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Peptide barcoding for establishment of new types of genotype–phenotype linkages

Measuring binding properties of binders (e.g., antibodies) is essential for developing useful experimental reagents, diagnostics, and pharmaceuticals. Display technologies can evaluate a large number of binders in a high-throughput manner, but the immobilization effect and the avidity effect prohibi...

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Autores principales: Miyamoto, Kana, Aoki, Wataru, Ohtani, Yuta, Miura, Natsuko, Aburaya, Shunsuke, Matsuzaki, Yusei, Kajiwara, Kaho, Kitagawa, Yoshinori, Ueda, Mitsuyoshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478338/
https://www.ncbi.nlm.nih.gov/pubmed/31013333
http://dx.doi.org/10.1371/journal.pone.0215993
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author Miyamoto, Kana
Aoki, Wataru
Ohtani, Yuta
Miura, Natsuko
Aburaya, Shunsuke
Matsuzaki, Yusei
Kajiwara, Kaho
Kitagawa, Yoshinori
Ueda, Mitsuyoshi
author_facet Miyamoto, Kana
Aoki, Wataru
Ohtani, Yuta
Miura, Natsuko
Aburaya, Shunsuke
Matsuzaki, Yusei
Kajiwara, Kaho
Kitagawa, Yoshinori
Ueda, Mitsuyoshi
author_sort Miyamoto, Kana
collection PubMed
description Measuring binding properties of binders (e.g., antibodies) is essential for developing useful experimental reagents, diagnostics, and pharmaceuticals. Display technologies can evaluate a large number of binders in a high-throughput manner, but the immobilization effect and the avidity effect prohibit the precise evaluation of binding properties. In this paper, we propose a novel methodology, peptide barcoding, to quantitatively measure the binding properties of multiple binders without immobilization. In the experimental scheme, unique peptide barcodes are fused with each binder, and they represent genotype information. These peptide barcodes are designed to have high detectability for mass spectrometry, leading to low identification bias and a high identification rate. A mixture of different peptide-barcoded nanobodies is reacted with antigen-coated magnetic beads in one pot. Peptide barcodes of functional nanobodies are cleaved on beads by a specific protease, and identified by selected reaction monitoring using triple quadrupole mass spectrometry. To demonstrate proof-of-principle for peptide barcoding, we generated peptide-barcoded anti-CD4 nanobody and anti-GFP nanobody, and determined whether we could simultaneously quantify their binding activities. We showed that peptide barcoding did not affect the properties of the nanobodies, and succeeded in measuring the binding activities of these nanobodies in one shot. The results demonstrate the advantages of peptide barcoding, new types of genotype–phenotype linkages.
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spelling pubmed-64783382019-05-07 Peptide barcoding for establishment of new types of genotype–phenotype linkages Miyamoto, Kana Aoki, Wataru Ohtani, Yuta Miura, Natsuko Aburaya, Shunsuke Matsuzaki, Yusei Kajiwara, Kaho Kitagawa, Yoshinori Ueda, Mitsuyoshi PLoS One Research Article Measuring binding properties of binders (e.g., antibodies) is essential for developing useful experimental reagents, diagnostics, and pharmaceuticals. Display technologies can evaluate a large number of binders in a high-throughput manner, but the immobilization effect and the avidity effect prohibit the precise evaluation of binding properties. In this paper, we propose a novel methodology, peptide barcoding, to quantitatively measure the binding properties of multiple binders without immobilization. In the experimental scheme, unique peptide barcodes are fused with each binder, and they represent genotype information. These peptide barcodes are designed to have high detectability for mass spectrometry, leading to low identification bias and a high identification rate. A mixture of different peptide-barcoded nanobodies is reacted with antigen-coated magnetic beads in one pot. Peptide barcodes of functional nanobodies are cleaved on beads by a specific protease, and identified by selected reaction monitoring using triple quadrupole mass spectrometry. To demonstrate proof-of-principle for peptide barcoding, we generated peptide-barcoded anti-CD4 nanobody and anti-GFP nanobody, and determined whether we could simultaneously quantify their binding activities. We showed that peptide barcoding did not affect the properties of the nanobodies, and succeeded in measuring the binding activities of these nanobodies in one shot. The results demonstrate the advantages of peptide barcoding, new types of genotype–phenotype linkages. Public Library of Science 2019-04-23 /pmc/articles/PMC6478338/ /pubmed/31013333 http://dx.doi.org/10.1371/journal.pone.0215993 Text en © 2019 Miyamoto et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Miyamoto, Kana
Aoki, Wataru
Ohtani, Yuta
Miura, Natsuko
Aburaya, Shunsuke
Matsuzaki, Yusei
Kajiwara, Kaho
Kitagawa, Yoshinori
Ueda, Mitsuyoshi
Peptide barcoding for establishment of new types of genotype–phenotype linkages
title Peptide barcoding for establishment of new types of genotype–phenotype linkages
title_full Peptide barcoding for establishment of new types of genotype–phenotype linkages
title_fullStr Peptide barcoding for establishment of new types of genotype–phenotype linkages
title_full_unstemmed Peptide barcoding for establishment of new types of genotype–phenotype linkages
title_short Peptide barcoding for establishment of new types of genotype–phenotype linkages
title_sort peptide barcoding for establishment of new types of genotype–phenotype linkages
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478338/
https://www.ncbi.nlm.nih.gov/pubmed/31013333
http://dx.doi.org/10.1371/journal.pone.0215993
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