Cross-Links of Quadruplex Structures from Human Telomeric DNA by Dinuclear Platinum Complexes Show the Flexibility of Both Structures

Abstract

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(NH(3))(2)}(2)H(2)N(CH(2))(n)NH(2)]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.

Polymorphism of human telomeric quadruplex structures

“…Because the K + structure is considered to be biologically more relevant due to the higher intracellular concentration of K + , it has been the subject of intense investigation [32][33][34][35][36][37][38][39][40][41][42][43][44][45], although the Na + structure was reported more than a decade ago [46]. In 2002, a crystal structure of the parallel-stranded G-quadruplex was reported using a 22-nt human telomeric sequence in the presence of K + [47].…”

GG sequence of DNA and the human telomeric sequence react with cis-diammine-diaquaplatinum at comparable rates

“…We have shown that the duplex and quadruplex It is worth noticing that only one cross-link of cisplatin was formed within the quadruplex structure of 35merG4, although two cross-links were formed within the quadruplex structure of the 22mer AG 3 (T 2 AG 3 ) 3 : the A1-G10 and A13-G22 cross-links [25]. We have previously proposed that both guanines could be platinated in spite of their involvement in G-quartet because they can leave reversibly the G-quartet rending their N 7 free from hydrogen bonds [26]. As no A13-G22 cross-link was formed within construct I, this indicates that its formation is impeded when a duplex DNA is linked at G22 that is the 3 0 extremity of the quadruplex (Fig.…”

“…The platinated products were treated with DMS/piperidine (probe of the free N 7 ) in Maxam-Gilbert sequencing conditions, following by deplatination reaction as described in [26]. DMS methylates N 7 of guanines and the treatment by piperidine induces a cleavage of the DNA at each methylated guanine.…”

“…1). Many works have evidenced that both parallel and anti-parallel structures co-exist in aqueous solution [18][19][20][21][22][23][24][25][26]. Moreover, a hybrid parallel/anti-parallel structure has been recently identified [27][28][29][30].…”

“…It is worth noticing that G10 and G22 were platinated in spite of the involvement of their N 7 in hydrogen bonding of the top G-quartet. It has been further explained by the flexibility of this G-quartet allowing some guanines to leave reversibly the G-quartet without defolding the quadruplex structure [26].…”