Cross-links of quadruplex structures from human telomeric DNA by dinuclear platinum complexes show the flexibility of both structures

The folding of AG(3)(T(2)AG(3))(3) was investigated in the presence of Na+ or K+ ions, by using the dinuclear platinum complexes [{trans-PtCl(NH3)(2)}(2)H2N(CH2)(n)NH2]Cl-2 (n = 2 or 6). AG(3)(T(2)AG(3))(3) has been previously found to adopt two different quadruplex structures: the antiparallel one in a solution containing Na+ and the parallel one in a K+-containing crystal. The two structures are strikingly distinct and are not expected to form the same platinum cross-links. Therefore, characterization of the cross-links formed with platinum complexes in solution allowed the predominant conformation(s) to be identified. The bases coordinating the platinum atoms were identified by chemical and 3'-exonuclease digestions. The observed cross-links showed that the parallel structure exists in solution whatever the cation and confirmed the existence of the antiparallel structure in the presence of both cations as previously reported from cross-linking experiments of AG(3)(T(2)AG(3))(3) by mononuclear platinum complexes. Furthermore, the major platinum cross-links were unexpectedly formed between two guanines belonging to the same G-quartet. Their formation was rationalized using molecular dynamics simulations in implicit solvent of the two quadruplex structures. It was shown that they were flexible, allowing some guanines to leave reversibly the top G-quartet and thus rendering their N-7 atom accessible to platinum complexes. Our results also suggest that the human telomere sequence could be a target for such platinum complexes.