title: Examination of bacterial inhibition using a catalytic DNA.
abstract: Determination of accurate dosage of existing antibiotics and discovery of new antimicrobials or probiotics entail simple but effective methods that can conveniently track bacteria growth and inhibition. Here we explore the application of a previously reported fluorogenic E. coli-specific DNAzyme (catalytic DNA), RFD-EC1, as a molecular probe for monitoring bacterial inhibition exerted by antibiotics and for studying bacterial competition as a result of cohabitation. Because the DNAzyme method provides a convenient way to monitor the growth of E. coli, it is capable of determining the minimal inhibitory concentration (MIC) of antibiotics much faster than the conventional optical density (OD) method. In addition, since the target for RFD-EC1 is an extracellular protein molecule from E. coli, RFD-EC1 is able to identify pore-forming antibiotics or compounds that can cause membrane leakage. Finally, RFD-EC1 can be used to analyse the competition of cohabitating bacteria, specifically the inhibition of growth of E. coli by Bacillus subtilis. The current work represents the first exploration of a catalytic DNA for microbiological applications and showcases the utility of bacteria-sensing fluorogenic DNAzymes as simple molecular probes to facilitate antibiotic and probiotic research.
authors.affiliation: Department of Chemistry, Tsinghua University, Beijing, China; Department of Biochemistry and Biomedical Sciences & Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; The State Key Laboratory Breeding Base & Shenzhen Key Laboratory of Chemical Biology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China.
authors.forename: Long
authors.initials: L
authors.lastname: Qu
authors.affiliation: Department of Biochemistry and Biomedical Sciences & Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
authors.forename: M Monsur
authors.initials: MM
authors.lastname: Ali
authors.affiliation: Department of Biochemistry and Biomedical Sciences & Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Sergio D
authors.initials: SD
authors.lastname: Aguirre
authors.affiliation: The State Key Laboratory Breeding Base & Shenzhen Key Laboratory of Chemical Biology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China.
authors.forename: Hongxia
authors.initials: H
authors.lastname: Liu
authors.affiliation: The State Key Laboratory Breeding Base & Shenzhen Key Laboratory of Chemical Biology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China.
authors.forename: Yuyang
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Biochemistry and Biomedical Sciences & Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
authors.forename: Yingfu
authors.initials: Y
authors.lastname: Li
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001412:Bacillus subtilis / Q000187:drug effects / Q000254:growth & development* / Q000302:isolation & purification; D021881:DNA, Catalytic / Q000378:metabolism*; D057075:Enzyme Assays / Q000379:methods; D004926:Escherichia coli / Q000187:drug effects* / Q000254:growth & development* / Q000302:isolation & purification; D008826:Microbial Sensitivity Tests; D015335:Molecular Probes / Q000378:metabolism*
chemical_list: D000900:Anti-Bacterial Agents; D021881:DNA, Catalytic; D015335:Molecular Probes