14
Bioorganic Chemistry
Intercalation to DNA by
an acridine derivative
(highlighted above,
chemical structure shown
below).
Planer structure
stacks between planer
base-pairs.
Binding to minor groove by
distamycin (highlighted
above, chemical structure
shown below).
Exclusive
hydrogen bond donation to
AT rich regions which are
exclusively hydrogen bond
accepting.
Binding to minor groove
by side by side polyamide
(highlighted above).
Sequence specificity tuned
by use of both pyrrole and
imidazole, the latter which is
able to accept a hydrogen
bond from G.
TA
N
O
N
H
N
N
N
H
H
O
N
H
O
N
N
H
O
N
N
NH
2
NH
2
O
H
+
N
O
O
H
N
H
N
N
N
N
H
N
Fig. 11
Major sites of small-molecule interaction with DNA. (left) intercalation by acridine
derivative (middle) minor groove binding by distamycin (right) minor groove binding by
side-by-side polyamide oligomers.
covalent modifcations (including bond
cleavage
and
alkylation)
oF
the
nu-
cleotides, sugars, and phosphate backbone
(±ig. 11).
A
well-studied
DNA-binding
sma
l
lmo
lecu
leisthenatura
lproductd
is
-
tamycin (±ig. 11), which has been shown
to bind noncovalently and selectively to the
minor groove oF AT-rich portions oF DNA.
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