Journal
FEBS JOURNAL
Volume 272, Issue 14, Pages 3531-3541Publisher
WILEY
DOI: 10.1111/j.1742-4658.2005.04773.x
Keywords
B-DNA double helix; base triplets; minor groove binder; netropsin; quantum chemical calculations
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The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using < smallcapitals > refmac 5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 angstrom, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.
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