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- Extends the ‘genetic alphabet’ by purine partnering with 5-(ß-D- ribofuranosyl)pyrimidine-2,4-diamine.
- Compatible with phosphoramidite synthesis cycle, however requires an extra deprotection reagent to remove the NPE groups.
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Xanthosine is a naturally occurring nucleoside containing a purine heterocycle that presents an H-bonding pattern to a complementary strand distinct from that presented by unmodified purines found in encoded oligonucleotides. Xanthosine has been proposed as a ‘universal base’, i.e. a heterocycle that can pair equally well with all four natural nucleosides.(1) As such, several studies have been carried out (as far back as the mid-1980s), incorporating deoxyxanthosine (dX) into oligonucleotides. However the expected base-pairing properties were not observed.
Other notable properties have been reported however. Benner and co-workers have described the extension of the ‘genetic alphabet’ by purine partnering dX with 5-(ß-D- ribofuranosyl)pyrimidine-2,4-diamine, a pyrimidine analogue presenting an H-bonding pattern complementary to dX.(2) dX has been used in the study of the physiologically important nitrosative deamination of DNA which is one of the main causes of genomic mutations.(3)
Although a number of monomers for the incorporation of dX have been reported (using phosphotriester or phosphoramidite chemistry), the most effective of these is the 2-(4-nitrophenyl)ethyl (NPE) O2/O6 doubly-protected monomer, our product 2'-Deoxyxanthosine-CE Phosphoramidite. This is used as per standard protocols, with an extra deprotection reagent to remove the NPE groups.
- (a) Double protection of the heterocyclic base of xanthosine and 2'-deoxyxanthosine, A. van Aerschot, M. Mag, P. Herdewijn and H. Vanderhaeghe, Nucleosides & Nucleotides, 8, 159-178, 1989; (b) Synthesis and properties of oligonucleotides containing 2'-deoxynebularine and 2'-deoxyxanthosine, R. Eritja, D.M. Horowitz, P.A. Walker, J.P. Ziehler-Martin, M.S. Boosalis, M.F. Goodman, K. Itakura and B.E. Kaplan, Nucleic Acids Research, 14, 8135-8153, 1986.
- Differential discrimination of DNA polymerases for variants of the non-standard nucleobase pair between xanthosine and 2,4-diaminopyridine, two components of an expanded genetic alphabet, M.J. Lutz, H.A. Held, M. Hottiger, U. Hübscher and S.A. Benner, Nucleic Acids Research, 24, 1308-1313, 1996.
- (a) Stability of 2'-deoxyxanthosine in DNA, V. Vongchampa, M. Dong, L. Gingipalli and P. Dedon, Nucleic Acids Research, 31, 1045-1051, 2003 ; (b) A bifunctional DNA repair protein from Ferroplasma acidarmanus exhibits O6-alkylguanine-DNA alkyltransferase and endonuclease V activities, S. Kanugula, G.T. Pauly, R.C. Moschel and A.E. Pegg, PNAS, 102, 3617-3622, 2005; (c) Synthesis and characterisation of oligonucleotides containing 2'-deoxyxanthosine using phosphoramidite chemistry, S.C. Jurczyk, J. Horlacher, K.G. Devined, S.A. Benner and T.R. Battersby, Helv. Chim. Acta., 83, 1517-1524, 2000; (d) Stability, miscoding potential and repair of 2'-deoxyxanthosine in DNA: Implications for nitric oxide-induced mutagenesis, G.E. Weunschell, T.R. O’Connor and J. Termini, Biochemistry, 42, 3608-3616, 2003.