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AutoPLP: A Padlock Probe Design Pipeline for Zoonotic Pathogens
Sowmya Ramaswamy Krishnan1,2, Ruben R G Soares3, Narayanan Madaboosi4
1Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
ACS Infectious Diseases
|February 15, 2023
Summary
A new pipeline, AutoPLP, automates the design of padlock probes (PLPs) for pathogen detection. This innovation enhances molecular diagnostics, enabling rapid identification of infectious agents like rabies virus and drug-resistant tuberculosis.
Area of Science:
- Molecular biology
- Bioinformatics
- Infectious disease diagnostics
Background:
- Novel zoonotic infections pose a growing threat to global health.
- Existing diagnostic methods require enhancement for rapid, molecular-level pathogen detection.
- Padlock probes (PLPs) combined with isothermal amplification offer high sensitivity and specificity but face design complexities.
Purpose of the Study:
- To develop an automated pipeline, AutoPLP, for designing padlock probes (PLPs).
- To overcome limitations in current PLP design for isothermal nucleic acid amplification techniques (NAAT).
- To facilitate the application of PLP-based diagnostics in point-of-care testing.
Main Methods:
- Developed AutoPLP, an integrated pipeline with three modules for automated PLP design.
- Pipeline modules include sequence curation, multiple sequence alignment, and conservation analysis.
- Incorporated experimental parameter filtration (Tm, GC content, secondary structure) and in silico validation against host genomes.
Main Results:
- AutoPLP automates the design of complete PLP sequences, including backbone and restriction site information.
- The pipeline successfully designed PLPs for detecting rabies virus.
- Demonstrated utility in designing probes for drug-resistant Mycobacterium tuberculosis strains.
Conclusions:
- AutoPLP streamlines the design of highly specific and sensitive padlock probes.
- The automated pipeline addresses key challenges in applying NAAT for pathogen detection.
- AutoPLP has significant potential for advancing molecular diagnostics in infectious disease surveillance.
