Probing the SELEX process with next-generation sequencing.
<h4>Background</h4>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-genera...
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2011
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oai:doaj.org-article:63aec77d91e042dc80de680b3675822a2021-11-18T07:31:14ZProbing the SELEX process with next-generation sequencing.1932-620310.1371/journal.pone.0029604https://doaj.org/article/63aec77d91e042dc80de680b3675822a2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22242135/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology</h4>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.<h4>Conclusions</h4>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.Tatjana SchützeBarbara WilhelmNicole GreinerHannsjörg BraunFranziska PeterMario MörlVolker A ErdmannHans LehrachZoltán KonthurMarcus MengerPeter F ArndtJörn GlöklerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 12, p e29604 (2011) |
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Medicine R Science Q Tatjana Schütze Barbara Wilhelm Nicole Greiner Hannsjörg Braun Franziska Peter Mario Mörl Volker A Erdmann Hans Lehrach Zoltán Konthur Marcus Menger Peter F Arndt Jörn Glökler Probing the SELEX process with next-generation sequencing. |
| description |
<h4>Background</h4>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.<h4>Methodology</h4>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.<h4>Conclusions</h4>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 |
article |
| author |
Tatjana Schütze Barbara Wilhelm Nicole Greiner Hannsjörg Braun Franziska Peter Mario Mörl Volker A Erdmann Hans Lehrach Zoltán Konthur Marcus Menger Peter F Arndt Jörn Glökler |
| author_facet |
Tatjana Schütze Barbara Wilhelm Nicole Greiner Hannsjörg Braun Franziska Peter Mario Mörl Volker A Erdmann Hans Lehrach Zoltán Konthur Marcus Menger Peter F Arndt Jörn Glökler |
| author_sort |
Tatjana Schütze |
| title |
Probing the SELEX process with next-generation sequencing. |
| title_short |
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_sort |
probing the selex process with next-generation sequencing. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2011 |
| url |
https://doaj.org/article/63aec77d91e042dc80de680b3675822a |
| work_keys_str_mv |
AT tatjanaschutze probingtheselexprocesswithnextgenerationsequencing AT barbarawilhelm probingtheselexprocesswithnextgenerationsequencing AT nicolegreiner probingtheselexprocesswithnextgenerationsequencing AT hannsjorgbraun probingtheselexprocesswithnextgenerationsequencing AT franziskapeter probingtheselexprocesswithnextgenerationsequencing AT mariomorl probingtheselexprocesswithnextgenerationsequencing AT volkeraerdmann probingtheselexprocesswithnextgenerationsequencing AT hanslehrach probingtheselexprocesswithnextgenerationsequencing AT zoltankonthur probingtheselexprocesswithnextgenerationsequencing AT marcusmenger probingtheselexprocesswithnextgenerationsequencing AT peterfarndt probingtheselexprocesswithnextgenerationsequencing AT jornglokler probingtheselexprocesswithnextgenerationsequencing |
| _version_ |
1718423347462668288 |