Skip to Main content Skip to Navigation
Journal articles

Compositional bias in naïve and chemically-modified phage-displayed libraries uncovered by paired-end deep sequencing

Abstract : Understanding the composition of a genetically-encoded (GE) library is instrumental to the success of ligand discovery. In this manuscript, we investigate the bias in GE-libraries of linear, macrocyclic and chemically post-translationally modified (cPTM) tetrapeptides displayed on the M13KE platform, which are produced via trinucleotide cassette synthesis (19 codons) and NNK-randomized codon. Differential enrichment of synthetic DNA {S}, ligated vector {L} (extension and ligation of synthetic DNA into the vector), naïve libraries {N} (transformation of the ligated vector into the bacteria followed by expression of the library for 4.5 hours to yield a "naïve" library), and libraries chemically modified by aldehyde ligation and cysteine macrocyclization {M} characterized by paired-end deep sequencing, detected a significant drop in diversity in {L} → {N}, but only a minor compositional difference in {S} → {L} and {N} → {M}. Libraries expressed at the N-terminus of phage protein pIII censored positively charged amino acids Arg and Lys; libraries expressed between pIII domains N1 and N2 overcame Arg/Lys-censorship but introduced new bias towards Gly and Ser. Interrogation of biases arising from cPTM by aldehyde ligation and cysteine macrocyclization unveiled censorship of sequences with Ser/Phe. Analogous analysis can be used to explore library diversity in new display platforms and optimize cPTM of these libraries.
Complete list of metadata

Cited literature [69 references]  Display  Hide  Download

https://hal.inrae.fr/hal-02623801
Contributor : Migration Prodinra <>
Submitted on : Tuesday, May 26, 2020 - 9:25:06 AM
Last modification on : Wednesday, May 12, 2021 - 3:42:41 AM

File

He_2018_Sci Rep_1.pdf
Publisher files allowed on an open archive

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

Bifang He, Katrina F. Tjhung, Nicholas J. Bennett, Ying Chou, Andrea Rau, et al.. Compositional bias in naïve and chemically-modified phage-displayed libraries uncovered by paired-end deep sequencing. Scientific Reports, Nature Publishing Group, 2018, 8 (1214), ⟨10.1038/s41598-018-19439-2⟩. ⟨hal-02623801⟩

Share

Metrics

Record views

415

Files downloads

35