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Deoxyxanthosine CE-Phosphoramidite

Deoxyxanthosine CE-Phosphoramidite

CAS No.:292050-43-2

Phosphoramidite used to incorporate a dX base into an oligonucleotide.

Key features

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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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Product information

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.


  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.

Applicable Products

LK2013 dU-CE Phosphoramidite
LK2016 dI-CE Phosphoramidite
LK2017 5-Me-dC(Bz)-CE Phosphoramidite
LK2145 2-Amino-dA-CE Phosphoramidite
LK2164 2'-Deoxyxanthosine-CE Phosphoramidite
LK2287 dU SynBase™ CPG 1000/110
LK2293 dI SynBase™ CPG 1000/110
LK2323 5-Me-dC SynBase™ CPG 1000/110
LK2529 5-Me-dC(Ac)-CE Phosphoramidite

Physical & Dilution Data

Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (LK4050). Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.


Mol. Formula

Mol. Wt.

Unit Wt.




LK2013 C39H47N4O8P 730.80 290.17 3.42 6.84 13.68
LK2016 C40H47N6O7 754.83 314.19 3.31 6.62 13.25
LK2017 C47H54N5O8P 847.90 303.21 2.95 5.90 11.79
LK2145 C58H83N10O6P 1047.33 328.22 2.39 4.77 9.55
LK2164 C56H61N8O12P 1069.12 330.20 2.34 4.68 9.35
LK2287 - - 290.17 - - -
LK2293 - - 314.19 - - -
LK2323 - - 303.21 - - -
LK2529 C42H52N5O8P 785.88 303.21 3.18 6.36 12.72


Couple the phosphoramidites LK2013, LK2016 and LK2017 using the standard method as recommended by synthesiser manufacturer with coupling times as per standard bases. 90s is recommended for 2529. A coupling time of 15min is recommended for LK2145. A coupling time of 3min is recommended for LK2164. The solid supports are used as per standard nucleoside supports.


For LK2013, LK2016, LK2017 and LK2529 standard oligonucleotide deprotection conditions can be applied when deprotecting an oligo containing these modifications, however LK2013, LK2016 and LK2529 are also compatible with AMA deprotection; typically 10min at 55oC.

LK2145 - Use AMA deprotection in conjunction with Ac-dC, rather than Bz-dC, or transamidation will occur. The supports are cleaved and deprotection carried out using the protocols required by the nucleobases.

LK2164 - Cleavage from support and primary deprotection is accomplished by treatment with ammonium hydroxide solution at room temperature for 24h.

After removing the solution1, the NPE groups are removed by treatment with 0.3M tetramethylguanidinium 2-nitrobenzaldoximate solution in water/dioxan (1:1) at 70°C for 48h. We find that this extended treatment is necessary to ensure complete removal of both of the NPE protecting groups.

It should be noted that this treatment generates a variety of low molecular weight by-products which are observed in the HPLC. Satisfactory results are obtained by de-salting the deprotection mixture into water using a NAP or G25 column before HPLC, from which the final oligonucleotide product can then be isolated.

Storage & Stability

Refrigerate dry compounds. Stability of phosphoramidites in solution is similar to standard dA, dC, dG and dT monomers.


  1. This is best achieved by removing the deprotection solution by G25 then freeze drying to remove the water. Heat cannot be used or the NPE groups would cleave.

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