Evidences for reaction mechanism of 9DB1 DNA catalyst

The first reported reaction mechanism of a DNAzyme, i.e. 9DB1, by using molecular dynamics (MD) simulations includes some ambiguities. We try to overcome some of these ambiguous aspects such as the role of mono and divalent metal ions and observed metal rescue effects by surveying the role of functional groups of original 9DB1 and a variety of its rate conserving and rate decreasing mutations via MD simulations. Conformational differences of these two distinct groups are responsible for their opposite rate trends. Blocking of the OH3' of acceptor nucleotide from effective attack by its hydrogen bond to O4' of donor nucleotide is observed in rate decreasing mutations. Our simulations manifest the role of Na⁺ and Mg²⁺ ions in bringing close to each other the ligated atoms. These findings along with observed conformational changes explain carefully the reported metal rescue effects for some phosphate groups.