Aptamer Selection Technology and Recent Advances

Molecular Therapy Nucleic Acids

Volumn 4, Issue 1, 2015, Pages e223-

  Blind, Michael ^a   Blank, Michael ^a  

^a Am Klopferspitz 19a   (Germany)

Author keywords

aptamer; bioinformatics; microfluidics; next generation sequencing; NGS; SELEX

Indexed keywords

APTAMER;

ARTICLE; BIOINFORMATICS; HIGH THROUGHPUT SEQUENCING; IN VITRO STUDY; MOLECULAR DIAGNOSIS; MOLECULAR LIBRARY; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; TECHNOLOGY;

EID: 84927717726     PISSN: None     EISSN: 21622531     Source Type: Journal    
DOI: 10.1038/mtna.2014.74     Document Type: Review

References (75)

1. Nimjee, SM, Rusconi, CP and Sullenger, BA (2005). Aptamers: an emerging class of therapeutics. Annu Rev Med 56: 555-583.
2. Keefe, AD, Pai, S and Ellington, A (2010). Aptamers as therapeutics. Nat Rev Drug Discov 9: 537-550.
3. Burnett, JC and Rossi, JJ (2012). RNA-based therapeutics: current progress and future prospects. Chem Biol 19: 60-71.
4. Wang, C, Liu, B, Lu, J, Zhang, G and Lu, A (2014). Strategies for combination of aptamer and targeted drug delivery. J Nanosci Nanotechnol 14: 501-512.
5. Mastronardi, E, Foster, A, Zhang, X and DeRosa, MC (2014). Smart materials based on DNA aptamers: taking aptasensing to the next level. Sensors (Basel) 14: 3156-3171.
6. Thiviyanathan, V and Gorenstein, DG (2012). Aptamers and the next generation of diagnostic reagents. Proteomics Clin Appl 6: 563-573.
7. Jayasena, SD (1999). Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin Chem 45: 1628-1650.
8. Ellington, AD and Szostak, JW (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
9. Gold, L and Tuerk, C (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
10. Gold, L, Ayers, D, Bertino, J, Bock, C, Bock, A, Brody, EN et al. (2010). Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS ONE 5: e15004.
11. Kuwahara, M and Obika, S (2013). In vitro selection of BNA (LNA) aptamers. Artif DNA PNA XNA 4: 39-48.
12. Kahvejian, A, Quackenbush, J and Thompson, JF (2008). What would you do if you could sequence everything? Nat Biotechnol 26: 1125-1133.
13. Dias-Neto, E, Nunes, DN, Giordano, RJ, Sun, J, Botz, GH, Yang, K et al. (2009). Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS ONE 4: e8338.
14. Ravn, U, Gueneau, F, Baerlocher, L, Osteras, M, Desmurs, M, Malinge, P et al. (2010). By-passing in vitro screening-next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res 38: e193.
15. 't Hoen, PA, Jirka, SM, Ten Broeke, BR, Schultes, EA, Aguilera, B, Pang, KH et al. (2012). Phage display screening without repetitious selection rounds. Anal Biochem 421: 622-631.
16. Mannocci, L, Zhang, Y, Scheuermann, J, Leimbacher, M, De Bellis, G, Rizzi, E et al. (2008). High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries. Proc Natl Acad Sci USA 105: 17670-17675.
17. Cho, M, Soo Oh, S, Nie, J, Stewart, R, Eisenstein, M, Chambers, J et al. (2013). Quantitative selection and parallel characterization of aptamers. Proc Natl Acad Sci USA 110: 18460-18465.
18. Ditzler, MA, Lange, MJ, Bose, D, Bottoms, CA, Virkler, KF, Sawyer, AW et al. (2013). High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Res 41: 1873-1884.
19. Cho, M, Xiao, Y, Nie, J, Stewart, R, Csordas, AT, Oh, SS et al. (2010). Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing. Proc Natl Acad Sci USA 107: 15373-15378.
20. Kupakuwana, GV, Crill, JE 2nd, McPike, MP and Borer, PN (2011). Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing. PLoS ONE 6: e19395.
21. Schütze, T, Wilhelm, B, Greiner, N, Braun, H, Peter, F, Mörl, M et al. (2011). Probing the SELEX process with next-generation sequencing. PLoS ONE 6: e29604.
22. Jolma, A, Kivioja, T, Toivonen, J, Cheng, L, Wei, G, Enge, M et al. (2010). Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res 20: 861-873.
23. Bayrac, AT, Sefah, K, Parekh, P, Bayrac, C, Gulbakan, B, Oktem, HA et al. (2011). In vitro Selection of DNA Aptamers to Glioblastoma Multiforme. ACS Chem Neurosci 2: 175-181.
