12
Bioorganic Chemistry
OCH
3
O
CH
3
O
O
N
1
O
O
Link to
resin
DMT protecting group
TCA
(DMT
cleavage)
O
DMT-O
N
2
O
P
(C
3
H
7
)
2
N
OCH
3
HO
O
N
1
O
O
Addition
N
N
N
H
N
(Tetrazole)
O
N
1
O
O
O
P
OCH
3
O
O
N
2
DMT-O
O
N
1
O
O
O
P
OCH
3
O
O
N
2
DMT-O
O
1. “Capping”
2. Oxidation
Fig. 8
Oligonucleotide synthesis begins with
the tethering of the Frst monomer to an
insoluble resin via an ester linkage to its 3
0
hydroxyl group. To prevent esteriFcation of the 5
0
hydroxyl instead, it is blocked with a dimethoxy
trityl group (DMT). After the ester linkage to
resin has been formed, the DMT group is cleaved
with acid. The next monomer (also 5
0
hydroxyl
DMT protected) contains a phosphoramidite
group attached to its 3
0
hydroxyl. The
displacement of the phosphoramidite amine by
the deprotected 5
0
hydroxyl is catalyzed by the
addition of tetrazole. ‘‘Capping’’ or acetylation of
the 5
0
hydroxyl group of any monomer that did
not react with the phosphoramidite prevents
errors from compounding. The capping prevents
the unreacted, and therefore incorrect, oligomer
from undergoing further chemistry. After the
coupling between monomers has taken place,
the phosphoramidite is oxidized to form the
phosphate triester using either hydrogen
peroxide or iodine. The DMT group is cleaved,
thereby releasing the 5
0
hydroxyl that can then
participate in the next round of monomer
addition. When the oligomer is complete, a Fnal
step of deprotection removes the Fnal DMT
group, any protecting groups on the nucleotide
bases, and converts the phosphate triester into
the naturally occurring diester.
this is that there is a destabilizing ef-
fect produced when like-charged species
are brought together. This is precisely the
situation with double-stranded DNA. The
distance between phosphate groups on op-
posite strands can be as little as 8
˚
A, thus
producing a signiFcant electrostatic repul-
sion. Obviously, there are enough other
interactions in dsDNA such as the hy-
drogen bonding between the base pairs
and van der Waals’ interactions between
stacked base pairs to overcome this desta-
bilizing influence. In the case of the PNA,
these positive interactions are maintained,
while the destabilizing electrostatic repul-
sion is eliminated. Thus, the stability of
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