Pseudouridine (ψ) is one of the most common modified nucleosides found in RNA.⁽¹⁾ The uracil nucleobase is identical to that found in uridine except that it is attached to the ribose ring via C5 rather than N1, i.e. it is a C-nucleoside. Thus, in addition to the ability to form Watson-Crick base pairs with adenosine in the normal manner, it has an additional hydrogen bond donor at N1. This difference can strongly influence the overall structure of an RNA oligonucleotide. The ability to install a ψ residue site-specifically allows the systematic study of its effect on the structure, function and stability of RNA. Several strategies have been reported for the incorporation of ψ during the chemical synthesis of RNA oligonucleotides.⁽²⁾ We now offer Pseudouridine CE-Phosphoramidite (BA0280) for this purpose. This particular version of pseudouridine phosphoramidite relies on standard cyanoethyl phosphoramidite coupling chemistry, 2'-O-TBDMS protection, and no nucleobase protecting groups.

Ref:

1. Charette, M.; Gray, M. W. IUBMB Life 2000, 49, 341-351.
2. (a) Hall, K. B.; McLaughlin, L. W. Nucleic Acids Res. 1992, 20, 1883-1889. See also reference (b) for a closely related phosphoramidite (NEtMe rather than N(i-Pr)2). (b) Gasparutto, D.; Livache, T.; Bazin, H.; Duplaa, A.-M.; Guy, A.; Khorlin, A.; Molko, D.; Roget, A.; Teoule, R. Nucleic Acids Res. 1992, 20, 5159-5166. This work describes a phosphoramidite similar to Pseudouridine CEP, but with an N-ethyl-N-methyl phosphoramidite. (c) Pieles, U.; Beijer, B.; Bohmann, K.; Weston, S.; O'Loughlin, S.; Adam, V.; Sproat, B. S. J. Chem. Soc., Perkin Trans. 1 1994, 3423-3429. This report describes a pseudouridine phosphoramidite bearing pivaloyloxymethyl protecting groups at N1 and N3 and an Fpmp group at the 2'-oxygen. See also the references provided therein for early non-phosphoramidite routes to pseudouridine incorporation. (d) Agris, P. F.; Malkiewicz, A.; Kraszewski, A.; Everett, K.; Nawrot, B.; Sochacka, E.; Jankowska, J.; Guenther, R. Biochemie 1995, 77, 125-134. (e) Meroueh, M.; Grohar, P. J.; Qiu, J.; SantaLucia, J., Jr.; Scaringe, S. A.; Chow, C. S. Nucleic Acids Res. 2000, 28, 2075-2083. This paper describes pseudouridine incorporation using the Scaringe/Dharmacon 2'-O-ACE method for RNA synthesis. See also: (f) Chui, H. M.-P.; Meroueh, M.; Scaringe, S. A.; Chow, C. S. Bioorg. Med. Chem. 2002, 10, 325-332 and © Chui, H. M.-P.; Desaulniers, J.-P.; Scaringe, S. A.; Chow, C. S. J. Org. Chem. 2002, 67, 8847-8854.