Quantification of evolved DNA-editing enzymes at scale with DEQSeq

We introduce DEQSeq, a nanopore sequencing approach that rationalizes the selection of favorable genome editing enzymes from directed molecular evolution experiments. With the ability to capture full-length sequences, editing efficiencies, and specificities from thousands of evolved enzymes simultan...

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Autores principales: Schmitt, Lukas Theo, Schneider, Aksana, Posorski, Jonas, Lansing, Felix, Jelicic, Milica, Jain, Manavi, Sayed, Shady, Buchholz, Frank, Sürün, Duran
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10626641/
https://www.ncbi.nlm.nih.gov/pubmed/37932818
http://dx.doi.org/10.1186/s13059-023-03097-3
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author Schmitt, Lukas Theo
Schneider, Aksana
Posorski, Jonas
Lansing, Felix
Jelicic, Milica
Jain, Manavi
Sayed, Shady
Buchholz, Frank
Sürün, Duran
author_facet Schmitt, Lukas Theo
Schneider, Aksana
Posorski, Jonas
Lansing, Felix
Jelicic, Milica
Jain, Manavi
Sayed, Shady
Buchholz, Frank
Sürün, Duran
author_sort Schmitt, Lukas Theo
collection PubMed
description We introduce DEQSeq, a nanopore sequencing approach that rationalizes the selection of favorable genome editing enzymes from directed molecular evolution experiments. With the ability to capture full-length sequences, editing efficiencies, and specificities from thousands of evolved enzymes simultaneously, DEQSeq streamlines the process of identifying the most valuable variants for further study and application. We apply DEQSeq to evolved libraries of Cas12f-ABEs and designer-recombinases, identifying variants with improved properties for future applications. Our results demonstrate that DEQSeq is a powerful tool for accelerating enzyme discovery and advancing genome editing research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03097-3.
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spelling pubmed-106266412023-11-07 Quantification of evolved DNA-editing enzymes at scale with DEQSeq Schmitt, Lukas Theo Schneider, Aksana Posorski, Jonas Lansing, Felix Jelicic, Milica Jain, Manavi Sayed, Shady Buchholz, Frank Sürün, Duran Genome Biol Method We introduce DEQSeq, a nanopore sequencing approach that rationalizes the selection of favorable genome editing enzymes from directed molecular evolution experiments. With the ability to capture full-length sequences, editing efficiencies, and specificities from thousands of evolved enzymes simultaneously, DEQSeq streamlines the process of identifying the most valuable variants for further study and application. We apply DEQSeq to evolved libraries of Cas12f-ABEs and designer-recombinases, identifying variants with improved properties for future applications. Our results demonstrate that DEQSeq is a powerful tool for accelerating enzyme discovery and advancing genome editing research. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03097-3. BioMed Central 2023-11-06 /pmc/articles/PMC10626641/ /pubmed/37932818 http://dx.doi.org/10.1186/s13059-023-03097-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Schmitt, Lukas Theo
Schneider, Aksana
Posorski, Jonas
Lansing, Felix
Jelicic, Milica
Jain, Manavi
Sayed, Shady
Buchholz, Frank
Sürün, Duran
Quantification of evolved DNA-editing enzymes at scale with DEQSeq
title Quantification of evolved DNA-editing enzymes at scale with DEQSeq
title_full Quantification of evolved DNA-editing enzymes at scale with DEQSeq
title_fullStr Quantification of evolved DNA-editing enzymes at scale with DEQSeq
title_full_unstemmed Quantification of evolved DNA-editing enzymes at scale with DEQSeq
title_short Quantification of evolved DNA-editing enzymes at scale with DEQSeq
title_sort quantification of evolved dna-editing enzymes at scale with deqseq
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10626641/
https://www.ncbi.nlm.nih.gov/pubmed/37932818
http://dx.doi.org/10.1186/s13059-023-03097-3
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