ArticleViruses2022
Analysis of Compositional Bias in a Commercial Phage Display Peptide Library by Next-Generation Sequencing.
Article in Viruses, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Phage Display as a Promising Platform for Peptide Drug Discovery.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Peptide-based drug design using generative AI.Chemical communications (Cambridge, England) · 2026Review
- Review
- Affinity-selected peptide ligands specifically bind i-motif DNA and modulate c-Myc gene expression.Nucleic acids research · 2025Article
- Review
- A comparative analysis of sequence composition in different lots of a phage display peptide library during amplification.Virology journal · 2025Article
- Application of phage surface display for the identification of EuFrontiers in bioengineering and biotechnology · 2025Article
- On the origin of non-specific binders isolated in the selection of phage display peptide libraries.Frontiers in microbiology · 2025Review
- Development of a new affinity maturation protocol for the construction of an internalizing anti-nucleolin antibody library.Scientific reports · 2024Article
- Review
- Phage libraries screening on P53: Yield improvement by zinc and a new parasites-integrating analysis.PloS one · 2024Article
- Propagation Capacity of Phage Display Peptide Libraries Is Affected by the Length and Conformation of Displayed Peptide.Molecules (Basel, Switzerland) · 2023Article
- Engineered M13 phage as a novel therapeutic bionanomaterial for clinical applications: From tissue regeneration to cancer therapy.Materials today. Bio · 2023Review
- Depth of Sequencing Plays a Determining Role in the Characterization of Phage Display Peptide Libraries by NGS.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The principal presumption of phage display biopanning is that the naïve library contains an unbiased repertoire of peptides, and thus, the enriched variants derive from the affinity selection of an entirely random peptide pool. In the current study, we utilized deep sequencing to characterize the widely used Ph.DTM-12 phage display peptide library (New England Biolabs). The next-generation sequencing (NGS) data indicated the presence of stop codons and a high abundance of wild-type clones in the naïve library, which collectively result in a reduced effective size of the library. The analysis of the DNA sequence logo and global and position-specific frequency of amino acids demonstrated significant bias in the nucleotide and amino acid composition of the library inserts. Principal component analysis (PCA) uncovered the existence of four distinct clusters in the naïve library and the investigation of peptide frequency distribution revealed a broad range of unequal abundances for peptides. Taken together, our data provide strong evidence for the notion that the naïve library represents substantial departures from randomness at the nucleotide, amino acid, and peptide levels, though not undergoing any selective pressure for target binding. This non-uniform sequence representation arises from both the M13 phage biology and technical errors of the library construction. Our findings highlight the paramount importance of the qualitative assessment of the naïve phage display libraries prior to biopanning.
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