24. Hoon, S, Zhou, B, Janda, KD, Brenner, S and Scolnick, J (2011). Aptamer selection by high-throughput sequencing and informatic analysis. BioTechniques 51: 413-416.
25. Thiel, KW, Hernandez, LI, Dassie, JP, Thiel, WH, Liu, X, Stockdale, KR et al. (2012). Delivery of chemo-sensitizing siRNAs to HER2+-breast cancer cells using RNA aptamers. Nucleic Acids Res 40: 6319-6337.
26. Berezhnoy, A, Stewart, CA, Mcnamara, JO 2nd, Thiel, W, Giangrande, P, Trinchieri, G et al. (2012). Isolation and optimization of murine IL-10 receptor blocking oligonucleotide aptamers using high-throughput sequencing. Mol Ther 20: 1242-1250.
27. Huang, YZ, Hernandez, FJ, Gu, B, Stockdale, KR, Nanapaneni, K, Scheetz, TE et al. (2012). RNA aptamer-based functional ligands of the neurotrophin receptor, TrkB. Mol Pharmacol 82: 623-635.
28. Zimmermann, B, Bilusic, I, Lorenz, C and Schroeder, R (2010). Genomic SELEX: a discovery tool for genomic aptamers. Methods 52: 125-132.
29. Klug, SJ, Hüttenhofer, A, Kromayer, M and Famulok, M (1997). In vitro and in vivo characterization of novel mRNA motifs that bind special elongation factor SelB. Proc Natl Acad Sci USA 94: 6676-6681.
30. Vater, A, Jarosch, F, Buchner, K and Klussmann, S (2003). Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX. Nucleic Acids Res 31: e130.
31. Jarosch, F, Buchner, K and Klussmann, S (2006). In vitro selection using a dual RNA library that allows primerless selection. Nucleic Acids Res 34: e86.
32. Pan, W, Xin, P, Patrick, S, Dean, S, Keating, C and Clawson, G (2010). Primer-free aptamer selection using a random DNA library. J Vis Exp 41: 2039.
33. Lai, YT and DeStefano, JJ (2011). A primer-free method that selects high-affinity single-stranded DNA aptamers using thermostable RNA ligase. Anal Biochem 414: 246-253.
34. Szeto, K, Latulippe, DR, Ozer, A, Pagano, JM, White, BS, Shalloway, D et al. (2013). RAPID-SELEX for RNA aptamers. PLoS ONE 8: e82667.
35. Mendonsa, SD and Bowser, MT (2005). In vitro selection of aptamers with affinity for neuropeptide Y using capillary electrophoresis. J Am Chem Soc 127: 9382-9383.
36. Mosing, RK, Mendonsa, SD and Bowser, MT (2005). Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. Anal Chem 77: 6107-6112.
37. Tang, J, Xie, J, Shao, N and Yan, Y (2006). The DNA aptamers that specifically recognize ricin toxin are selected by two in vitro selection methods. Electrophoresis 27: 1303-1311.
38. Mallikaratchy, P, Stahelin, RV, Cao, Z, Cho, W and Tan, W (2006). Selection of DNA ligands for protein kinase C-delta. Chem Commun (Camb) : 3229-3231.
39. Yang, J and Bowser, MT (2013). Capillary electrophoresis-SELEX selection of catalytic DNA aptamers for a small-molecule porphyrin target. Anal Chem 85: 1525-1530.
40. Nie, H, Chen, Y, Lü, C and Liu, Z (2013). Efficient selection of glycoprotein-binding DNA aptamers via boronate affinity monolithic capillary. Anal Chem 85: 8277-8283.
41. Berezovski, M, Musheev, M, Drabovich, A and Krylov, SN (2006). Non-SELEX selection of aptamers. J Am Chem Soc 128: 1410-1411.
42. Berezovski, MV, Musheev, MU, Drabovich, AP, Jitkova, JV and Krylov, SN (2006). Non-SELEX: selection of aptamers without intermediate amplification of candidate oligonucleotides. Nat Protoc 1: 1359-1369.
43. Tok, J, Lai, J, Leung, T and Li, SF (2010). Selection of aptamers for signal transduction proteins by capillary electrophoresis. Electrophoresis 31: 2055-2062.
44. Ashley, J, Ji, K and Li, SF (2012). Selection of bovine catalase aptamers using non-SELEX. Electrophoresis 33: 2783-2789.
45. Nitsche, A, Kurth, A, Dunkhorst, A, Pänke, O, Sielaff, H, Junge, W et al. (2007). One-step selection of Vaccinia virus-binding DNA aptamers by MonoLEX. BMC Biotechnol 7: 48.
46. Haberland, A, Wallukat, G, Dahmen, C, Kage, A and Schimke, I (2011). Aptamer neutralization of beta1-adrenoceptor autoantibodies isolated from patients with cardiomyopathies. Circ Res 109: 986-992.
47. Jing, M and Bowser, MT (2011). Isolation of DNA aptamers using micro free flow electrophoresis. Lab Chip 11: 3703-3709.
