Single-step discovery of high-affinity RNA ligands by UltraSelex

Area of Science:

• Biochemistry
• Molecular Biology
• Biotechnology

Background:

• Aptamers are nucleic acid ligands with diverse applications, including therapeutics and diagnostics.
• Traditional aptamer discovery (SELEX) is laborious, time-consuming, and may yield suboptimal candidates.
• There is a need for faster, more efficient aptamer discovery methods.

Purpose of the Study:

• To develop a rapid, noniterative method for discovering high-affinity RNA aptamers.
• To demonstrate the utility of the new method for identifying aptamers against diverse targets.
• To enable rapid inference of minimal aptamer motifs.

Main Methods:

• UltraSelex combines biochemical partitioning, high-throughput sequencing, and computational rank modeling.
• This noniterative approach streamlines the aptamer selection process.
• The method achieves aptamer discovery in approximately one day.

Main Results:

• UltraSelex successfully identified high-affinity RNA aptamers targeting a silicon rhodamine dye and two proteins.
• Identified aptamers enabled live-cell RNA imaging and efficient inhibition of SARS-CoV-2 RNA-dependent RNA polymerase and HIV reverse transcriptase.
• Minimal aptamer motifs were readily inferred from the ranked sequences.

Conclusions:

• UltraSelex offers a significantly faster alternative to conventional aptamer discovery.
• The method accelerates the identification of novel aptamers for drug candidates and diagnostic tools.
• UltraSelex facilitates rapid development of aptamer-based technologies.