Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

Nucleic Acids Research

Volumn 43, Issue 12, 2015, Pages 5699-5707

  Hoinka, Jan ^a   Berezhnoy, Alexey ^b   Dao, Phuong ^a   Sauna, Zuben E ^c   Gilboa, Eli ^b   Przytycka, Teresa M ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^c CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; INTERLEUKIN 10 RECEPTOR ALPHA;

ARTICLE; BINDING AFFINITY; COMPUTER MODEL; CONTROLLED STUDY; ENZYME ANALYSIS; GENE MUTATION; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC PROCEDURES; HIGH THROUGHPUT SYSTEMATIC EVOLUTION OF LIGANDS BY EXPONENTIAL ENRICHMENT; HUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS; ALGORITHM; COMBINATORIAL CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; HIGH THROUGHPUT SEQUENCING; METABOLISM; MUTAGENESIS; MUTATION; PROCEDURES; STATISTICAL MODEL; VALIDATION STUDY;

ALGORITHMS; APTAMERS, NUCLEOTIDE; COMPUTER SIMULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERLEUKIN-10 RECEPTOR ALPHA SUBUNIT; MODELS, STATISTICAL; MUTAGENESIS; MUTATION; SELEX APTAMER TECHNIQUE; SOFTWARE;

EID: 84938542141     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv308     Document Type: Article

References (84)

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32. Hoinka, J., Berezhnoy, A., Sauna, Z.E., Gilboa, E. and Przytycka, T.M. (2014) AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application. In: 18th Annual International Conference on Research in Computational Molecular Biology. Springer, Pittsburgh, Pennsylvania, pp. 115-128.
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48. Ishihama, A., Kori, A., Koshio, E., Yamada, K., Maeda, H., Shimada, T., Makinoshima, H., Iwata, A. and Fujita, N. (2014) Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli. J. Bacteriol., 196, 2718-2727.
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53. Park, J.-W., Jin Lee, S., Choi, E.-J., Kim, J., Song, J.-Y. and Bock Gu, M. (2014) An ultra-sensitive detection of a whole virus using dual aptamers developed by immobilization-free screening. Biosens. Bioelectron., 51, 324-329.
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61. Thiel, W.H., Thiel, K.W., Flenker, K.S., Bair, T., Dupuy, A.J., McNamara, J.O. 2nd, Miller, F.J. and Giangrande, P.H. (2015) Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells. Methods Mol. Biol., 1218, 187-199.
62. Jiang, P., Meyer, S., Hou, Z., Propson, N.E., Soh, H.T., Thomson, J.A. and Stewart, R. (2014) MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers. Bioinformatics, 30, 2665-2667.
63. Beier, R., Boschke, E. and Labudde, D. (2014) New strategies for evaluation and analysis of SELEX experiments. Biomed. Res. Int., 2014, 849743.
64. Hoon, S., Zhou, B., Janda, K.D., Brenner, S. and Scolnick, J. (2011) Aptamer selection by high-throughput sequencing and informatic analysis. Biotechniques, 51, 413-416.
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67. Stoltenburg, R., Reinemann, C. and Strehlitz, B. (2007) SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng., 24, 381-403.
68. Eaton, B.E., Gold, L., Hicke, B.J., Janjic, N., Jucker, F.M., Sebesta, D.P., Tarasow, T.M., Willis, M.C. and Zichi, D.A. (1997) Post-SELEX combinatorial optimization of aptamers. Bioorg. Med. Chem., 5, 1087-1096.
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71. Ditzler, M.A., Lange, M.J., Bose, D., Bottoms, C.A., Virkler, K.F., Sawyer, A.W., Whatley, A.S., Spollen, W., Givan, S.A. and Burke, D.H. (2013) High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Res., 41, 1873-1884.
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74. Hoinka, J., Berezhnoy, A., Sauna, Z.E., Gilboa, E. and Przytycka, T.M. (2014) AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application. In: 18th Annual International Conference on Research in Computational Molecular Biology. Springer, Pittsburgh, Pennsylvania, pp. 115-128.
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77. Layzer, J.M. and Sullenger, B.A. (2007) Simultaneous generation of aptamers to multiple gamma-carboxyglutamic acid proteins from a focused aptamer library using DeSELEX and convergent selection. Oligonucleotides, 17, 1-11.
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79. Cho, M., Xiao, Y., Nie, J., Stewart, R., Csordas, A.T., Oh, S.S., Thomson, J.A. and Soh, H.T. (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl. Acad. Sci., 107, 15373-15378.
80. Thiel, W.H., Bair, T., Peek, A.S., Liu, X., Dassie, J., Stockdale, K.R., Behlke, M.A., Miller, F.J. Jr and Giangrande, P.H. (2012) Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PloS One, 7, e43836.
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82. Swofford, D.L. (2003) 4.0 ed. Sinauer Associates, Sunderland, Massachusetts, pp. PAUP. Phylogenetic Analysis Using Parsimony (and Other Methods).
83. Cho, M., Xiao, Y., Nie, J., Stewart, R., Csordas, A.T., Oh, S.S., Thomson, J.A. and Soh, H.T. (2010) Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc. Natl. Acad. Sci., 107, 15373-15378.
84. Ozer, A., Pagano, J.M. and Lis, J.T. (2014) New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. Mol. Ther. Nucleic Acids, 3, e183.