A novel protecting strategy for internucleosidic phosphate and phosphorothioate groups

The utility of 2-(N-isopropyl-N-anisoylamino)ethyl group for protection of internucleosidic phosphate linkages in oligonucleotide synthesis was studied. The group demonstrated high coupling yields, favorable deprotection kinetics and a high hydrolytic stability of phosphoramidite building blocks. The mechanism of deprotection was established using a model phosphate triester.     

A NOVEL PROTECTING STRATEGY FOR INTERNUCLEOSIDIC PHOSPHATE AND PHOSPHOROTHIOATE GROUPS

The utility of 2–(N–isopropyl–N–anisoylamino)ethyl group for protection of internucleosidic phosphate linkages in oligonucleotide synthesis was studied. The group demonstrated high coupling yields, favorable deprotection kinetics and a high hydrolytic stability of phosphoramidite building blocks. The mechanism of deprotection was established using a model phosphate triester.     

Synthesis of oligonucleotides with sequences identical with or analogous to the 3''-end of 16S ribosomal RNA of Escherichia coli: preparation of m-6-2-A-C-C-U-C-C and A-C-C-U-C-m-4-2C via phosphotriester intermediates.

The synthesis of two fully-protected hexanucleotides (11a and 11b) via a phosphotriester approach, which is based on the use of two types of protecting groups for the internucleotide linkages, i.e. one 2,2,2-tribromo-ethyl at the 5'-terminus and four 2-chlorophenyl groups for the remaining linkages, is reported. The hexanucleotides 11a and 11b, assembled via a block-wise two-step phosphotriester method, can be deblocked conveniently to give the two hexamers 12a and 12b containing only 3'leads to5' internucleotide linkages.     

Rapid synthesis of long-chain deoxyribooligonucleotides by the N-methylimidazolide phosphotriester method.

A modified phosphotriester method has been employed for the efficient chemical synthesis of long-chain deoxyribooligonucleotides. During the course of this work, a general and rapid procedure was developed for the preparation of 24-62-mers in solution. Preparative reversed phase column chromatography on silanized silica gel was used to purify triester intermediates starting from 10-mers. The rapid synthesis of 32-mer and 42-mer on glass and silica gel supports using suitably protected 2-8-mer blocks as coupling units has been also accomplished. In particular, a convenient procedure for the solid-phase synthesis of oligonucleotide blocks bearing 3'-terminal phosphodiester groups is described.     

NBS-DMSO as a nonaqueous nonbasic oxidation reagent for the synthesis of oligonucleotides

A new method for the oxidation of nucleoside phosphite triester into phosphate triester under nonbasic and nonaqueous conditions using NBS-DMSO in CH(3)CN has been developed. The utility of this method for solution- and solid-phase synthesis of oligonucleotide is demonstrated.     

l-Methyl-Z-(2′-Hydroxyphenyl)Imidazole–A Catalytic Phosphate protecting group in deoxyoligonucleotide synthesis

Abstract

The rate of condensation using the phosphate triester method of deoxyoligonucleotide synthesis is dramatically increased by the introduction of a phosphate protecting group bearing a nuclcophilic catalyst in the proper position. Following condensation (resulting in the formation of a phosphate triester) the catalytic protecting group can be removed leaving a dinucleotide, or the condensation reaction can be repeated to synthesize an oligonucleotide. This development is a significant advance in the chemical synthesis of deoxyoligonucleotides.     

Synthesis of chimeric oligonucleotides containing internucleosidic phosphodiester and S-pivaloylthioethyl phosphotriester residues

Novel oligonucleotide analogs that bear phosphodiester and bioreversible S-pivaloyl 2-mercaptoethyl (SPME) phosphate triester internucleosidic linkages are described. Their synthesis employs a novel methodology of oligonucleotide deprotection under mild, non-aqueous conditions.     

Synthesis of phosphate-branched oligonucleotides

A solid-phase synthesis for phosphate-branched oligonucleotides is described. The method is based on coupling of a single nucleoside phosphorodiamidite to terminal hydroxyl functions of two solid-supported oligonucleotides. After oxidation of the phosphite triester obtained to a phosphate triester, the third branch is assembled by conventional phosphoramidite chemistry.     

A rapid and convenient synthesis of poly-thymidylic acid by the modified triester approach.

