Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment

Nucleic Acids Research

Volumn 43, Issue 12, 2015, Pages

  Levay, Agata ^a   Brenneman, Randall ^a   Hoinka, Jan ^b   Sant, David ^a   Cardone, Marco ^c   Trinchieri, Giorgio ^c   Przytycka, Teresa M ^b   Berezhnoy, Alexey ^a,d  

^a UNIVERSITY OF MIAMI   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; CD137 ANTIGEN; HIGH AFFINITY APTAMER LIGAND; INTERLEUKIN 10 RECEPTOR ALPHA; UNCLASSIFIED DRUG; INTERLEUKIN 10 RECEPTOR; LIGAND; TNFRSF9 PROTEIN, HUMAN;

ARTICLE; BINDING AFFINITY; BIOINFORMATICS; COMBINATORIAL CHEMISTRY; CROSS REACTION; EMULSION POLYMERASE CHAIN REACTION; HIGH THROUGHPUT SEQUENCING; IN VITRO STUDY; ISOLATION PROCEDURE; MUTAGENESIS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; ANIMAL; GENE LIBRARY; HUMAN; METABOLISM; MOUSE; MUTATION; PROCEDURES;

ANIMALS; ANTIGENS, CD137; APTAMERS, NUCLEOTIDE; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIGANDS; MICE; MUTATION; POLYMERASE CHAIN REACTION; RECEPTORS, INTERLEUKIN-10; SELEX APTAMER TECHNIQUE;

EID: 84942087540     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv534     Document Type: Article

References (48)

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25. Aggarwal, S. (2012) What's fueling the biotech engine - 2011 to 2012. Nat. Biotech., 12, 1191-1197.
26. Parsons, H.L., Earnshaw, J.C., Wilton, J., Johnson, K.S., Schueler, P.A., Mahoney, W. and McCafferty, J. (1996) Directing phage selections towards specific epitopes. Protein Eng., 9, 1043-1049.
27. Beck, A., Wurch, T., Bailly, C. and Corvaia, N. (2010) Strategies and challenges for the next generation of therapeutic antibodies. Nat. Rev. Immunol., 10, 345-352.
28. Burton, D.R., Poignard, P., Stanfield, R.L. and Wilson, I.A. (2012) Broadly neutralizing antibodies present new prospects to counter highly antigenically diverse viruses. Science, 337, 183-186.
29. Bostrom, J., Yu, S.F., Kan, D., Appleton, B.A., Lee, C.V., Billeci, K., Man, W., Peale, F., Ross, S., Wiesmann, C. et al. (2009) Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site. Science, 323, 1610-1614.
30. Pastor, F., Kolonias, D., Giangrande, P.H. and Gilboa, E. (2010) Induction of tumor immunity by targeted inhibition of nonsense mediated mRNA decay. Nature, 465, 227-231.
31. Dassie, J.P., Liu, X.Y., Thomas, G.S., Whitaker, R.M., Thiel, K.W., Stockdale, K.R., Meyerholz, D.K., McCaffrey, A.P., McNamara, J.O. 2nd and Giangrande, P.H. (2009) Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat. Biotechnol., 27, 839-849.
32. Ni, X., Zhang, Y., Ribas, J., Chowdhury, W.H., Castanares, M., Zhang, Z., Laiho, M., Deweese, T.L. and Lupold, S.E. (2011) Prostate-targeted radiosensitization via aptamer-shRNA chimeras in human tumor xenografts. J. Clin. Invest., 121, 2383-2390.
33. Neff, C.P., Zhou, J., Remling, L., Kuruvilla, J., Zhang, J., Li, H., Smith, D.D., Swiderski, P., Rossi, J.J. and Akkina, R. (2011) An aptamer-siRNA chimera suppresses HIV-1 viral loads and protects from helper CD4(+) T cell decline in humanized mice. Sci. Transl. Med., 3, 66ra66.
34. Wheeler, L.A., Trifonova, R., Vrbanac, V., Basar, E., McKernan, S., Xu, Z., Seung, E., Deruaz, M., Dudek, T., Einarsson, J.I. et al. (2011) Inhibition of HIV transmission in human cervicovaginal explants and humanized mice using CD4 aptamer-siRNA chimeras. J. Clin. Invest., 121, 2401-2412.
35. 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. U.S.A., 107, 15373-15378.
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37. 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.
38. Berezhnoy, A., Stewart, C.A., McNamara, J., Thiel, W., Giangrande, P., Trinchieri, G. and Gilboa, E. (2012) Isolation & optimization of murine IL-10 receptor blocking oligonucleotide aptamers using high-throughput sequencing. Mol. Ther., 20, 1242-1250.
39. Hoinka, J., Berezhnoy, A., Dao, P., Sauna, Z.E., Gilboa, E. and Przytycka, T.M. (2015) Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery. Nucleic Acids Res., doi: 10.1093/nar/gkv308.
40. Agresti, J.J., Kelly, B.T., Jäschke, A. and Griffiths, A.D. (2005) Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization. Proc. Natl. Acad. Sci. U.S.A., 102, 16170-16175.
41. Shao, K., Ding, W., Wang, F., Li, H., Ma, D. and Wang, H. (2011) Emulsion PCR: a high efficient way of PCR amplification of random DNA libraries in aptamer selection. PLoS One, 6, e24910.
42. Yufa, R., Krylova, S.M., Bruce, C., Bagg, E.A., Schofield, C.J. and Krylov, S.N. (2015) Emulsion PCR significantly improves nonequilibrium capillary electrophoresis of equilibrium mixtures-based aptamer selection: allowing for efficient and rapid selection of aptamer to unmodified ABH2 protein. Anal. Chem., 87, 1411-1419.
43. 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.
44. White, R., Rusconi, C., Scardino, E., Wolberg, A., Lawson, J., Hoffman, M. and Sullenger, B. (2001) Generation of species cross-reactive aptamers using 'toggle' SELEX. Mol. Ther., 4, 567-573.
45. Musheev, M.U. and Krylov, S.N. (2006) Selection of aptamers by systematic evolution of ligands by exponential enrichment: addressing the polymerase chain reaction issue. Anal. Chim. Acta, 564, 91-96.
46. Cho, M., Soo Oh, S., Nie, J., Stewart, R., Eisenstein, M., Chambers, J., Marth, J.D., Walker, F., Thomson, J.A. and Soh, H.T. (2013) Quantitative selection and parallel characterization of aptamers. Proc. Natl. Acad. Sci. U.S.A., 110, 18460-18465.
47. Gong, Q., Wang, J., Ahmad, K.M., Csordas, A.T., Zhou, J., Nie, J., Stewart, R., Thomson, J.A., Rossi, J.J. and Soh, H.T. (2012) Selection strategy to generate aptamer pairs that bind to distinct sites on protein targets. Anal. Chem., 84, 5365-5371.
48. Rockey, W.M., Hernandez, F.J., Huang, S.Y., Cao, S., Howell, C.A., Thomas, G.S., Liu, X.Y., Lapteva, N., Spencer, D.M., McNamara, J.O. et al. (2011) Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling. Nucleic Acids Ther., 21, 299-314.