48. Cox, JC and Ellington, AD (2001). Automated selection of anti-protein aptamers. Bioorg Med Chem 9: 2525-2531.
49. Cox, JC, Hayhurst, A, Hesselberth, J, Bayer, TS, Georgiou, G and Ellington, AD (2002). Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res 30: e108.
50. Cox, JC, Rajendran, M, Riedel, T, Davidson, EA, Sooter, LJ, Bayer, TS et al. (2002). Automated acquisition of aptamer sequences. Comb Chem High Throughput Screen 5: 289-299.
51. Qian, J, Lou, X, Zhang, Y, Xiao, Y and Soh, HT (2009). Generation of highly specific aptamers via micromagnetic selection. Anal Chem 81: 5490-5495.
52. Lou, X, Qian, J, Xiao, Y, Viel, L, Gerdon, AE, Lagally, ET et al. (2009). Micromagnetic selection of aptamers in microfluidic channels. Proc Natl Acad Sci USA 106: 2989-2994.
53. Oh, SS, Ahmad, KM, Cho, M, Kim, S, Xiao, Y and Soh, HT (2011). Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels. Anal Chem 83: 6883-6889.
54. Ahmad, KM, Oh, SS, Kim, S, McClellen, FM, Xiao, Y and Soh, HT (2011). Probing the limits of aptamer affinity with a microfluidic SELEX platform. PLoS ONE 6: e27051.
55. Huang, CJ, Lin, HI, Shiesh, SC and Lee, GB (2010). Integrated microfluidic system for rapid screening of CRP aptamers utilizing systematic evolution of ligands by exponential enrichment (SELEX). Biosens Bioelectron 25: 1761-1766.
56. Huang, CJ, Lin, HI, Shiesh, SC and Lee, GB (2012). An integrated microfluidic system for rapid screening of alpha-fetoprotein-specific aptamers. Biosens Bioelectron 35: 50-55.
57. Lai, HC, Wang, CH, Liou, TM and Lee, GB (2014). Influenza A virus-specific aptamers screened by using an integrated microfluidic system. Lab Chip 14: 2002-2013.
58. Stoltenburg, R, Nikolaus, N and Strehlitz, B (2012). Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics. J Anal Methods Chem 2012: 415697.
59. Nikolaus, N and Strehlitz, B (2014). DNA-aptamers binding aminoglycoside antibiotics. Sensors (Basel) 14: 3737-3755.
60. Bock, LC, Griffin, LC, Latham, JA, Vermaas, EH and Toole, JJ (1992). Selection of singlestranded DNA molecules that bind and inhibit human thrombin. Nature 355: 564-566.
61. Beier, R, Pahlke, C, Quenzel, P, Henseleit, A, Boschke, E, Cuniberti, G et al. (2014). Selection of a DNA aptamer against norovirus capsid protein VP1. FEMS Microbiol Lett 351: 162-169.
62. Thiel, WH, Bair, T, Peek, AS, Liu, X, Dassie, J, Stockdale, KR et al. (2012). Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PLoS ONE 7: e43836.
63. Katoh, K, Kuma, K, Toh, H and Miyata, T (2005). MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518.
64. Nawrocki, EP, Kolbe, DL and Eddy, SR (2009). Infernal 1.0: inference of RNA alignments. Bioinformatics 25: 1335-1337.
65. Zuker, M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
66. Brown, JW, Birmingham, A, Griffiths, PE, Jossinet, F, Kachouri-Lafond, R, Knight, R et al. (2009). The RNA structure alignment ontology. RNA 15: 1623-1631.
67. Lorenz, R, Bernhart, SH, Höner Zu Siederdissen, C, Tafer, H, Flamm, C, Stadler, PF et al. (2011). ViennaRNA Package 2.0. Algorithms Mol Biol 6: 26.
68. Weinberg, Z and Breaker, RR (2011). R2R-software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics 12: 3.
69. Kang, KN and Lee, YS (2013). RNA aptamers: a review of recent trends and applications. Adv Biochem Eng Biotechnol 131: 153-169.
70. Lollo, B, Steele, F and Gold, L (2014). Beyond antibodies: new affinity reagents to unlock the proteome. Proteomics 14: 638-644.
71. Wang, AZ and Farokhzad, OC (2014). Current progress of aptamer-based molecular imaging. J Nucl Med 55: 353-356.
72. Hong, P, Li, W and Li, J (2012). Applications of aptasensors in clinical diagnostics. Sensors (Basel) 12: 1181-1193.
73. Ohuchi, S (2012). Cell-SELEX Technology. Biores Open Access 1: 265-272.
74. Guo, KT, Ziemer, G, Paul, A and Wendel, HP (2008). CELL-SELEX: Novel perspectives of aptamer-based therapeutics. Int J Mol Sci 9: 668-678.
75. Blank, M (2014). Bringing light into the black box of SELEX experiments. Aptamers 2014 Oxford Proceeding: 17-18.