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416 Carbohydrates

nucleotide (one having a phosphate group on C-5 and an cleoside, such as a 5 -dimethoxytrityl-2 -deoxynucleoside

acetyl group on O-3 ) with a nucleotide or an oligonu- having a 3 -p-nitrophenylsuccinoyl group. The addition

cleotide having a blocked phosphate group on C-5 and a of successive deoxynucleotides to this support-bound

free hydroxyl group in position 3 . The second type, those deoxynucleoside is carried out by (a) removal of the

terminally phosphated at C-3 , are usually prepared from trityl (DMT) protecting group with trichloroacetic acid;

nucleosides phosphated at C-3 (which are not available (b) condensing with a tritylated deoxynucleoside 3 -

commercially). The monomers are acetylated on O-5 and phosphoramidite, to yield a deoxydinucleoside phosphite

treated with other monomers having free hydroxyl groups triester; (c) oxidizing of the phosphite triester to a phos-
on C-5 and a blocked phosphate group on C-3 to obtain phate triester with iodine (see Scheme 31). Repetitions of

the desired oligonucleotide. this sequence have been used to synthesize DNA segments
In both cases, it is necessary to block the phosphate containing up to 200 deoxynucleotides. Once a synthesis
groups to prevent the formation of anhydrides (pyrophos- is complete, the oligodeoxynucleotide is removed from
phates). This is done by treating the nucleotide with the column, freed of protecting groups, and isolated by
3-hydroxypropanonitrile to obtain an ester removable with gel electrophoresis and purified by HPLC.
alkali (β elimination). Other phosphate-blocking groups
include PhCH 2 O (CH 2 ) 2 NH 2 , which forms an amide
hydrolyzable by acids. SEE ALSO THE FOLLOWING ARTICLES
The coupling of the two nucleotide moieties involves
formation of a phosphoric diester from a monoester (or a
BIOPOLYMERS • PHYSICAL ORGANIC CHEMISTRY • PULP
triester from a diester). The reaction is catalyzed by such
AND PAPER
condensing agents as dicyclohexylcarbodiimide (DCC), a
reagent extensively used in peptide synthesis, or arylsul-
fonyl chlorides (for example, 2,4,6-trimethylphenyl- or BIBLIOGRAPHY
2,4,6-triisopropylphenylsulfonyl chloride).
All nucleotides possessing primary amino groups (three
Aspinall, G. O., ed. (1982). “The Polysaccharides,” Academic Press,
of the four bases present in DNA and RNA nucleotides),
New York.
namely adenylic, guanylic, and cytidylic acid, must have Boons G. J., ed. (1998). “Carbohydrate Chemistry,” Academic and Pro-
their amino groups protected to prevent the formation of fessional.
amide ester bridges (instead of diester phosphate bridges). Ginsberg, V., and Robbins, P. W. (1991). “Biology of Carbohydrates,”
The primary amino group of adenylic acid is usually pro- Jai Press, Tokyo.
Robert M. Giuliano, R. M., ed. (1992). “Cycloaddition Reactions in
tected by a benzoyl (or p-methoxybenzoyl) group. This is
Carbohydrate Chemistry,” ACS Symposium Series, Washington D.C.
achieved by treating the nucleotide with an excess of ben- Gyorgydeak, Z., and Pelyvas, Z. F. (1998). “Monosaccharide Sugars,”
zoyl chloride and removing the undesired benzoyl groups Academic Press, New York.
with alkali. Guanylic acid is usually protected by reac- Hanessian, S. (1983). “Total Synthesis of Natural Products,” Pergamon,
tion with N,N-dimethylformamide diethyl acetal to give Oxford,England.
Horton, D., ed. (1995). “Advances in Carbohydrate Chemistry and
a readily removable Schiff base. Finally, cytidylic acid is
Biochemistry,” Vol. 50, Academic Press, New York.
protected by formation of a carbamate (see Scheme 30). Horton, D., ed. (1996). “Advances in Carbohydrate Chemistry and
Biochemistry,” Vol. 51, Academic Press, New York.
Horton, D., ed. (1997). “Advances in Carbohydrate Chemistry and
C. Formation on Automated Oligonucleotide Biochemistry,” Vol. 52, Academic Press, New York.
Synthesizers Horton, D., ed. (1998). “Advances in Carbohydrate Chemistry and
Biochemistry,” Vol. 53, Academic Press, New York.
The phosphite triester approach is commonly used with Horton, D., ed. (1999). “Advances in Carbohydrate Chemistry and
automatic synthesizers. The phosphite ester formed is ox- Biochemistry,” Vol. 54, Academic Press, New York.
idized at the end of each sequence to a phosphate ester. Kennedy, J. F., ed. (1988). “Carbohydrate Chemistry,” Clarendon Press,
Typically, a deoxynucleoside 3 -phosphoramidite is added Oxford, England.

Ogura, H., Hasegawa, A., and Suami, T. (1992). “Carbohydrate Synthetic
toagrowingDNAsegmentthatislinkedtoasilicasupport.
Methods,” Kondasha, Tokyo.
The silica is first reacted with a 3-aminopropyl triethoxysi- Postema, M. H. D. (1995). “C–Glycosides Syntheses,” CRC Press,
lane linker and then with an appropriate tritylated nu- Cleveland.