Unraveling the Mechanism of a DNA Nanotechnology: The 10-23 Dnazyme

Many emerging DNA nanotechnologies are difficult or even impossible to crystallize, frustrating attempts to connect their structure and function.  Using a straightforward multi-scale simulation approach, we developed an atomic scale model of one such nanotechnology that has resisted attempts at crystallization, the widely used 10-23 DNAzyme.  Deoxyribozymes (DNAzymes) are a new class of small catalytic oligodeoxynucleotides composed entirely of DNA.  The 10-23 DNAzyme consists of a conserved 15-base catalytic core that is flanked by binding arms typically 7-10 bases in length with sequence complementary to a target single-stranded RNA molecule.  The 10-23 DNAzyme is capable of cleaving at a purine-pyrimidine junction with both high turnover rate and substrate affinity.  The ability of the 10-23 DNAzyme to cleave an RNA substrate has lead to both in vitro and in vivo applications although the evidence for its biochemical activity remains indirect.  Our simulations suggest a plausible mechanism for the catalysis of RNA cleavage by this single-stranded DNA molecule.  Two critical structural features were found:  (i) the unstacking and rotation of the RNA nucleotide at the cleavage site, and (ii) the formation of electrostatic traps for cofactor metal ions.