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Nucleic Acids Research Advance Access originally published online on May 3, 2008
Nucleic Acids Research 2008 36(10):3508-3514; doi:10.1093/nar/gkn245
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Nucleic Acids Research, 2008, Vol. 36, No. 10 3508-3514
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Crystal structure of trioxacarcin A covalently bound to DNA

Roland Pfoh1, Hartmut Laatsch2 and George M. Sheldrick1,*

1Lehrstuhl für Strukturchemie, Georg-August-Universität, Tammannstr. 4, 37077 and 2Institut für Organische und Biomolekulare Chemie, Georg-August-Universität, Tammannstr. 2, 37077 Göttingen, Germany

*To whom correspondence should be addressed. Tel: +49 551 393021; Fax: +49 551 3922582; Email: gsheldr{at}shelx.uni-ac.gwdg.de

Received March 17, 2008. Revised April 16, 2008. Accepted April 16, 2008.

We report a crystal structure that shows an antibiotic that extracts a nucleobase from a DNA molecule ‘caught in the act’ after forming a covalent bond but before departing with the base. The structure of trioxacarcin A covalently bound to double-stranded d(AACCGGTT) was determined to 1.78 Å resolution by MAD phasing employing brominated oligonucleotides. The DNA–drug complex has a unique structure that combines alkylation (at the N7 position of a guanine), intercalation (on the 3'-side of the alkylated guanine), and base flip-out. An antibiotic-induced flipping-out of a single, nonterminal nucleobase from a DNA duplex was observed for the first time in a crystal structure.


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