Oligonucleotides Containing Modified Phosphodiester Linkages

A method for the synthesis of N3 -P5 phosphoramidite internucleoside linkages has been reported. The solid-supported chain assembly, which proceeds from 5 -3 utilises a support bound 3 -dideoxyamino nucleoside coupling with a 

Peptide nucleic acid (PNA) has received considerable attention for several years as a candidate for antisense exploitation. Several publications have addressed the physical and biological properties, applications and characterisation of PNA and modified PNAs. One problem associated with PNA is its poor solubility. There has therefore been interest in the synthesis of mixed PNA-DNA chimeras and the introduction of charge into the PNA monomer itself. Phosphonate PNA 157a has been prepared using the aminomethylpho-sphonate 157b. Proline derived PNA monomers 158 have been described.  

A dimer block assembly strategy has been utilised to synthesise oligonucleotides with a triazole (159a b) or imidazole (159c d) internucleoside linkage. 

DNA containing 2, 5 -phosphodiester linkages (160) has been prepared and its properties have been investigated. The 2, 5 -linked DNA was found to 

Circular oligonucleotides (DNA dumbbells) are of interest for the study of DNA structure and their resistance to exonucleases. Lim and Hunt have compared enzymatic and chemical methodologies for the synthesis of circular DNA. Chemical ligation utilising cyanogen bromide was found to be faster and less costly than the use of DNA ligase.  

Oligonucleotides containing phosphorothioate intemucleoside linkages (122) have been of interest for several years now. Full details describing the stereospecific synthesis of phosphorothioates using the oxathiaphospholane monomers 

Kuimelis and McLaughlin have prepared an oligonucleotide containing an intemucleoside 5 -phosphorothiolate RNA linkage Although em- 

N-Pent-4-enoyl protected nucleosides (see section of DNA synthesis) have been utilised in an /f-phosphonate-mediated assembly of oligomers containing methyl phosphotriester (138) and phosphoramidite (139) linkages - The stereospecific conversion of /f-phosphonates into phosphoramidites upon treatment with butylamine in carbon tetrachloride has been monitored by NMR and found to proceed with inversion of stereochemistry at phosphorus.  

The synthesis of methylene(methylamino) linked oligonucleotides (144) has been automated and performed on solid phase. Oligonucleotides having hydroxymethylphosphonate intemucleotide linkages (145) have been synthesised from the corresponding /f-phosphonate via a trimethylphosphite intermediate (146). 2  

Oligonucleotides containing the sulfide linked dinucleoside units (147a-d) have been prepared and their preference for binding to RNA has been explored. A series of modified oligonucleotides containing the intemucleotide linkages 

A synthetic procedure has been developed which enables the (Rp)-diastereoisomer of dinucleoside methanephosphonates to be prepared in up to 79% diastereomeric excess.Reaction of dichloromethylphosphine with the 3 -hydroxy function of an otherwise protected nucleoside at -80 C gives the chloromethylphosphlne (81) as a 1 1 mixture of dlastereoisomers as determined by n.m.r. Stereochemical induction therefore occurs in the subsequent 

Anti-sense ollgodeoxyribonucleotides containing either phosphorothioate or natural linkages have been shown to inhibit the replication and expression of human immunodeficiency virus already growing in tissue culture (MOLT-3 cells).The efficiency of inhibition is much greater than that observed with random and homo-oligomers of the same length and reinforces the concept 

The formation of a triple-helix with dA19.dT19.dT19 has been studied in which one of the homo-pyrimidine oligodeoxyrlbonucleotlde strands is replaced with the analogous strand containing all methanephosphonate linkages.In contrast to a previous report there was no evidence for triple-helix formation. 

Nucleoside 3 -0-phosphonothioates (95) are also useful synthetic precursors for phosphorodlthloate-containlng oligonucleotides and can be prepared in 80-90Z yield by reaction of a suitably protected nucleoside with phosphinic acid in the presence of plvaloyl chloride and subsequent oxidation with elemental sulphur. 

Oligodeoxyrlbonucleotide analogues containing flexible aliphatic, non-ionic, achiral spacers are of interest as potential anti-sense agents. Analogues containing the 3 0-5 C oxyacetamide linkage were first reported in 1974, and an improved procedure for their preparation has recently been published. The pyridinium salts of 5 -azido-3 -0-carboxymethyl nucleosides 

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The ability to synthesise oligonucleotides containing modified phosphodiester linkages continues to be of great interest in the therapeutic area. In particular it is desirable to confer through these modifications enhanced cell permeability properties and nuclease resistance. Several previous candidates that confer these properties have modified the pho,sphodiester linkage in such a way that creates a chiral centre at phosphorus. The resultant complex mixture of diastereoisomers all meet the above requirements to different extents, Over the past year efforts have therefore concentrated on the synthesis of achiral alternative linkages or stereospecific syntheses of chiral phosphate modifications. A number of literature summaries in this area have appeared recently. 

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