Oligonucleotide methylphosphonate

Miller, P.S. (1991). Oligonucleotide methylphosphonates as antisense reagents. Bio/Technology 9,358 362. 

Jayaraman, K., McParland, K., Miller, P., and Tso, P.O.P. 1981. Non-ionic oligonucleoside methylphosphonates. 4. Selective inhibition of Escherichia coli protein synthesis and growth by non-ionic oligonucleotides complementary to the 3 end of 16S ribosomal-RNA. Proc. Natl. Acad. Sci. U.S.A. 78 1537-1541. 

Structures of oligonucleotides with modified backbone include an NMR study of the duplex d(TGTTTGGC) with diasteromerically pure Rp or Sp methylphos-phonates of the duplex d(CCAAACA). Substitution was carried out using either all Rp or a single central Sp in an otherwise Rp oligonucleotide. The methyl-phosphonate strand showed increased dynamics relative to the phosphodiester strand, and whilst sugars in the phosphodiester strand are C -endo, in the methylphosphonate strand they are an intermediate C4-endo. The introduction... 

T. R. Baker, T. Keough, R.L.M. Dobson, T.A. Riley, J.A. Hasselfield, P.E. Hesselberth, Antisense DNA oligonucleotides I the use of ESI-MS-MS for the sequence verification of methylphosphonate oligodeoxyribo-nucleotides. Rapid Commun. Mass Spectrom., 7 (1993) 190. 

This year s nucleotide and nucleic acid literature has been dominated by interest in internucleoside linkages. A number of approaches to novel internucleoside linkages in dimers have been published in addition to stereoselective routes to phosphorothioate and methylphosphonate linkages. In some cases these studies have also extended to the oligonucleotide level. In addition a number of novel nucleotide analogues have been described. One of the most exciting areas in the field of nucleic acid chemistry is the application of in vitro selection techniques and these are reviewed for the first time. 

J. A. Hesselberth, P.E. Antisense DNA Oligonucleotides. II The Use of Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for the Sequence Verification of Methylphosphonate Oligodeoxyribonucleotides, Rapid Commun. Mass Spectrom. 7, 195-200 (1993). 

Bohringer, M.P., Graff, D., and Caruthers, M.H., Synthesis of 5 -deoxy-5 -methylphosphonate linked thymidine oligonucleotides. Tetrahedron Lett., 34, 2723, 1993. 

With respect to pharmacokinetics it is obvious that biotransformation of natural or only slightly modified natural oligonucleotides - mainly by action of nucleases - is a major obstacle towards application of such compounds. It is not surprising that first of all a variety of modifications of the labile phosphodiester bond has been developed, with phosphorothioate and methylphosphonate groups being hitherto the most successful approaches (see section 6). This report will also include structures such as peptide nucleic acids (PNAs), which are promising bio-isosteres of natural lead structures (see section 10.1). 

The use of methylphosphonates (12) as antisense compounds has been reviewed by several authors [83,84]. Very good nuclease resistance and a different mechanism of membrane penetration are the most remarkable features of this ODN modification [85]. The lack of anionic charge however renders the compounds relatively insoluble in water. Drug/target duplexes do not activate RNase-H. Therefore, high concentrations of up to 100 pM are required to achieve antisense activity. Nevertheless, methylphosphonates seem to be suited elements of chimeric oligonucleotides. 

Gray G D, Basu S, Wickstrom E (1997). Transformed and immortalized cellular uptake of oligodeoxynucleoside phosphorothioates, 3 -alkylamino oligonucleotides, 2 -0-methyl oligoribonucleotides, oligodeoxynucleoside methylphosphonates, and peptide nucleic acids. Biochem. Pharmacol. 53 1465-1476. 

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