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2'-Deoxyxanthosine CE-Phosphoramidite (dX CE-Phosphoramidite)

2'-Deoxyxanthosine CE-Phosphoramidite (dX CE-Phosphoramidite)

CAS No.:292050-43-2

Useful phosphoramidite for the incorporation of 2'-deoxyxanthosine (dX) nucleotides into oligonucleotides.
  • Extends the ‘genetic alphabet’ by purine partnering with 5-(ß-Dribofuranosyl)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 (X) and 2'-deoxyxanthosine (dX), the products of deamination of G and dG, have been incorporated into oligonucleotides,(1) imparting a variety of properties to these nucleic acids. The pKa of the proton at N3 of dX is 5.5-5.7.1b,1h therefore dX is present as a mono-anion to the extent of about 95% at neutral pH. dX residues have the same hydrogen-bond donor/acceptor pattern as thymidine, thus allowing base-pairing with dA.1h This leads to a distortion of the helix, since two purines are paired. Stronger base stacking interactions are apparent. Duplex stability variations as a function of the opposing base pair have been studied.1d,1h dX is susceptible to depurination under acidic conditions, forming abasic sites.1b,1h At pH 4, dX depurinates more quickly than dG by a factor of about 1000. At neutral pH, dX has about the same stability as dG. The recognition and excision of dX by base excision repair enzymes has been studied.1b dX has been considered to be a promiscuous or universal nucleoside.1a,1h dX may expand the genetic code when paired to a pyrimidine-2,4-diamine C-nucleoside.1e Studies of polymerase-mediated incorporation of various nucleotides opposite dX have been carried out.1b,1d The presence of dX residues may lead to triplexes, quartets, and other G-stranded structures.1h We offer the 2'-Deoxyxanthosine-CE Phosphoramidite (BA0313), featuring 2-(4-nitrophenyl)ethyl (NPE) protecting groups at O2 and O6.1a,1b

Ref:

  1. (a) Jurczyk, S. C.; Horlacher, J.; Devined, K. G.; Benner, S. A.; Battersby, T. R. Helv. Chim. Acta 2000, 83, 1517-1524. (b) Weunschell, G. E.; O'Connor, T. R.; Termini, J. Biochemistry, 2003, 42, 3608-3616. (c) Tuschl, T.; Ng, M. M. P.; Pieken, W.; Benseler, F.; Eckstein, F. Biochemistry 1993, 32, 11658-11668. (d) Eritja, R.; Horowitz, D. M.; Walker, P. A.; Ziehler-Martin, J. P.; Boosalis, M. S.; Goodman, M. F.; Itakura, K.; Kaplan, B. E. Nucleic Acids Res. 1986, 14, 8135-8153. (e) Van Aerschot, A.; Mag, M.; Herdewijn, P.; Vanderhaeghe, H. Nucleosides Nucleotides Nucleic Acids 1989, 8, 159-178. (f) Lutz, M. J.; Held, H. A.; Hottiger, M.; Hubscher, U.; Benner, S. A. Nucleic Acids Res. 1996, 24, 1308-1313. (g) Groebke, K.; Hunziker, J.; Fraser, W.; Peng, L.; Diederichsen, U.; Zimmermann, K.; Holzner, A.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1998, 81, 375. (h) Seela, F.; Shaikh, K. I. Helv. Chim. Acta 2006, 89, 2794-2814.

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