APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data

Bioinformatics (Oxford, England) - Tập 32 Số 2 - Trang 161-164 - 2016
Jimmy Caroli1, Cristian Taccioli1, Adriana De La Fuente2, Paolo Serafini2, Silvio Bicciato1
11 Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy and
22 Department of Microbiology & Immunology, UM/Sylvester Comprehensive Cancer Center, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA

Tóm tắt

Abstract Motivation: Aptamers are synthetic nucleic acid molecules that can bind biological targets in virtue of both their sequence and three-dimensional structure. Aptamers are selected using SELEX, Systematic Evolution of Ligands by EXponential enrichment, a technique that exploits aptamer-target binding affinity. The SELEX procedure, coupled with high-throughput sequencing (HT-SELEX), creates billions of random sequences capable of binding different epitopes on specific targets. Since this technique produces enormous amounts of data, computational analysis represents a critical step to screen and select the most biologically relevant sequences. Results: Here, we present APTANI, a computational tool to identify target-specific aptamers from HT-SELEX data and secondary structure information. APTANI builds on AptaMotif algorithm, originally implemented to analyze SELEX data; extends the applicability of AptaMotif to HT-SELEX data and introduces new functionalities, as the possibility to identify binding motifs, to cluster aptamer families or to compare output results from different HT-SELEX cycles. Tabular and graphical representations facilitate the downstream biological interpretation of results. Availability and implementation: APTANI is available at http://aptani.unimore.it. Contact:  [email protected] Supplementary information:  Supplementary data are available at Bioinformatics online.

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Tài liệu tham khảo

Alam, 2015, FASTAptamer: a bioinformatic toolkit for high-throughput sequence analysis of combinatorial selections, Mol. Ther. Nucleic Acids, 4, e230, 10.1038/mtna.2015.4

Bowser, 2005, SELEX: just another separation?, Analyst, 130, 128, 10.1039/b412492h

Denman, 1993, Using RNAFOLD to predict the activity of small catalytic RNAs, BioTechniques, 15, 1090

Ditzler, 2013, High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase, Nucleic Acids Res., 41, 1873, 10.1093/nar/gks1190

Hofacker, 1994, Fast folding and comparison of RNA secondary structures, Monatshefte f. Chemie, 125, 167, 10.1007/BF00818163

Hoinka, 2012, Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers, Bioinformatics, 28, i215, 10.1093/bioinformatics/bts210

Hoinka, 2014, AptaCluster—a method to cluster HT-SELEX aptamer pools and lessons from its application, Res. Comput. Mol. Biol., 8394, 115, 10.1007/978-3-319-05269-4_9

Keefe, 2010, Aptamers as therapeutics, Nat. Rev. Drug Discov., 9, 537, 10.1038/nrd3141

Kim, 2011, An RNA aptamer that specifically binds pancreatic adenocarcinoma up-regulated factor inhibits migration and growth of pancreatic cancer cells, Cancer Lett., 313, 76, 10.1016/j.canlet.2011.08.027

Lorenz, 2011, ViennaRNA package 2.0, Algorithms Mol. Biol., 6, 26, 10.1186/1748-7188-6-26

Popenda, 2012, Automated 3D structure composition for large RNAs, Nucleic Acids Res., 40, e112, 10.1093/nar/gks339

Roth, 2012, Aptamer-mediated blockade of IL4Rα triggers apoptosis of MDSCs and limits tumor progression, Cancer Res., 72, 1373, 10.1158/0008-5472.CAN-11-2772

Sievers, 2011, Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol. Syst. Biol., 7, 539, 10.1038/msb.2011.75

Thiel, 2012, Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection, PLoS One, 7, e43836, 10.1371/journal.pone.0043836

Tucker, 2012, G-quadruplex DNA aptamers and their ligands: structure, function and application, Curr. Pharm. Des., 18, 2014, 10.2174/138161212799958477

Wang, 2011, Aptamers as therapeutics in cardiovascular diseases, Curr. Med. Chem., 18, 4169, 10.2174/092986711797189673

Wuchty, 1999, Complete suboptimal folding of RNA and the stability of secondary structures, Biopolymers, 49, 145, 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G

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Bioinformatics (Oxford, England)

Tập 32 Số 2

161-164

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