Post-Selection Methods for Analyzing mRNA Display Selections and Optimization of Hits.

Pearl Qi, Colin M Leaf, Richard W Roberts, Terry T Takahashi

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Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

4 authors.

Pearl QiMork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA.

Colin M LeafDepartment of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.

Richard W RobertsMork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA. richrob@usc.edu.

Terry T TakahashiDepartment of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA. tttakaha@usc.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

mRNA display enables the selection of peptide and protein ligands from libraries containing more than a trillion unique sequences. Identifying optimal target binders, however, requires extensive post-selection analysis and optimization, which is often more challenging than the selection itself. Here, we outline general strategies for analyzing mRNA display selections with the goal of advancing a small set of high-quality ligands for further study. We describe methods for sequencing and analyzing selection pools to identify potential binders, followed by experimental approaches to validate target binding and characterize ligand-target interactions. We present strategies for constructing second-generation libraries to improve initial hits, along with more specialized selection techniques for further improving binding affinity and/or protease resistance. Together, these methods provide a comprehensive strategy for post-selection analysis and the development of optimized ligands for downstream applications.

Indexed as

RNA, MessengerDirected Molecular EvolutionGene LibraryHigh-Throughput Nucleotide SequencingLigandsPeptide LibraryPeptidesProtein BindingProtein EngineeringLigandsPeptide LibraryPeptidesRNA, MessengerDirected evolution, RNA-protein fusionHigh-throughput sequencingIn vitro selectionMachine learningmRNA displayPost-selection analysisProtein engineering

Identifiers

PMID42400847

DOI10.1021/acs.analchem.0c01867

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.