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Probing the SELEX Process with Next-Generation Sequencing
BACKGROUND: SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing off...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248438/ https://www.ncbi.nlm.nih.gov/pubmed/22242135 http://dx.doi.org/10.1371/journal.pone.0029604 |
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author | Schütze, Tatjana Wilhelm, Barbara Greiner, Nicole Braun, Hannsjörg Peter, Franziska Mörl, Mario Erdmann, Volker A. Lehrach, Hans Konthur, Zoltán Menger, Marcus Arndt, Peter F. Glökler, Jörn |
author_facet | Schütze, Tatjana Wilhelm, Barbara Greiner, Nicole Braun, Hannsjörg Peter, Franziska Mörl, Mario Erdmann, Volker A. Lehrach, Hans Konthur, Zoltán Menger, Marcus Arndt, Peter F. Glökler, Jörn |
author_sort | Schütze, Tatjana |
collection | PubMed |
description | BACKGROUND: SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing offers the opportunity to open the black box and observe a large part of the population dynamics during the selection process. METHODOLOGY: We have performed a semi-automated SELEX procedure on the model target streptavidin starting with a synthetic DNA oligonucleotide library and compared results obtained by the conventional analysis via cloning and Sanger sequencing with next-generation sequencing. In order to follow the population dynamics during the selection, pools from all selection rounds were barcoded and sequenced in parallel. CONCLUSIONS: High affinity aptamers can be readily identified simply by copy number enrichment in the first selection rounds. Based on our results, we suggest a new selection scheme that avoids a high number of iterative selection rounds while reducing time, PCR bias, and artifacts. |
format | Online Article Text |
id | pubmed-3248438 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-32484382012-01-12 Probing the SELEX Process with Next-Generation Sequencing Schütze, Tatjana Wilhelm, Barbara Greiner, Nicole Braun, Hannsjörg Peter, Franziska Mörl, Mario Erdmann, Volker A. Lehrach, Hans Konthur, Zoltán Menger, Marcus Arndt, Peter F. Glökler, Jörn PLoS One Research Article BACKGROUND: SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing offers the opportunity to open the black box and observe a large part of the population dynamics during the selection process. METHODOLOGY: We have performed a semi-automated SELEX procedure on the model target streptavidin starting with a synthetic DNA oligonucleotide library and compared results obtained by the conventional analysis via cloning and Sanger sequencing with next-generation sequencing. In order to follow the population dynamics during the selection, pools from all selection rounds were barcoded and sequenced in parallel. CONCLUSIONS: High affinity aptamers can be readily identified simply by copy number enrichment in the first selection rounds. Based on our results, we suggest a new selection scheme that avoids a high number of iterative selection rounds while reducing time, PCR bias, and artifacts. Public Library of Science 2011-12-29 /pmc/articles/PMC3248438/ /pubmed/22242135 http://dx.doi.org/10.1371/journal.pone.0029604 Text en Schütze 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Schütze, Tatjana Wilhelm, Barbara Greiner, Nicole Braun, Hannsjörg Peter, Franziska Mörl, Mario Erdmann, Volker A. Lehrach, Hans Konthur, Zoltán Menger, Marcus Arndt, Peter F. Glökler, Jörn Probing the SELEX Process with Next-Generation Sequencing |
title | Probing the SELEX Process with Next-Generation Sequencing |
title_full | Probing the SELEX Process with Next-Generation Sequencing |
title_fullStr | Probing the SELEX Process with Next-Generation Sequencing |
title_full_unstemmed | Probing the SELEX Process with Next-Generation Sequencing |
title_short | Probing the SELEX Process with Next-Generation Sequencing |
title_sort | probing the selex process with next-generation sequencing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248438/ https://www.ncbi.nlm.nih.gov/pubmed/22242135 http://dx.doi.org/10.1371/journal.pone.0029604 |
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