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.

Ref:

1. (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.
2. 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.
3. (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.