A complex formed by molecules of topotecan (TPT), an inhibitor of human DNA topoisomerase I, with duplexes of DNA and of synthetic polydeoxyribonucleotides. This complex is prevalent in the case of TPT binding to linear double-stranded polynucleotides (except for the case of poly(dA-dT)·(poly(dA-dT)) at neutral pH and low ionic strength (1 mM sodium cacodylate, pH 6.8). The complex is characterized by a negative linear dichroism band in the TPT absorption region in the long-wavelength part of the spectrum.

We have shown the following: (i) TPT forms dimers in solution (1). (ii) Mainly TPT dimers bind to DNA (2). (iii) TPT dimers bind at the minor groove (3, 4). (iv) They bind mainly to GC pairs (curves of TPT binding to polymers with different GC content were obtained) (3, 5); it was supposed that the carbonyl of the D ring of TPT interacts with the 2-amino group of guanine, because it is the only group differing GC from AT in the minor groove (3, 5). (v) TPT dimers stimulate formation of quadruplexes and higher-order structures, in which TPT dimers play the role of ?clamps? (3, 5). (vi) The long axis of TPT dimer in these complexes forms an angle of ~60° with the long axis of DNA (4).

The models proposed for the TPT lactone dimer interaction with two intersecting duplexes poly(dG)·poly(dC) (see figure) as well as with two antiparallel duplexes of this polymer include the above-mentioned carbonyl--amino group H-bonding (iv).



TPT is a derivative of camptothecin (CPT). Both form dimers, which are quite similar and have a helical dyad axis (1, 5). In complexes with DNA the plane of their chromophores forms an angle of ~60° with the long axis of DNA. Therefore, we believe that the proposed model of TPT interaction with DNA is general for all CPT derivatives able to form dimers of such geometry.

Experiments with TPT were carried out in solutions of low ionic strength, because under these conditions DNA duplexes acquire additional rigidity (2); this stimulates formation of regular ?clamps? of TPT dimers between them, which creates an ordered structure amenable to physicochemical investigation. Such complexes model the contacts that emerge between two sites of adjacent duplexes in circular supercoiled DNA.

The study was partially supported by the Russian Foundation for Basic Research (grants 01-04-48657, 01-03-32669, 02-04-48339).