Journal article
Enhancement of DNAzymatic activity using iterative in silico maturation
RA Fenati, Z Chen, Y Yamagishi, K Tsukakoshi, K Ikebukuor, A Manian, SP Russo, T Yamazaki, AV Ellis
Journal of Materials Chemistry B | ROYAL SOC CHEMISTRY | Published : 2022
DOI: 10.1039/d2tb01638a
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 ..
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Grants
Awarded by Australian Government
Funding Acknowledgements
The authors would like to thank Ms Satomi Kohara and Ms Satomi Magae for their technical assistance in the experiments for the electrophoresis and CD analyses. The authors would like to thank Dr Peter Sherrell for their guidance on structuring this paper. The authors also thank the Flinders University of South Australia/National Institute of Materials Science (NIMS). This work was conducted at the NIMS Molecule and Material Synthesis platform. This work was supported by the Nanotechnology Platform Program of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. This work was supported by the Australian Government through the Australian Research Council (ARC) under the Discovery Project (project number DP190100055), the Centre of Excellence schemes (project number CE170100026), and the Japan Society for the Promotion of Science Kakenhi (grant number 17KK0122). This work was also supported by computational resources provided by the Australian Government through the National Computational Infrastructure National Facility and the Pawsay Supercomputer Centre.