy used in the new synthesis is that allyloxycarbonyl and allyl groups are used for the protection of two guanine bases and two internucleotide bonds, respectively. These four allylic protectors can be removed all at once by the organopalladium-catalyzed reaction under neutral conditions. Thus, deprotection of the protected cGpGp precursor was achieved in the present synthesis in a shorter step and under milder conditions than the deprotection achieved in the existing synthesis, which uses diphenylacetyl and o-chlorophenyl groups as protectors for two guanine bases and two internucleotide bonds, respectively, whose full removal requires two different procedures including rather harsh basic treatment. As a result, technical loss and decomposition of the target product in the new synthesis is remarkably reduced.

Highly efficient solid phase synthesis of oligonucleotide analogs containing phosphorodithioate linkages.

A triester method for the synthesis of deoxynucleoside phosphorodithioate dimers is described. The phosphorodithioate linkage is introduced using a new dithiophosphorylating reagent DPSE-SP(S)Cl(2)where DPSE = 2-diphenylmethylsilylethyl. This group is removed quickly using tetra-butylammonium fluoride leading to the quantitative formation of phosphorodithioate diesters uncontaminated with the corresponding phosphorothioates. The utility of this group is demonstrated by the synthesis of a penta-decathymidylic acid, [T(PS(2))T(PO(2))](7)T, which contains alternating phosphorodithioate/phosphate diester internucleotide linkages.

ChemInform Abstract: Synthesis of Deoxyribonucleoside Phosphorodithioate Dimers by a Triester Method

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Synthesis of Deoxyribonucleoside Phosphorodithioate Dimers by a Triester Method

Modified oligodeoxynucleotides have recently received much attention due to their therapeutic applications. Among the more promising are phosphorodithioates where both nonbridging oxygen atoms in the phosphate diesters are replced by sulfur. Deoxynucleoside phosphorodithioate dimers have been prepared in several ways, using H-phosphonate, phosphordiamidite, phosphoramidite, and thiophosphoramidite methods. Reports have also appeared on the synthesis of oligonucleotides with alternating phosphodiester and dithiophosphodiester linkages, as well as one on ribonucleoside dimers. Of the above methods, the thiophosphoramidite method has been applied successfully for the preparation of mixed base oligonucleotides containing contiguous phosphorodithioate linkages. However, this method gives products which contain varying amounts of phosphorothioate linkages (2 − 10%) due to factors associated with the involvement of trivalent thiophosphorus compounds. In addition, the thiophosphoramidite synthons are difficult to purify on silica gel column, and have a tendency to dismutate in presence of acidic catalysts such as tetrazole. The thiophosphite intermediate which is formed is also unstable to tetrazole. Similarly in the thio- and dithio-H-phosphonate method, the primary coupling products are unstable to catalysts, pivaloyl chloride and iodine. Recently, Dahl et al reported1–2 synthesis of dimers and oligomers upto octamer which also leads to formation of small amounts of phosphorothioate linkages. In additon, about 1.2% per phosphorodithioate linkage of the oligomer is cleaved during

Solution Phase Synthesis of an Oligodeoxyribonucleotide Phosphorothioate for Therapeutic Applications

Solution phase synthesis of an oligodeoxyribonucleotide phosphorothioate Octamer (5′-TTGGGGTT) using phosphorothioate triester method is reported.

Synthesis of Liposomal Phospholipid‐(N4‐palmitoyl‐1‐β‐D‐arabinofuranosylcytosine) Conjugates and Evaluation of Their Cytostatic Activity against l1210 Murine Leukemia

AbstractN4‐Palmitoyl‐araC, a prodrug of the cytostatic compound 1‐β‐D‐arabinofuranosylcytosine (araC), was linked by means of the triester method to the phospholipids (2‐chlorophenyl) (1,2‐di‐O‐palmitoylglyceryl) phosphate, (2‐chlorophenyl) (1,2‐di‐O‐octadecylglyceryl) phosphate and (2‐chlorophenyl) (1‐O‐octadecyl‐2‐O‐palmitoylglyceryl) phosphate. In the first step of these gram‐scale syntheses phospholipid‐(N4‐palmitoyl‐araC) conjugates were obtained the linkage of which was accomplished via a triester group. In the second step the final condensates were obtained through transformation of the triester into a diester linkage by removal of the 2‐chlorophenyl group. The cytostatic activity of these compounds which form stable liposomal preparations together with matrix lipids was evaluated according to the L1210 mouse leukemia model. The conjugates containing a triester linkage were shown to be ineffective, whereas those with a diester linkage display a significantly higher antitumor activity as compared to N4‐palmitoyl‐araC and araC. With the diester 6a–8a 80–100% of the treated animals were cured at a total dose of 200 μmol/kg, whereas with araC given at a fourfold higher concentration none of the treated mice survived.

