Examination of bacterial inhibition using a catalytic DNA

PLoS One. 2014 Dec 22;9(12):e115640. doi: 10.1371/journal.pone.0115640. eCollection 2014.


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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacillus subtilis / drug effects
  • Bacillus subtilis / growth & development*
  • Bacillus subtilis / isolation & purification
  • DNA, Catalytic / metabolism*
  • Enzyme Assays / methods
  • Escherichia coli / drug effects*
  • Escherichia coli / growth & development*
  • Escherichia coli / isolation & purification
  • Microbial Sensitivity Tests
  • Molecular Probes / metabolism*


  • Anti-Bacterial Agents
  • DNA, Catalytic
  • Molecular Probes

Grant support

The research work was supported by the Natural Sciences and Engineering Research Council of Canada Discovery Grant (227594-2009), the Ministry of Science and Technology of China (2012ZX09506001-010), and National Natural Science Foundation of China (No. 21302108). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.