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(ImHpPyPy)2 AGTACT |
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X-ray crystal structure of the polyamide
ImHpPyPy-β-Dp bound as a homodimer in the minor groove to the target DNA sequence, 5'-AGTACT-3'.
Imidazole (Im), 3-hydroxypyrrole (Hp), and pyrrole (Py) residues are shown in red, yellow, and white,
respectively. This structure demonstrates the complete set of pairing rules for specific recognition of
all four Watson-Crick base pairs by Im/Hp/Py polyamides. Im/Py ring pairings target G·C base
pairs via a directional hydrogen bond between the N-3 of Im and exocyclic amine of G. T·A vs
A·T discrimination is achieved by Hp/Py and Py/Hp pairs, respectively. The 3-hydroxy of the Hp
residue makes a hydrogen bond to the O-2 carbonyl of T and provides steric bulk that favors the
asymmetric cleft on the T side of a T·A base pair. Further details of the structure can be found in
Kielkopf et. al. and an overview of polyamide:DNA recognition
is also provided. |
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