Enhancement of DNAzymatic activity using iterative in silico maturation

Abstract

DNAzyme-based (catalytic nucleic acid) biosensing technology is recognised as a valuable biosensing tool in diagnostic medicine and seen as a cheaper, more stable alternative to antibodies or enzymes. However, like enzyme discovery, no method exists to predict DNAzyme sequences that result in high catalytic activity using computer software (in silico). In this work, iterative in silico maturation and in vitro evaluation were applied to a DNAzyme oligodeoxynucleotide (ODN) sequence to elucidate novel synthetic sequences with enhanced DNAzyme activity. An already well-known model DNAzyme, the G-quadruplex/hemin complex, was iterated over eight generations to elucidate synthetic sequences that were up to five times faster than the original parent sequence. By combining molecular dynamics simulations, we found that the POD-mimicking activities were largely affected by docking modes and the tightness of locking between complexes. Ultimately, the theoretical models showed significant sequence-dependencies.