ISSN 1068-1620, Russian Journal of Bioorganic Chemistry, 2009, Vol. 35, No. 2, pp. 250–253. © Pleiades Publishing, Ltd., 2009.
Original Russian Text © V.A. Efimov, A.V. Aralov, S.V. Fedunin, V.N. Klykov, O.G. Chakhmakhcheva, 2009, published in Bioorganicheskaya Khimiya, 2009, Vol. 35, No. 2,
pp. 270–273.
LETTERS TO THE EDITOR
An Azidomethyl Protective Group in the Synthesis
of Oligoribonucleotides by the Phosphotriester Method
V. A. Efimov1, A. V. Aralov, S. V. Fedunin, V. N. Klykov, and O. G. Chakhmakhcheva
Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences,
ul. Miklukho-Maklaya 16/10, GSP Moscow, 117997 Russia
Received September 26, 2008; in final form, October 8, 2008
Abstract—A rapid and effective method of an automatic oligoribonucleotide synthesis alternative to the phos-
phoramidite one was developed. This method is based on the phosphotriester approach to internucleotide bond
formation under intramolecular O-nucleophilic catalysis and the use of an azidomethyl group for protection of
a nucleotide 2'-hydroxyl function.
Key words: azidomethyl group, rapid phosphotriester method, oligoribonucleotides, synthesis
DOI: 10.1134/S1068162009020149
INTRODUCTION
idues [3]. In addition, the potential of this method for
preparation of stereospecific oligonucleotide phospho-
rothioate analogues was shown [4, 5].
Natural and modified oligonucleotides are universal
tools for the solution of a wide range of problems in
molecular biology, gene engineering, biotechnology,
and medicine.2 Recently, synthetic RNA fragments,
particularly, ribozymes and small double-stranded
RNA interferences, which are widely used in functional
genomics and regarded as potential drugs, have
attracted the interest of numerous research groups.
Therefore, the necessity of the development of effective
methods of chemical synthesis of natural RNA frag-
ments and their analogues with predetermined proper-
ties has increased.
Unlike deoxyribonucleotides, ribonucleotides con-
tain additional 2'-OH groups, which considerably ham-
pers synthesis of their oligomers and makes the choice
of protective groups for this function one of the crucial
steps of the oligoribonucleotide synthesis. A protective
2'-OH group must be stable both in the process of chain
elongation and upon removal of other protective
groups, and must be removed at the last step under con-
ditions preventing degradation of the resulting oligori-
bonucleotide. For blocking 2'-OH groups in the phos-
phoramidite method,
a
tert-butyldimethylsilyl
Until now, the phosphoramidite method was the
only well-developed method of oligoribonucleotide
synthesis [1]. However, due to its chemical specific fea- and bis(2-acetoxyethoxy)methyl (ACE) [8] groups are
(TBDMS) [6], triisopropylsilyloxymethyl (TOM) [7],
tures it cannot be used for the synthesis of some modi-
fied oligonucleotides, particularly derivatives contain-
ing strong electrophilic centers (for example, azide or
N-oxide groups) or stereospecific phosphorothioate
analogues of nucleic acids.
used. However, all of them suffer from some disadvan-
tages which complicate the synthesis. In particular,
bulky TBDMS and TOM groups raise spatial hin-
drances that results in an increase in internucleotide
coupling time and yield reduction, whereas the synthe-
sis of ANA phosphoroamidite derivatives is difficult
and commercially unreasonable.
The phosphotriester method involving é-nucleo-
philic intramolecular catalysis at the stage of internu-
cleotide bond formation is an alternative approach to
the oligoribonucleotide synthesis. Earlier, it was suc-
cessfully used for the synthesis of natural oligodeoxyri-
bonucleotides [2] as well as modified oligonucleotides
containing 2'-azido- and 2'-amino-2'-deoxyuridine res-
In the process of development of effective
approaches to the synthesis of natural and modified oli-
goribonucleotides by the phosphotriester method under
intramolecular é-nucleophilic catalysis, we screened
various groups for the ribonucleotide 2'-OH hydroxyl
protection that met the requirements of the phosphotri-
ester approach. One of the selected groups was a 2'-é-
azidomethyl one. The preparation and properties of 2'-
é-azidomethyl nucleoside derivatives were described
earlier [9], but this group was not used in the phosphor-
amidite and H-phosphonate methods of oligonucle-
1
Corresponding author; phone: +7 (495) 336-5911; fax: +7 (495)
330-6738; e-mail: eva@mx.ibch.ru
2
Abbreviations: MTM, methylthiomethyl group; NBS-C1, 2-
nitrobenzenesulfenyl chloride; TBAF, tetrabutylammonium fluo-
ride; TIPDS-Cl , 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane;
2
TPS-C1, 2,4,6-triisopropylbenzenesulfonyl chloride; DBU, 1,8-
diazabicyclo[5.4.0]undec-7-ene.
250