Solid Phase Synthesis of 2′, 5′-Oligoadenylates Containing 3′-Fluorinated Ribose

Abstract 2′, 5′-phosphodiester bond-linked oligoadenylate trimers with 3′-fluoro-3′-deoxyadenosine residues incorporated at specific positions of the nucleotide sequence were synthesized by the solid phase phosphite triester (phosphoramidite) method. The syntheses were in the 2′ to 5′ direction and were performed manually using commercially available microcolumns. The oligonucleotides were 5′-end phosphorylated on the support before deprotection.

Solution-phase synthesis of phosphorothioate oligodeoxynucleosides by the phosphotriester method.

A "phosphorothioate triester method" was investigated for the solution-phase synthesis of phosphorothioate oligonucleosides. Using fully protected 3'-phosphorothiolate thymidine bearing O-cyanoethyl and S-2,4-dichlorobenzyl groups as phosphorothioate protecting groups, decathymidine nonaphosphorothioate was efficiently assembled through a blockwise procedure. Two side reactions occurred during the deprotection steps: breakage of internucleoside linkages (1.8% per linkage) and formation of phosphate diester linkages (0.9%). Substitution of the dichlorobenzyl group by the more labile 4-nitrobenzyl S-protecting group reduced the extent of internucleoside bond breakage by one-half.

Synthesis, and Some Properties of, Amphiphilic Dinucleoside Phosphate Derivatives of 3′-azido-2′,3′-dideoxythymidine (AZT)

N4-hexadecyl-5′-0-(4-monomethoxytrityl)-2′-deoxycytidine-3′-hydrogenphosphate was reacted with 3′-azido-2′,3′-dideoxythymidine (AZT) according to the hydrogenphosphate method to yield N4-hexadecyl-2′-deoxycytidylyl-(3′-5)-3′-azido-2′,3′-dideoxythymidine. N4-palmitoyl-5′-O-(4-monomethoxytrityl)-2′-deoxycytidine-3′-(2-chlorophenyl)-phosphate was condensed to AZT using the triester method to give N4-palmitoyl-2′-deoxycytidylyl-(3′-5′)-3,-azido-2′,3′-dideoxythymidine. Both dinucleosidephosphates have amphiphilic properties and represent a new class of AZT derivatives in which the polar AZT-5′-monophosphate is masked with lipophilic deoxycytidine residues of variable stability. The AZT derivatives are water soluble, by forming micelles, and as a result of their amphiphilic nature, they can be incorporated into the lipid membranes of liposomes. In contrast to the micellar drug preparations, the liposomal formulations were shown to exert no lytic activity on human erythrocytes. Both AZT derivatives have anti HIV-1 activity in vitro.

Preparation of oligodeoxyribonucleoside phosphorodithioates by a triester method.

A method to prepare thymidine phosphorodithioate dimers (ref. 1) has been extended to allow the preparation of oligo-2'-deoxyribonucleotide phosphorodithioates containing all four bases. The method is suitable for large-scale synthesis and gives phosphorodithioates without phosphorothioate impurities (31P nmr, detection limit 0.5 to 1%). Oligonucleotides up to octamers which contain -0-(PS2-)-0- linkages at all positions have been prepared by block synthesis in solution. The phosphorodithioate linkage is introduced by the reaction of a 5'-O, N-protected nucleoside (or oligonucleotide) with a dithiophosphorylating agent RSP(S)(ODhbt)2, R = 2,4-dichlorobenzyl, Dhbt = 3,4-dihydro-4-oxo-benzotriazin-3-yl, followed by coupling of the product to a 3'-O,N-protected nucleoside (or oligonucleotide). This method gives pure protected oligodeoxyribonucleoside phosphorodithioates, and phosphorothioate linkages are only introduced if contact with conc. aqueous ammonia during or after deblocking is unduly prolonged.

2',5'-Oligoadenylate:antisense chimeras--synthesis and properties.

We have synthesized a novel bioconjugate which joins an antisense oligonucleotide to a unique and potent inhibitor of translation,pn5'A2'(p5'A2')mp5'A(2-5A). Two residues of 4-hydroxybutyl phosphate were employed as linkers to attach the 2',5'-oligoadenylate moiety through its 2'-terminus to the 5'-terminus of the chosen antisense sequence, (dT)20. The syntheses were carried on a solid support according to the phosphite triester method of DNA synthesis (Letsinger, R.L., Lunsford, W.B. (1976) J. Am. Chem. Soc. 98, 3655-3661; Beaucage, S.L., and Caruthers, M.H. (1981) Tetrahedron Lett. 22, 1859-1862). The generated 2-5A antisense chimeras retained both the ability of the 2-5A molecule to activate the 2-5A-dependent RNase as well as the ability of the oligo(dT) moiety to hybridize to the complementary poly(A). Moreover, the chimera, when annealed to its target nucleic acid sequence, was still effectively bound to the 2-5A-dependent nuclease. The methodology described represents a new approach to the selective modulation of mRNA expression.

