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  Probing the SELEX Process with Next-Generation Sequencing

Schütze, T., Wilhelm, B., Greiner, N., Braun, H., Peter, F., Mörl, M., et al. (2011). Probing the SELEX Process with Next-Generation Sequencing. PLoS ONE, 6(12): e29604. doi:10.1371/journal.pone.0029604.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E3E1-9 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-E3E2-7
Genre: Journal Article

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© 2011 Schütze et al. 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 credited.
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 Creators:
Schütze, Tatjana1, Author              
Wilhelm, Barbara2, Author
Greiner, Nicole1, Author              
Braun, Hannsjörg3, Author
Peter, Franziska4, Author
Mörl, Mario4, Author
Erdmann, Volker A.5, Author
Lehrach, Hans1, Author              
Konthur, Zoltán6, Author              
Menger, Marcus7, Author
Arndt, Peter F.8, Author              
Glökler, Jörn1, Author              
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1433550              
2Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_persistent22              
3Alacris Theranostics GmbH, Berlin, Germany, ou_persistent22              
4Institute of Biochemistry, Universität Leipzig, Leipzig, Germany, ou_persistent22              
5Institute for Chemistry/Biochemistry, Free University Berlin, Berlin, Germany, ou_persistent22              
6In vitro Ligand Screening (Zoltán Konthur), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1479653              
7RiNA RNA-Netzwerk Technologien GmbH, Berlin, Germany, ou_persistent22              
8Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, Berlin, Germany, ou_1479638              

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 Abstract: 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.

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Language(s): eng - English
 Dates: 2011-12-29
 Publication Status: Published online
 Pages: -
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 Table of Contents: -
 Rev. Method: Peer
 Identifiers: PMC: 3248438
DOI: 10.1371/journal.pone.0029604
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Title: PLoS ONE
Source Genre: Journal
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Publ. Info: San Francisco, USA : Public Library of Science
Pages: - Volume / Issue: 6 (12) Sequence Number: e29604 Start / End Page: - Identifier: Other: PLoS One
Other: plos
Other: plosone
ISSN: 1932-6203