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In silico maturation of binding-specificity of DNA aptamers against Proteus mirabilis
Nasa Savory1, Danielle Lednor, Kaori Tsukakoshi
1Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
Abstract:
Proteus mirabilis is a prominent cause of catheter-associated urinary tract infections (CAUTIs) among patients undergoing long-term bladder catheterization. There are currently no effective means of preventing P. mirabilis infections, and strategies for prophylaxis and rapid early diagnosis are urgently required. Aptamers offer significant potential for development of countermeasures against P. mirabilis CAUTI and are an ideal class of molecules for the development of diagnostics and therapeutics. Here we demonstrate the application of Cell-SELEX to identify DNA aptamers that show high affinity for P. mirabilis. While the aptamers identified displayed high affinity for P. mirabilis cells in dot blotting assays, they also bound to other uropathogenic bacteria. To improve aptamer specificity for P. mirabilis, an in silico maturation (ISM) approach was employed. Two cycles of ISM allowed the identification of an aptamer showing 36% higher specificity, evaluated as a ratio of binding signal for P. mirabilis to that for Escherichia coli (also a cause of CAUTI and the most common urinary tract pathogen). Aptamers that specifically recognize P. mirabilis would have diagnostic and therapeutic values and constitute useful tools for studying membrane-associated proteins in this organism.
Insights
Researchers developed DNA aptamers to detect Proteus mirabilis, a common cause of catheter-associated urinary tract infections (CAUTIs). Aptamer specificity was enhanced using in silico maturation, offering potential for new diagnostics and therapeutics against CAUTI.
Area of Science:
- Biotechnology
- Microbiology
- Molecular Biology
Background:
- Proteus mirabilis is a major cause of catheter-associated urinary tract infections (CAUTIs).
- Current prevention and rapid diagnosis strategies for P. mirabilis CAUTIs are lacking.
- DNA aptamers show promise for developing diagnostics and therapeutics against P. mirabilis.
Purpose of the Study:
- To identify DNA aptamers with high affinity and specificity for Proteus mirabilis.
- To improve aptamer specificity for P. mirabilis using in silico maturation (ISM).
- To explore the diagnostic and therapeutic potential of specific aptamers against P. mirabilis.
Main Methods:
- Cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was used to identify initial DNA aptamers.
- Dot blotting assays were performed to assess aptamer binding affinity.
- In silico maturation (ISM) was applied to enhance aptamer specificity against P. mirabilis.
Main Results:
- DNA aptamers with high affinity for P. mirabilis were identified using Cell-SELEX.
- Initial aptamers showed cross-reactivity with other uropathogenic bacteria.
- Two cycles of ISM improved aptamer specificity by 36% compared to Escherichia coli.
Conclusions:
- Developed aptamers demonstrate potential for specific detection of Proteus mirabilis.
- Enhanced aptamers could serve as tools for diagnosing and treating P. mirabilis CAUTIs.
- These aptamers may also be valuable for studying P. mirabilis membrane proteins.
