THE CRYSTAL STRUCTURE OF 9-AMINO-[N-(2-DIMETHYL-AMINO)PROPYL]ACRIDINE-4-CARBOXAMIDE BOUND TO D(CGTACG)₂: A COMPARISON OF STRUCTURES OF D(CGTACG)₂ COMPLEXED WITH INTERCALATORS IN THE PRESENCE OF COBALT

Adrienne Adams,^a, J. Mitchell Guss,^a William A. Denny,^b and Laurence P.G. Wakelin^c

^aSchool of Molecular & Microbial Biosciences, University of Sydney, NSW 2006, Australia; ^bAuckland Cancer Society Research Centre, Faculty of Medicine and Health Science, University of Auckland, Private Bag 92019, Auckland, New Zealand; ^cSchool of Medical Sciences, University of New South Wales, NSW 2052, Australia (a.adams@mmb.usyd.edu.au)

The structure of the complex formed between an inactive derivative of the clinical trial anti-cancer drug and topoisomerase II poison DACA (9-amino-[N-(2-dimethyl-amino)propyl]acridine-4-carboxamide) and d(CGTACG)₂ has been solved and refined to a resolution of 1.55 Å. The complex crystallised in space group C222. An asymmetric unit comprises 2 strands of DNA, one disordered drug molecule, 2 cobalt (II) ions, 2 disordered magnesium ions and 32 water molecules. The DNA helices stack in continuous columns with their central 4 base pairs adopting a B-like motif. The terminal GC base pairs engage in different interactions. At one end of the duplex there is a CpG dinucleotide overlap modified by ligand intercalation and terminal cytosine exchange between symmetry-related duplexes. An intercalation complex is formed involving four DNA duplexes, four disordered ligand molecules, and two pairs of base tetrads. The other end of the DNA is frayed with the terminal guanine lying in the minor groove of the next duplex in the column. The structure is stabilised by guanine N7/cobalt (II) coordination. We compare our structure with the six published structures of d(CGTACG)₂ complexed with intercalators in the presence of cobalt [1-4] and find them all to be very similar. The seven structures appear to be independent of biological activity and sidechain configuration and dependent mainly on the presence of an intercalator and cobalt ions. It is likely that many different intercalators, besides those discussed here, would be capable of forming a similar structure with d(CGTACG)₂ in the presence of cobalt. Intercalators appear to destabilise B-DNA in the presence of cobalt ions and promote formation of multistranded DNA structures. Although we find no evidence for biological significance of this structure in terms of topoisomerase activity, this does not exclude the possibility that this is an important property of intercalators which may have an effect on other biological processes.

References

1 Adams, A., Guss, J. M., Collyer, C. A., Denny, W. A., Prakash, A. S., and Wakelin, L. P. G. (2000) Mol. Pharmacol. 58, 649-58.

2 Thorpe, J. H., Hobbs, J. R., Todd, A. K., Denny, W. A., Charlton, P., and Cardin, C. J. (2000) Biochemistry 39, 15055-61.

3 Yang, X.-l., Robinson, H., Gao, Y.-G., and Wang, A. H. J. (2000) Biochemistry 39, 10950-57.

4 Teixeira, S. C. M., Thorpe, J. H., Todd, A. K., Powell, H. R., Adams, A., Wakelin, L. P. G., Denny, W. A., and Cardin, C. J. (2002) J. Mol. Biol. 323, 167-71.