Local conformational changes in the 8–17 deoxyribozyme core induced by activating and inactivating divalent metal ions. Issue 41 (12th October 2017)

• Record Type: Journal Article
• Authors: Peracchi, Alessio; Bonaccio, Maria; Credali, Alfredo
• Is Part Of: Organic & biomolecular chemistry. Volume 15:Issue 41(2017)
• Page Start: 8802
• Page End: 8809
• Publication Date: 2017-10-12
• Subjects: Chemistry, Organic -- Periodicals; Bioorganic chemistry -- Periodicals; Chemistry, Physical organic -- Periodicals; 547
• DOI: 10.1039/c7ob02001e
• Languages: English
• ISSNs: 1477-0520

Abstract

Abstract : Placing 2-aminopurine at position 15 of the 8–17 DNAzyme allows the detection of a specific metal-induced conformational change, apparently coupled to the activation of catalysis. Abstract : The 8–17 deoxyribozyme (DNAzyme) is a catalytic DNA molecule capable of cleaving specific RNA substrates. The deoxyribozyme is activated by a wide variety of divalent metal ions, from Mg 2+ to Pb 2+, with just a few exceptions. It is not clear if metal ions are directly involved in catalysis, or are required to attain an active conformation, or both. In particular, the connection between metal-induced global structural rearrangements and catalysis is not straightforward. To gain more information on the local structural changes induced by metal ions, we introduced fluorescent 2-aminopurine (2-Ap) residues at different positions of the 8–17 'core'. We found that a construct containing 2-Ap at position 15 was best suited to monitor conformational changes in the presence of Mg 2+, Ca 2+ or Mn 2+ . Binding of these activating metal ions caused a local rearrangement at position 15, apparently entailing decreased stacking of the 2-Ap base. The metal dependence for such conformational change was generally hyperbolic (suggesting it mirrored the binding by a single metal ion) and yielded apparent dissociation constants close to those required for activation. In contrast, Cu 2+, a divalent metal ion which does not support catalysis, caused in the deoxyribozyme a slow, reversible inactivation, which correlated with a very distinct conformational change at position 15.