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Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs
Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material res...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759992/ https://www.ncbi.nlm.nih.gov/pubmed/33261041 http://dx.doi.org/10.3390/v12121360 |
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author | Braun, Robert Schönberger, Nora Vinke, Svenja Lederer, Franziska Kalinowski, Jörn Pollmann, Katrin |
author_facet | Braun, Robert Schönberger, Nora Vinke, Svenja Lederer, Franziska Kalinowski, Jörn Pollmann, Katrin |
author_sort | Braun, Robert |
collection | PubMed |
description | Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material research. However, limitations of traditional phage display hinder the identification process. Growth-based library biases and target-unrelated peptides often result in the dominance of parasitic sequences and the collapse of library diversity. This study describes the effective enrichment of specific peptide motifs potentially binding to arsenic as proof-of-concept using the combination of PSD and NGS. Arsenic is an environmental toxin, which is applied in various semiconductors as gallium arsenide and selective recovery of this element is crucial for recycling and remediation. The development of biomolecules as specific arsenic-binding sorbents is a new approach for its recovery. Usage of NGS for all biopanning fractions allowed for evaluation of motif enrichment, in-depth insight into the selection process and the discrimination of biopanning artefacts, e.g., the amplification-induced library-wide reduction in hydrophobic amino acid proportion. Application of bioinformatics tools led to the identification of an SxHS and a carboxy-terminal QxQ motif, which are potentially involved in the binding of arsenic. To the best of our knowledge, this is the first report of PSD combined with NGS of all relevant biopanning fractions. |
format | Online Article Text |
id | pubmed-7759992 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-77599922020-12-26 Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs Braun, Robert Schönberger, Nora Vinke, Svenja Lederer, Franziska Kalinowski, Jörn Pollmann, Katrin Viruses Article Next generation sequencing (NGS) in combination with phage surface display (PSD) are powerful tools in the newly equipped molecular biology toolbox for the identification of specific target binding biomolecules. Application of PSD led to the discovery of manifold ligands in clinical and material research. However, limitations of traditional phage display hinder the identification process. Growth-based library biases and target-unrelated peptides often result in the dominance of parasitic sequences and the collapse of library diversity. This study describes the effective enrichment of specific peptide motifs potentially binding to arsenic as proof-of-concept using the combination of PSD and NGS. Arsenic is an environmental toxin, which is applied in various semiconductors as gallium arsenide and selective recovery of this element is crucial for recycling and remediation. The development of biomolecules as specific arsenic-binding sorbents is a new approach for its recovery. Usage of NGS for all biopanning fractions allowed for evaluation of motif enrichment, in-depth insight into the selection process and the discrimination of biopanning artefacts, e.g., the amplification-induced library-wide reduction in hydrophobic amino acid proportion. Application of bioinformatics tools led to the identification of an SxHS and a carboxy-terminal QxQ motif, which are potentially involved in the binding of arsenic. To the best of our knowledge, this is the first report of PSD combined with NGS of all relevant biopanning fractions. MDPI 2020-11-27 /pmc/articles/PMC7759992/ /pubmed/33261041 http://dx.doi.org/10.3390/v12121360 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Braun, Robert Schönberger, Nora Vinke, Svenja Lederer, Franziska Kalinowski, Jörn Pollmann, Katrin Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title | Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_full | Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_fullStr | Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_full_unstemmed | Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_short | Application of Next Generation Sequencing (NGS) in Phage Displayed Peptide Selection to Support the Identification of Arsenic-Binding Motifs |
title_sort | application of next generation sequencing (ngs) in phage displayed peptide selection to support the identification of arsenic-binding motifs |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759992/ https://www.ncbi.nlm.nih.gov/pubmed/33261041 http://dx.doi.org/10.3390/v12121360 |
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