ChemInform Abstract: Deoxynucleoside Phosphorodithioates. Preparation by a Triester Method.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Incorporation of dA opposite N3-ethylthymidine terminates in vitro DNA synthesis

N3-Ethylthymidine (N3-Et-dT) was site specifically incorporated into a 17-nucleotide oligomer to investigate the significance of DNA ethylation at the central hydrogen-bonding site (N3) of thymine. The 5'-(dimethoxytrityl)-protected N3-Et-dT was converted to the corresponding 3'-phosphoramidite and used to incorporate N3-Et-dT at a single site in the oligonucleotide during synthesis by the phosphite triester method. The purified N3-Et-dT-containing oligomer was ligated to a second 17-mer to yield a 34-nucleotide template with N3-Et-dT present at position 26 from the 3'-end. The template DNA, which corresponds to a specific sequence at gene G of bacteriophage phi X174, was used to study the specificity of nucleotide incorporation opposite N3-Et-dT. At 10 microM dNTP and 5 mM Mg2+, N3-Et-dT blocked DNA synthesis by Escherichia coli polymerase I (Klenow fragment): 96% immediately 3' to N3-Et-dT and 4% after incorporation of a nucleotide opposite N3-Et-dT (incorporation-dependent blocked product). DNA replication past the lesion (postlesion synthesis) was negligible. Incorporation opposite N3-Et-dT increased with increased dNTP concentrations, reaching 35% at 200 microM. Postlesion synthesis remained negligible. DNA sequencing of the incorporation-dependent blocked product revealed that dA is incorporated opposite N3-Et-dT consistent with the "A" rule in mutagenesis. Formation of the N3-Et-dT.dA base pair at the 3'-end of the growing chain terminated DNA synthesis. These results implicate N3-Et-dT as a potentially cytotoxic lesion produced by ethylating agents.

ChemInform Abstract: The Automation of DNA Synthesis

To date, three chemical protocols have been used in the solid phase synthesis of DNA. These are: 1) The triester method developed by Gait and Itakura; 2) The methyl phosphoramidite method developed by Carruthers; 3) The cyanoethyl phosphoramidite (CED phosphoramidite) method, a modification of method number 2

Deoxynucleoside phosphorodithioates. Preparation by a triester method

A series of active esters of dithiophosphoric acid ( 3) have been prepared and their properties as potential precursors for dideoxynucleoside phosphorodithioates evaluated.

ChemInform Abstract: Durenesulfonic Acid Derivatives as New Condensing Reagents in the Nucleotide Synthesis Following the Triester Method.

ChemInform Abstract: Durenesulfonic Acid Derivatives as New Condensing Reagents in the Nucleotide Synthesis Following the Triester Method.

Synthesis of 2'-end lipophilized derivatives of 2'-5'-triadenylates

Synthesis of protected derivatives of 2-5 A3 core starting from 2',3'-O-ethoxymethylene-N6-benzoyladenosine (I) by traizolidate and/or modified triester method are described. Preparation of adenylyl-(2'-5')-adenylyl-(2'-5')-2'-3'-O-(1-methoxyhexadecylidene)adenosine (X), adenylyl-(2'-5')-adenylyl-(2'-5')-2'-3'-O-palmitoyladenosine (XIII) and 5'-phosphoryladenyl-(2'-5')-adenylyl-(2'-5')-2'-3'-O-(1-methoxyhexadecylidene)adenosine (XVI) are described.

Chiral synthesis of D- and L-myo-inositol 1,4,5-trisphosphate.

Chiral inositols (D-chiro-inositol from D-pinitol and L-chiro-inositol from L-quebrachitol) were converted to the 3,4-di-O-benzyl ethers, which were selectively benzoylated to yield the 1,2,5-tri-O-benzoyl-3,4-di-O-benzyl-chiro-inositols. The free hydroxyl group in each derivative was inverted by way of the trifluoromethane sulfonate ester to provide D- and L-1,2,4-tri-O-benzoyl-5,6-di-O-benzyl-myo-inositol. Hydrogenolysis to remove the benzyl ether groups gave the enantiomeric 1,2,4-tri-O-benzoyl-myo-inositols, which were phosphorylated by a dibenzylphosphite triester method. After hydrogenolysis and saponification of the derivatives, the D- and L-myo-inositol 1,4,5-trisphosphates were isolated as the crystalline cyclohexylammonium salts in gram quantity.

Chemical synthesis and cloning of secretin gene.

A DNA duplex coding for the 27 amino acids of secretin has been synthesized and cloned. In designing the sequence of the gene, computer analysis has been applied. The following factors have been considered: selection of codon usage in favour of expression in yeast; design of various sites useful in gene cloning, gene modification and expressed product purification; avoiding the repeat sequences which may interfere in the ligation of the synthetic fragments. The synthesis involved preparation of 12 oligodeoxyribonucleotides (12-mer to 24-mer in length) by phosphate triester and phosphite triester method, purification by polyacrylamide gel electrophoresis (PAGE). A new plasmid pWS1 was constructed by insertion of the enzymatic ligated gene fragment into plasmid pWR13.