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  Probing the SELEX Process with Next-Generation Sequencing

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

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7923-9 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7927-1
Genre: Journal Article

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 Creators:
Schutze, T.1, Author              
Wilhelm, B.2, Author              
Greiner, N.1, Author              
Braun, H., Author
Peter, F., Author
Morl, M., Author
Erdmann, V. A., Author
Lehrach, H.1, Author              
Konthur, Z.3, Author              
Menger, M., Author
Arndt, P. F.2, Author              
Glokler, J.1, Author              
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
2Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              
3In vitro Ligand Screening (Zoltán Konthur), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479653              

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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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 Dates: 2011
 Publication Status: Published in print
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 Rev. Method: -
 Identifiers: eDoc: 584794
DOI: 10.1371/journal.pone.0029604
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Title: PLoS ONE
Source Genre: Journal
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Pages: - Volume / Issue: 6 (12) Sequence Number: - Start / End Page: e29604 - e29604 Identifier: ISSN: 1932-6203 (Electronic)