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Nucleic Acids Research, 1995, Vol. 23, No. 8 1333-1340
© 1995

STRUCTURAL BIOLOGY

Evidence for DAPI intercalation in CG sites of DNA oligomer [d(CGACGTCG)]2: a 1H NMR study

Edoardo Trotta*, Ettore D'Ambrosio, Giampietro Ravagnan and Maurizio Paci1

Istituto di Medicina Sperimentale CNR, Viale Marx 15, 00137 Roma, Italy 1Dipartimento di Scienze e Tecnologie Chimiche, Universita' di Roma ‘Tor Vergata’ Roma, Italy

* To whom correspondence should be addressed

Received January 13, 1995. Revised March 1, 1995. Accepted March 1, 1995.

The interaction between 4',6-diamidino-2-phenylindole (DAPI) and the DNA oligomer [d(CGACGTCG)]2 has been investigated by proton one- and two-dimensional NMR spectroscopy in solution. Compared with the minor groove binding of the drug to [d(GCGATCCG)]2 previously studied by NMR spectroscopy, the interaction of DAPI with [d(CGACGTCG)]2 appears markedly different and gives results typical of a binding mechanism by intercalation. C:G imino proton signals of the [d(CGACGTCG)]2 oligomer as well as DAPI resonances appear strongly upfield shifted and sequential dipolar connectivities between cytosine and guanine residues show a clear decrease upon binding. Moreover, protons lying in both the minor and major grooves of the DNA double helix appear involved in the interaction, as evidenced principally by intermolecular drug-DNA NOEs. In particular, the results Indicate the existence of two stereochemically non-equivalent intercalation binding sites located in the central and terminal adjacent C:G base pairs of the palindromic DNA sequence. Different lifetimes of the complexes were also observed for the two sites of binding. Moreover, due to the fast exchangeon the NMR timescale between free and bound species, different interactions in dynamic equilibrium with the observed intercalative bindings were not excluded.


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