Collis, Alana E.C.
(2008)
The synthesis of vinylphosphonate-linked RNA.
PhD thesis, University of Nottingham.
Abstract
An introductory chapter discusses the steric block, RNase H and RNA interference antisense mechanisms and the application of antisense nucleic acids as therapeutic agents. Examples of existing chemical modifications of the sugar and backbone regions of nucleic acids are given, followed by the introduction of the vinylphosphonate modification. The vinylphosphonate has previously been examined in DNA and has been synthesised by either Pd(0) catalysed cross-coupling of an H-phosphonate with a vinyl bromide, or by the cross-metathesis of a vinylphosphonate with a terminal olefin.
This thesis details the first examples of the vinylphosphonate modification in RNA. The initial aim of this project was the synthesis of a range of nucleosides where the 5'-C-O was replaced by a vinyl bromide carbon-carbon double bond.
Starting from alpha-D-glucose, acid catalysed formation of the 1,2:5,6-diisopropylidene alpha-D-glucofuranose was carried out followed by protection of the 3-OH as an acetate. The 5,6-isopropylidene was then subjected to H5IO6 mediated one-pot hydrolysis-oxidative cleavage to obtain the 5-aldehyde. Wittig olefination using CBr4 and Ph3P led to the dibromo olefin which was then stereoselectively reduced using dimethyl phosphite and diisopropylamine to obtain the pure trans-vinyl bromide. Following hydrolysis of the acetate, the stereochemistry of the 3-OH was then inverted by sequential oxidation and reduction. With the correct stereochemistry, the 3-OH was protected as the 2-methylnaphthyl ether. The 1,2-isopropylidene moiety was then hydrolysed and acetylated to the bis-acetate which was subjected to Vorbruggen conditions obtaining the uridine (93%), adenosine (77%), cytidine (30) and guanosine (63%) vinyl bromide nucleosides. The 2'-OAc of the nucleosides were hydrolysed to the 2'-OH in yields of 74-92%. The uridine 2'-OH was protected as the 2'-OTBS ether (98%), analogous to the commercially available phosphoramidites used in automated oligonucleotide synthesis. Similarly, the adenosine and uridine nucleosides could also be blocked as the 2'-OMe (59% and 73% respectively). In the case of the uridine vinyl bromide, the 3'-O-(2-methylnaphthyl) protecting group was cleaved using DDQ, this then enabled the vinylphosphonate-linked uridine dinucleotides to be functionalised at the 3'-OH as the cyanoethyl phosphoramidite using N,N-diisopropyl-2-cyanoethyl-chlorophosphoramidite, DIPEA and DMAP in dichloromethane (2'-OTBS 74%, 2'-OMe 41%). These could then be used in automated solid phase oligonucleotide synthesis.
The H-phosphonates were prepared in a single step form the commercially available phosphoramidites using a tetrazole. These were then coupled to the vinyl bromide nucleosides using standard conditions of Pd(OAc)2 (0.2 eq.), dppf (0.4 eq.) and propylene oxide (20 eq.) in THF at 70 oC in a sealed vial for 6 hours. A range of vinylphosphonate-linked dinucleotides were accessed in yields of 61-99%.
A detailed experimental section at the end of this thesis describes the procedures used in the synthesis and the analysis of the structures obtained.
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