146 Chapter 4
synthesis with either dichloroacetic acid or trichloroacetic acid in non-aqueous solvent, conditions that
prevent other side reactions, such as depurination. During deprotection, the bright orange-red DMT cation
is liberated and is used as a measure of the yield of coupling of that nucleoside unit (Section 4.1.4).
4.1.2.3 Introduction of Phosphate. In the original chemistry developed by Khorana and co-workers
(phosphodiester, Section 4.1.3), deoxynucleoside 5-phosphates were used as building blocks. In other
chemistries developed more recently 5-O-dimethoxytrityl-(N-acylated)-2-deoxynucleosides are phosphor-
ylated or phosphitylated at the 3-hydroxyl group (Figure 4.5). In these cases the products of synthesis after
assembly of the oligonucleotide are phosphate triesters, where the internucleoside phosphate carries a pro-
tecting group. In phosphotriesterchemistry [P(V)] the best protecting groups are aryl (usually mono- or
di-chlorophenyl derivatives). This is because an aryl phosphodiester is a much more reactive deoxynucleo-
side building block than an alkyl phosphodiester in a coupling reaction. For example, 5-O-dimethoxytrityl-
N^6 -benzoyl-2-deoxyadenosine gives the corresponding 3-O-(2-chlorophenyl) phosphodiester by reaction
OMe
MeO
Figure 4.4 The 4,4-dimethoxyphenylmethyl (dimethoxytrityl, DMT) group
N
N
N
N NHBz
O
HO
HO
BzCl
BzCl
TMSCl
NaOH
NH 4 OH
N
N
N
N NBz 2
O
BzO
BzO
Route A
Per-acylation
Route B
Transient protection
N
N
N
N NH 2
O
HO
HO
N
N
N
N NH 2
O
TMSO
TMSO N
N
N
N NBz 2
O
TMSO
TMSO
Figure 4.3 Routes to N^6 -benzoyl-2-deoxyadenosine