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Published on: September 21, 2017
Biophysical evaluation of antiparallel triplexes for biosensing and biomedical applications
Arnau Domínguez1, Raimundo Gargallo2, Carlos Cuestas-Ayllón3
1Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
Polypyrimidine-rich hairpins (PPRHs) targeting SARS-CoV-2 were studied. Their binding affinity and stability depend on length, GC content, and pyrimidine interruptions, crucial for triplex formation and biosensing applications.
Area of Science:
- Molecular Biology
- Biophysics
- Genomics
Background:
- Polypyrimidine sequences are targets for antiparallel clamps forming triplex structures.
- Applications in biosensing and therapeutics exist, but biophysical properties are not fully understood.
Purpose of the Study:
- To evaluate the biophysical properties of polypyrimidine-rich hairpins (PPRHs) targeting the SARS-CoV-2 genome.
- To understand factors influencing PPRH binding affinity and stability for improved design.
Main Methods:
- Polyacrylamide gel electrophoresis (PAGE)
- Circular dichroism (CD) spectroscopy
- Multivariate analysis
- Thermal lateral flow sensing device
Main Results:
- PPRHs targeting SARS-CoV-2 showed variable binding affinities influenced by length, GC content, and pyrimidine interruptions.
- Intramolecular and intermolecular equilibria were affected by these factors, indicating polymorphic behavior.
- Functionality in a thermal lateral flow sensing device correlated well with biophysical properties and detection limits.
Conclusions:
- Critical factors for designing effective PPRHs targeting viral genomes via triplex structures under neutral conditions were identified.
- This research enhances understanding for developing targeted biosensing and therapeutic strategies.