By using anhydrous triethylamine-pyridine to selectively remove the cyanoethyl group from the fully protected oligonucleotide, a substantial improvement has been achieved in yields and the rates of condensation by the modified triester approach from the 5' leads to 3' end. The unreacted oligonucleotide containing the 5'-hydroxy group was removed by treatment with bis (triazolyl)-p-chlorophenyl phosphate after each condensation in situ. These modifications, as exemplified by the synthesis of fully protected T12, T18, T24 and T38 in 80%, 77%, 70% and 50% yields respectively, should allow the ready synthesis of polynucleotides of even longer chain lengths by purely chemical methods.     

SYNTHESIS OF CHIMERIC OLIGONUCLEOTIDES CONTAINING INTERNUCLEOSIDIC PHOSPHODIESTER AND S–PIVALOYLTHIOETHYL PHOSPHOTRIESTER RESIDUES

Novel oligonucleotide analogs that bear phosphodiester and bioreversible Õ–pivaloyl 2–mercaptoethyl (SPME) phosphate triester internucleosidic linkages are described. Their synthesis employs a novel methodology of oligonucleotide deprotection under mild, non-aqueous conditions.     

Synthesis of Chimerical Oligonucleotides Containing Internucleosidic Phosphodiester and S-Pivaloyl Mercaptoethyl Phosphotriester Linkages

Abstract

Novel oligonucleotide analogs that bear phosphodiester and bioreversible S-pivaloyl 2-mercaptoethyl (SPME) phosphate triester internucleosidic linkages and their thioate analogs are described. Their synthesis involves new methodology for the deprotection of base-labile oligonucleotides.     

Site-localized mutagenesis directed by phosphotriester analogs of oligonucleotides

17- and 20-mer oligodeoxyribonucleotides and their analogues, containing one to four phosphate groups esterified with ethyl alcohol in different positions of oligonucleotide chain, were synthesized by modified triester method. Ethylated di- and trinucleotide blocks were prepared by transesterification method from chlorophenyl derivatives. The structures of the oligonucleotides were confirmed by Maxam-Gilbert sequencing method. Oligonucleotides were not totally complementary to the N-terminal region of lac Z'gene (coding for N-terminal fragment of beta-galactosidase) of phage M13mpB DNA and induced the formation of the proposed deletion mutant DNA M13mp1 delta T. Phosphotriester analogues were more effective mutagens as compared to phosphodiester oligonucleotides due to their stability to nucleases. The use of E. coli DNA-polymerase I provided the increase in the mutant yields in case of the phosphotriester analogues. The stability of the analogues to 5'----3'----5'-endonuclease action, the specificity of oligonucleotide: DNA binding and the structure of mutant DNA were studied by the Sanger sequencing method.     

A new approach to the synthesis of branched and branched cyclic oligoribonucleotides.

The six-step synthesis of the di-triethylammonium salt of 5[prime]-O -trityl-6-N-pivaloyladenosine-2[prime]-(H -phosphonate)-3'-[(2-chlorophenyl) phosphate]9 from 3', 5'- O -(1,1,3,3-tetraisopropyldisiloxan-1,3-diyl)-6-N-pivaloyla denosine1in 68% overall yield is described. Compound9is converted into a branched pentaribonucleoside tetraphosphate 24 and a branched cyclic pentaribonucleotide ('lariat') 25 by solution phase triester chemistry involving both H-phosphonate and conventional phosphotriester coupling reactions. The monomeric building block 9 is proposed as a universal synthon for the preparation of branched and branched cyclic oligoribonucleotides derived from adenosine.     

New efficient sulfurizing reagents for the preparation of oligodeoxyribonucleotide phosphorothioate analogues.

A set of new sulfurizing agents representing disulfides of arylsulfonic acids has been developed for the automated synthesis of phosphorothioate oligonucleotide analogues via the phosphoramidite method. These reagents, such as bis(benzenesulfonyl)disulfide, bis(p-toluenesulfonyl)disulfide, bis(p-methoxybenzensulfonyl)disulfide, and bis (p-chlorobenzenesulfonyl) disulfide, are easily prepared crystalline solid compounds. They are relatively inexpensive, easy to handle, and efficiently convert internucleotide cyanoethyl phosphite to the phosphorothioate triester within 1-2 min. The efficiency of phosphorothioate oligonucleotide synthesis with the use of these reagents is comparable to that of phosphodiester oligonucleotides.     

