Refining the Results of a Classical SELEX Experiment by Expanding the Sequence Data Set of an Aptamer Pool Selected for Protein A

International Journal of Molecular Sciences
Regina Stoltenburg, Beate Strehlitz

Abstract

New, as yet undiscovered aptamers for Protein A were identified by applying next generation sequencing (NGS) to a previously selected aptamer pool. This pool was obtained in a classical SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiment using the FluMag-SELEX procedure followed by cloning and Sanger sequencing. PA#2/8 was identified as the only Protein A-binding aptamer from the Sanger sequence pool, and was shown to be able to bind intact cells of Staphylococcus aureus. In this study, we show the extension of the SELEX results by re-sequencing of the same aptamer pool using a medium throughput NGS approach and data analysis. Both data pools were compared. They confirm the selection of a highly complex and heterogeneous oligonucleotide pool and show consistently a high content of orphans as well as a similar relative frequency of certain sequence groups. But in contrast to the Sanger data pool, the NGS pool was clearly dominated by one sequence group containing the known Protein A-binding aptamer PA#2/8 as the most frequent sequence in this group. In addition, we found two new sequence groups in the NGS pool represented by PA-C10 and PA-C8, respectively, which also have high specificity for Protein A. ...Continue Reading

References

Aug 30, 1990·Nature·A D Ellington, J W Szostak
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Jun 26, 2003·Nucleic Acids Research·Michael Zuker
Jul 14, 2007·Biomolecular Engineering·Regina StoltenburgBeate Strehlitz
Jul 31, 2007·Genome Biology·Susan M HuseDavid Mark Welch
Aug 23, 2008·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Ruud H Deurenberg, Ellen E Stobberingh
Aug 30, 2008·Analytical Chemistry·Johanna-Gabriela WalterThomas Scheper
Apr 15, 2010·BMC Bioinformatics·Beifang NiuWeizhong Li
Aug 14, 2010·Proceedings of the National Academy of Sciences of the United States of America·Minseon ChoH Tom Soh
Dec 14, 2011·BioTechniques·Shawn HoonJonathan Scolnick
Jan 14, 2012·PloS One·Tatjana SchützeJörn Glökler
Mar 22, 2012·Molecular Therapy : the Journal of the American Society of Gene Therapy·Alexey BerezhnoyEli Gilboa
Jul 26, 2012·Journal of Biomedicine & Biotechnology·Lin LiuMaggie Law
Mar 23, 2013·International Journal of Medical Microbiology : IJMM·Michael Otto
May 2, 2013·Biotechnology Advances·Filip RadomFilip Jeleń
Dec 18, 2013·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Martin E Stryjewski, G Ralph Corey
May 8, 2014·BioMed Research International·Jhalka KadariyaDipendra Thapaliya
Jun 1, 2014·Journal of Pharmaceutical and Biomedical Analysis·Zsuzsanna SzeitnerTamás Mészáros
Jan 13, 2015·Analytical and Bioanalytical Chemistry·Kathryn R RileyKeith Bonin
Feb 25, 2015·Biotechnology Advances·Mariia DarmostukTomas Ruml
Jul 3, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Hongguang Sun, Youli Zu
Jul 21, 2015·Analytical Chemistry·Maureen McKeagueMaria C DeRosa
Jul 30, 2015·PloS One·Regina StoltenburgBeate Strehlitz
Feb 13, 2016·The Analyst·Muslum Ilgu, Marit Nilsen-Hamilton
Apr 9, 2016·ACS Combinatorial Science·Stefania ValenzanoMichelangelo Pascale
Apr 26, 2016·Methods : a Companion to Methods in Enzymology·Yi Xi Wu, Young Jik Kwon
May 14, 2016·Analytical and Bioanalytical Chemistry·Shunxiang GaoLianghua Wang
Jun 1, 2016·Chemistry : a European Journal·Huimin ZhangChaoyong Yang
Jun 18, 2016·Methods : a Companion to Methods in Enzymology·Kenan JijakliKourosh Salehi-Ashtiani
Aug 21, 2016·Journal of Chromatography. a·Kathryn R RileyChrista L Colyer
Nov 4, 2016·Nature Reviews. Drug Discovery·Jiehua Zhou, John Rossi
Nov 16, 2016·Molecular Therapy. Nucleic Acids·Christopher H StuartWilliam H Gmeiner
Dec 16, 2016·Pharmaceuticals·Nam Nguyen QuangFrédéric Ducongé
Jan 1, 2015·Molecular Therapy. Nucleic Acids·Michael Blind, Michael Blank
Mar 16, 2017·Journal of Biological Engineering·Ho Bin Seo, Man Bock Gu
Sep 22, 2017·PloS One·Mario Martínez SoldevillaFernando Pastor
Oct 19, 2017·International Journal of Molecular Sciences·Zhenjian ZhuoBaoting Zhang
Nov 3, 2017·The Analyst·Sean K Dembowski, Michael T Bowser
Nov 22, 2017·International Journal of Molecular Sciences·Peggy ReichDieter Beckmann
Dec 1, 2017·International Journal of Molecular Sciences·Andrew B KinghornJulian A Tanner

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Citations

Jun 26, 2020·BMC Bioinformatics·Shintaro KatoTakafumi Aoki
Jul 28, 2020·International Journal of Molecular Sciences·Nevina E Trunzo, Ka Lok Hong
Oct 9, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Natalia Komarova, Alexander Kuznetsov
Jul 13, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Alexander Eisold, Dirk Labudde
Nov 26, 2020·International Journal of Molecular Sciences·Natalia KomarovaAlexander Kuznetsov
Dec 31, 2020·International Journal of Molecular Sciences·Mia StromSarah Shigdar

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Methods Mentioned

BETA
biosensors
SELEX
biosensor
electrophoresis
nucleotide exchange
PCR

Software Mentioned

MUSCEL
CLC Sequence Viewer
mfold
BIAevaluation
OriginPro
cutadapt

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