Identification of intrinsic dynamics in a DNA sequence preferentially cleaved by topoisomerase II enzyme
Résumé
The topoisomerases II enzymes are essential enzymes which modulate the DNA topology and have a role in the chromatin compaction. While the enzyme appears to recognize and cleave the DNA in a non random fashion, the factors which underlie the enzyme specificity remain an enigma. To gain new insights in these topics, we undertake, using NMR and molecular dynamics (MD) methods, studies of the structural and dynamical features of a 21 bp DNA segment preferentially cleaved by topoisomerases II. The large size of the oligonucleotide did not hamper the determination of structures of a sufficient quality and numerous interesting correlations between helicoidal parameters already depicted in crystals and molecular dynamics simulations are recovered here. The main feature of the sequence is the occurrence of a large opening of the bases pairs in a four residues AT rich region located immediately in 5' of one of the cleaved site. This opening seems to be largely dependant on sequence context since similar opening is not found in the other AT bases pairs of the sequence. Furthermore, two adenines of the same portion of the oligonucleotide present slow internal motions at the NMR time scale, revealing particular base dynamics. In conclusion this AT-rich region is those presenting the most salient characters in the sequence and could be involved in the preferential cleavage by topoisomerase II. The examination of preferred sites in the literature pointed out the frequent occurring of AT rich sequences, namely the MARs, SARs sequences, at the sites cleaved by topoisomerase II. We could infer that the particular flexibility of these sequences play an important role to enable the formation of a competent cleavage complex. The sequences could be then selected rather on their facility to undertake conformational change during the complex formation than purely on the basis of the binding affinity.