Enzymatic and Hybridization Properties of Oligonucleotide Analogues Containing Novel Phosphotriester Internucleotide Linkage

Abstract

Enhanced cellular uptake, stable and discriminating hybridization and increased stability in biological media are of particular interest for oligonucleotides of potential therapeutic application. Additionally, toxicity or immunogenicity of the oligonucleotide analogues and their biodegradation products should be minimized by minimal alteration of the biological structure and effort and cost of bulk production should be as low as possible by using a standard automated synthesis protocol. Oligonucleotide phosphotriesters with oligoethyleneglycol substituents show promise to ideally combine all these advantages. Here we describe the hybridization properties and the stability of modified oligonucleotides containing triester internucleotide linkages substituted with α,ω-dihydroxy-(3,6-dioxa)-octan-1-yl group (“triethyleneglycol triester linkages”) towards enzymatic degradation. The triester linkages are stable towards exo- and endonucleases. Regardless of number and position of triester linkages, the modified oligonucleotides showed practically no decrease of T_m in hybridization studies with complementary biological oligonucleotides. In further enzymatic studies the modified oligonucleotides were highly stable towards nucleases in human blood serum.     

Efficient synthesis of the cholinephosphate phospholipid headgroup

In search of an efficient method to prepare cholinephosphate headgroups in phospholipids under mild conditions (where the diacylglycerol moiety is not subject to oxidation), a method was developed for phosphorylation using a trialkyl phosphite and I2. The active intermediate is a phosphoryl iodide formed by oxidation of the phosphite with I2. 2-Bromoethanol, dimethyl chlorophosphite, and an alcohol (diglyceride) are converted to a phosphate triester in a one-pot reaction with high yield. In the second reaction, the phosphate triester is demethylated, and the ethyl bromide group is converted to choline by treatment with aqueous trimethylamine. This procedure is applied to the synthesis of hexadecylphosphocholine, and 1,2-didecanoyl-1-deoxy-1-thio-sn-glyceryo-3-phosphocholine.     

The chemical synthesis of oligoribonucleotides VII. A comparison of condensing agents in the coupling of silylated ribonucleosides.

The t-butyldimethylsilyl group is shown to be an ideal protecting group for the 2T-hydroxyl function of ribonucleosides during the synthesis of ribonucleotides using any of nine commonly used condensing agents. The phosphite coupling procedure compares favorably with all of the widely used condensing agents and provides a most convenient route to the key intermediates in the "modified" triester strategy.     

Formation of 4,4'-dimethoxytrityl-C-phosphonate oligonucleotides

Incomplete sulfurization during solid-phase synthesis of phosphorothioate oligonucleotides using phosphoramidite chemistry was identified as the cause of formation of two new classes of process-related oligonucleotide impurities containing a DMTr-C-phosphonate (DMTr=4,4'-dimethoxytrityl) moiety. Phosphite triester intermediates that failed to oxidize (sulfurize) to the corresponding phosphorothioate triester react during the subsequent acid-induced (dichloroacetic acid) detritylation with the DMTr cation or its equivalent in an Arbuzov-type reaction. This leads to formation of DMTr-C-phosphonate mono- and diesters resulting in oligonucleotides modified with a DMTr-C-phosphonate moiety located internally or at the 5'terminal hydroxy group. DMTr-C-phosphonate derivatives are not detected when optimized sulfurization conditions are employed.     

Diastereomeric Process Control in the Synthesis of Oligodeoxyribonucleotide Phosphorothioates

Abstract

The emergence of antisense and antigene oligonucleotides as potential sequenceselective inhibitors of gene expression is evidenced by the growing number of ongoing clinicals trials against a variety of diseases. First generation antisense therapeutics utilize a uniformly modified oligodeoxyribonucleotide phosphorothioate where one non-bridging oxygen atom is formally replaced by sulfur, because natural DNA is unstable towards extra- and intracellular enzymes. Phosphoramidite chemistry has been widely used for the synthesis of phosphorothioate oligonucleotides because of its potential for automation, high coupling efficiency, ease of site-specific thioate linkage incorporation, and ready scalability. The large scale solid-supported synthesis of phosphorothioates is presently carried out by initial formation of the internucleotidic phosphite linkage followed by sulfurization of the phosphite triester to phosphorothioate using the Beaucage reagent. The resulting O,O-linked phosphorothioate diester linkage in the oligonucleotide is a chiral functional group. For a typical 20-mer there are 524,288 (2¹⁹) possible diastereoisomers. Separation and individual quantification of this number of diastereomers is currently not feasible. In addition, the best reported methods for stereocontrolled synthesis of phosphorothioate oligomers are not presently useful for drug synthesis; that is, since net 100% enantiomeric excess is not achieved in the coupling step, the oligomeric product still consists of the same mixture of Sp and Rp diastereomers, except that the levels of all but one isomer are reduced to low individual levels. As a result, even a small change in the and Sp phosphorothioate diesters, due to racemization during coupling, indicating that the overall synthetic process is stereo reproducible and under inherent process control.