ASSET: A Framework for Decoding Aptamer Specificity of an Enriched Library by Next-Generation Sequencing of...

Area of Science:

• Biotechnology
• Molecular Biology
• Genomics

Background:

• The SELEX process identifies RNA and DNA aptamers through sequencing selection rounds.
• Current methods infer aptamer specificity from enrichment patterns, lacking direct quantification.

Purpose of the Study:

• To introduce Aptamer Specificity Sequencing for Efficient Targeting (ASSET) for direct quantification of aptamer specificity.
• To enable robust classification of aptamers as true or false positives/negatives.

Main Methods:

• ASSET utilizes next-generation sequencing (NGS) with an internal reference sequence for normalization.
• It calculates statistically significant aptamer specificity scores and generates specificity profiles.
• Integrates ASSET scores with conventional SELEX sequencing data.

Main Results:

• ASSET specificity scores strongly correlate with experimentally measured specificity.
• The method allows for effective separation of true positive aptamers from false positives.
• ASSET demonstrates superior performance compared to abundance or enrichment metrics.

Conclusions:

• ASSET provides a more effective metric for selecting lead aptamer candidates post-SELEX.
• This framework accelerates aptamer discovery for therapeutic and diagnostic applications.
• ASSET enhances the reliability and efficiency of aptamer identification.