Minor groove binding compounds related to distamycin A bind DNA with high sequence selectivity, recognizing sites which contain various combinations of A·T and G·C base pairs. These molecules have the potential to deliver cross-linking agents to the minor groove of a target DNA sequence. We have studied the covalent DNA-DNA cross-linked complex of 2,3-bis(hydroxymethyl)pyrrole-distamycin and [d(CGCGAATTCGCG)]2. The alkylating pyrrole design is based on the pharmacophore of mitomycin C and is similar in substructure to another important class of natural products, the oxidatively activated pyrrolizidine alkaloids. Ligand-DNA NOEs confirm that the tri(pyrrole-carboxamide) unit of the ligand is bound in the minor groove of the central A+T tract. Unexpectedly, it is shifted by 1 bp with respect to the distamycin A binding site on this DNA sequence. The cross-link bridges the 2-amino position of two guanine residues, G4 and G22. The C3·G22 and G4·C21 base pairs exhibit Watson-Crick base pairing, with some local distortion, as evidenced by unusual intensities observed for DNA-DNA NOE cross-peaks. The model is compared with a related structure of a cross-linked mitomycin C:DNA complex.
|Number of pages||8|
|Journal||Nucleic Acids Research|
|State||Published - 1996|
Bibliographical noteFunding Information:
This work was supported in part by National Institutes of Health grants GM-43219 (DEW) and GM-45804 (PBH), post-doctoral fellowship GM-14966 (HPS), through instrumentation grants from the US Department of Energy, DE FG05-86ER75281, and the National Science Foundation, DMB 86-09305 and BBS 87-20134, and by the Director, Office of Biological and Environmental Research, General Sciences Division of the US Department of Energy under contract no. DE-AC03-76SF00098 (DEW).
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