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Sequence-dependent DNA flexibility mediates DNase I cleavage.

Abstract : Understanding the preference of nonspecific proteins for certain DNA structural features requires an accurate description of the properties of free DNA, especially regarding their possible predisposition to adopt a conformation that favors the formation of a complex. Exploiting previous exhaustive NMR studies performed on free DNA oligomers, we investigated the molecular basis of DNase I sensitivity under conditions where DNase I binding limits the probability of cleavage. We showed that cleavage intensity was correlated with adjacent 3' phosphate linkage flexibility, monitored by (31)P chemical shifts. Examining NMR-refined DNA structures highlighted that sequence-dependent flexible phosphates were associated with large minor groove variations that may promote the affinity of DNase I, according to relevant DNA-protein complexes. In sum, this work demonstrates that specificity in DNA-DNase I interaction is mediated by DNA flexibility, which influences the induced-fit transitions required to form productive complexes.
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Brahim Heddi, Josephine Abi-Ghanem, Marc Lavigne, Brigitte Hartmann. Sequence-dependent DNA flexibility mediates DNase I cleavage.. Journal of Molecular Biology, Elsevier, 2010, 395 (1), pp.123-33. ⟨10.1016/j.jmb.2009.10.023⟩. ⟨pasteur-01416864⟩

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