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A Highly Specific DNA Aptamer for RNase H2 from Clostridium difficile.

Jiuxing Li1, Jimmy Gu1, Hongfen Zhang1,2

  • 1M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.

ACS Applied Materials & Interfaces
|January 7, 2021
PubMed
Summary

Researchers developed a specific DNA aptamer for Clostridium difficile RNase H2. This aptamer shows high binding affinity and can differentiate C. difficile in cell lysates, aiding diagnostics and drug development.

Keywords:
Clostridium difficileRNase H2SELEXaptamersspecificity

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Area of Science:

  • Molecular biology
  • Biochemistry
  • Biotechnology

Background:

  • High specificity molecular recognition elements are crucial for diagnostics and drug design.
  • RNase H2 is a ubiquitous enzyme, presenting a challenge for specific targeting.

Purpose of the Study:

  • To develop a highly specific DNA aptamer targeting RNase H2 from Clostridium difficile.
  • To assess the aptamer's binding affinity and specificity for diagnostic and therapeutic applications.

Main Methods:

  • Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was employed to generate the aptamer.
  • The aptamer was minimized to 40 nucleotides.
  • Binding affinity (Kd) and inhibition constant (IC50) were determined.
  • A fluorescent version was used in cell lysate assays.

Main Results:

  • A DNA aptamer with high specificity for Clostridium difficile RNase H2 was successfully generated and minimized.
  • The aptamer demonstrated a dissociation constant (Kd) of 1.8 ± 0.5 nM and an inhibition constant (IC50) of 7.1 ± 0.6 nM.
  • Specificity was significantly higher (2 orders of magnitude) compared to RNase H2 from control bacteria.
  • The fluorescent aptamer could distinguish C. difficile in cell lysate assays.

Conclusions:

  • Highly specific aptamers can be developed even for ubiquitous proteins like RNase H2.
  • The developed aptamer offers a promising tool for specific C. difficile detection.
  • This aptamer-protein combination holds potential for diagnostic tests and drug development.