Targeting a conserved structural element from the SARS-CoV-2 genome using l-DNA aptamers

Area of Science:

• Molecular Biology
• Virology
• Biotechnology

Background:

• COVID-19 pandemic caused by SARS-CoV-2.
• Focus on viral proteins, but RNA structures are also potential targets.
• SARS-CoV-2 stem-loop II-like motif (s2m) is conserved and has diagnostic/therapeutic potential.

Purpose of the Study:

• Identify high-affinity l-DNA aptamers against the SARS-CoV-2 s2m RNA.
• Evaluate aptamer selectivity and potential for diagnostic and therapeutic applications.

Main Methods:

• Selection and optimization of l-DNA aptamers (l-C1t and l-C3t) against s2m RNA.
• Binding affinity (Kd) measurements using nanomolar range.
• Assessing selectivity against monomeric s2m, homodimer duplex, and related viral RNAs (SARS-CoV-1).
• Analyzing conformational changes induced by aptamer binding.

Main Results:

• Optimized aptamers l-C1t and l-C3t bind s2m RNA with nanomolar affinity.
• Aptamers selectively differentiate monomeric s2m from its homodimer.
• Aptamers distinguish between SARS-CoV-2 and SARS-CoV-1 s2m RNAs.
• Aptamer binding induces significant conformational changes in s2m structure.

Conclusions:

• l-DNA aptamers are feasible tools for targeting SARS-CoV-2 RNA structures.
• l-C1t and l-C3t aptamers offer potential for COVID-19 diagnosis and treatment.
• Nuclease resistance and selectivity of l-aptamers enable development of novel probes for s2m function analysis.