Tetrahedron
Letters
Tetrahedron Letters 45 (2004) 9529–9531
Oligoribonucleotide synthesis by the use of
1-(2-cyanoethoxy)ethyl (CEE) as a 20-hydroxy protecting group
Tadashi Umemoto and Takeshi Wada*
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo,
Bioscience Bldg 702, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
Received 30 September 2004; revised 20 October 2004; accepted 22 October 2004
Available online 11 November 2004
Abstract—A novel method for the synthesis of oligoribonucleotides using 1-(2-cyanoethoxy)ethyl (CEE) as a 20-hydroxy protecting
group has been developed. A CEE group was introduced to the 20-position of N-acyl-30,50-O-silyl-protected ribonucleosides under
acidic conditions in good yields. The 20-O-CEE group was found to be stable in an aqueous or ethanolic ammonia and was quickly
removed by treatment with anhydrous tetrabutylammonium fluoride (TBAF). A combination of the use of N-acyl and 20-O-CEE
protecting groups enabled a reliable and complete two-step deprotection, first with NH3–EtOH, then with TBAF in THF, without
cleavage of internucleotidic linkages.
Ó 2004 Elsevier Ltd. All rights reserved.
Chemically synthesized oligoribonucleotides have be-
come increasingly important since the discovery of small
interfering RNAs (siRNAs).1 The mammalian siRNAs
consist of only 21–23 nucleotides,2,3 and their chain
lengths are suitable for chemical synthesis. Many re-
search groups have successfully synthesized RNAs by
various strategies.4 Compared with DNA, each nucleo-
tide unit of RNA contains an additional 20-hydroxy
group, which has to be protected regioselectively. 20-O-
TBDMS-Protection has been widely used for the
oligoribonucleotide synthesis by the phosphoramidite
approach.5 However, 20-O-TBDMS-protected mono-
mers possess lower coupling efficiency compared with
that of 20-deoxyribonucleoside derivatives due to the
steric hindrance of the TBDMS group. In recent years,
new protecting groups have been reported for the 20-
hydroxy function, such as fluoride-labile silicon-based
protecting groups6,7 and acid-labile acetals8–10 as well
as orthoester-type protecting groups.11 The acetal-type
protecting groups have excellent features such as capa-
bility for the 20-O-selective protection and lower steric
hindrance. However, these protecting groups are some-
what unstable under the strong acidic conditions pre-
scribed for the deprotection of the 50-O-DMTr group.
It has been reported that the introduction of an elec-
tron-withdrawing group to an acetal function stabilizes
the protecting group under acidic conditions.8,9 Pfleidrer
and co-workers have reported that the 1-(2-cyanoeth-
oxy)ethyl (CEE) was an acid-stable 20-hydroxy protect-
ing group for uridine.9 However, this stabilized acetal
group requires drastic acidic conditions for complete re-
moval. Therefore, the CEE group has not hitherto been
applied for oligoribonucleotide synthesis. In this letter,
we wish to report the application of a CEE group as
the first example of a base-labile acetal-type of 20-hydr-
oxy protection group for oligoribonucleotide synthesis.
The 20-O-CEE-protected ribonucleoside 30-phosphor-
amidite building blocks 4a–d were synthesized via the
N-acyl-50,30-O-(tetraisopropyldisiloxan-1,3-diyl)-protected
nucleosides 1a–d. Compounds 1a,b and d were allowed
to react with vinyloxypropionitrile12 in the presence of
p-toluenesulfonic acid in 1,4-dioxane to give the 20-O-
CEE-protected nucleosides (2a,b and d) in 94–97%
yields.9 In the case of the N-2-phenoxyacetylguanosine
derivative 1c, a side reaction occurred under the same
conditions. Therefore, the reaction was carried out in
the presence of pyridinium p-toluenesulfonate at 55°C
to afford 2c in an acceptable yield (75%). The selective
deprotection of the 30,50-cyclic silyl ethers was achieved
by treatment of 2 with 5equiv of tetrabutylammonium
fluoride (TBAF) and 6equiv of acetic acid in THF.9
The resulting intermediates bearing the free 50-OH were
Keywords: Oligoribonucleotide; Chemical synthesis; Protecting group.
*
Corresponding author. Tel./fax: +81 4 7136 3612; e-mail: wada@
k.u-tokyo.ac.jp
0040-4039/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2004.10.151