Identification and characterization of an eIF4e DNA aptamer that inhibits proliferation with high throughput sequencing

Molecular Therapy Nucleic Acids

Volumn 3, Issue , 2014, Pages e217-

  Guo, Wei Mei ^a   Kong, Kiat Whye ^a   Brown, Christopher John ^a   Quah, Soo Tng ^a   Yeo, Hui Ling ^a   Hoon, Shawn ^a,b   Seow, Yiqi ^a  

^a Agency for Science   (Singapore)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

Aptamer; eIF4e; Proliferation; SELEX

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; INITIATION FACTOR 4E; SHORT HAIRPIN RNA; SMALL INTERFERING RNA;

ARTICLE; CANCER INHIBITION; CELL CULTURE; CELL LOSS; CELL PROLIFERATION; CELL VIABILITY; CONTROLLED STUDY; DRUG IDENTIFICATION; DRUG PROTEIN BINDING; FEMALE; GEL MOBILITY SHIFT ASSAY; HEK293 CELL LINE; HELA CELL LINE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PURIFYING SELECTION; TRANSLATION INITIATION; WESTERN BLOTTING;

EID: 84925269992     PISSN: None     EISSN: 21622531     Source Type: Journal    
DOI: 10.1038/mtna.2014.70     Document Type: Article

References (29)

1. Ellington, AD and Szostak, JW (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
2. Tuerk, C and Gold, L (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
3. Huizenga, DE and Szostak, JW (1995). A DNA aptamer that binds adenosine and ATP. Biochemistry 34: 656-665.
4. Wen, AQ, Yang, QW, Li, JC, Lv, FL, Zhong, Q and Chen, CY (2009). A novel lipopolysaccharide-antagonizing aptamer protects mice against endotoxemia. Biochem Biophys Res Commun 382: 140-144.
5. 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.
6. Stojanovic, MN, de Prada, P and Landry, DW (2001). Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc 123: 4928-4931.
7. Gronewold, TM, Glass, S, Quandt, E and Famulok, M (2005). Monitoring complex formation in the blood-coagulation cascade using aptamer-coated SAW sensors. Biosens Bioelectron 20: 2044-2052.
8. McNamara, JO 2nd, Andrechek, ER, Wang, Y, Viles, KD, Rempel, RE, Gilboa, E et al. (2006). Cell type-specific delivery of siRNAs with aptamer-siRNA chimeras. Nat Biotechnol 24: 1005-1015.
9. Gu, F, Zhang, L, Teply, BA, Mann, N, Wang, A, Radovic-Moreno, AF et al. (2008). Precise engineering of targeted nanoparticles by using self-assembled biointegrated block copolymers. Proc Natl Acad Sci USA 105: 2586-2591.
10. Teng, Y, Girvan, AC, Casson, LK, Pierce, WM Jr, Qian, M, Thomas, SD et al. (2007). AS1411 alters the localization of a complex containing protein arginine methyltransferase 5 and nucleolin. Cancer Res 67: 10491-10500.
11. Marimuthu, C, Tang, TH, Tominaga, J, Tan, SC and Gopinath, SC (2012). Single-stranded DNA (ssDNA) production in DNA aptamer generation. Analyst 137: 1307-1315.
12. Boiziau, C, Dausse, E, Yurchenko, L and Toulmé, JJ (1999). DNA aptamers selected against the HIV-1 trans-activation-responsive RNA element form RNA-DNA kissing complexes. J Biol Chem 274: 12730-12737.
13. 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.
14. 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.
15. 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.
16. Ditzler, MA, Lange, MJ, Bose, D, Bottoms, CA, Virkler, KF, Sawyer, AW et al. (2013). Highthroughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase. Nucleic Acids Res 41: 1873-1884.
17. 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.
18. Montanaro, L and Pandolfi, PP (2004). Initiation of mRNA translation in oncogenesis: the role of eIF4E. Cell Cycle 3: 1387-1389.
19. Graff, JR and Zimmer, SG (2003). Translational control and metastatic progression: enhanced activity of the mRNA cap-binding protein eIF-4E selectively enhances translation of metastasis-related mRNAs. Clin Exp Metastasis 20: 265-273.
20. Blagden, SP and Willis, AE (2011). The biological and therapeutic relevance of mRNA translation in cancer. Nat Rev Clin Oncol 8: 280-291.
21. Mochizuki, K, Oguro, A, Ohtsu, T, Sonenberg, N and Nakamura, Y (2005). High affinity RNA for mammalian initiation factor 4E interferes with mRNA-cap binding and inhibits translation. RNA 11: 77-89.
22. Zuker, M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
23. Soni, A, Akcakanat, A, Singh, G, Luyimbazi, D, Zheng, Y, Kim, D et al. (2008). eIF4E knockdown decreases breast cancer cell growth without activating Akt signaling. Mol Cancer Ther 7: 1782-1788.
24. Di Giusto, DA and King, GC (2004). Construction, stability, and activity of multivalent circular anticoagulant aptamers. J Biol Chem 279: 46483-46489.
25. Mahlknecht, G, Maron, R, Mancini, M, Schechter, B, Sela, M and Yarden, Y (2013). Aptamer to ErbB-2/HER2 enhances degradation of the target and inhibits tumorigenic growth. Proc Natl Acad Sci USA 110: 8170-8175.
26. Latham, JA, Johnson, R and Toole, JJ (1994). The application of a modified nucleotide in aptamer selection: novel thrombin aptamers containing 5-(1-pentynyl)-2'-deoxyuridine. Nucleic Acids Res 22: 2817-2822.
27. Kimoto, M, Yamashige, R, Matsunaga, K, Yokoyama, S and Hirao, I (2013). Generation of high-affinity DNA aptamers using an expanded genetic alphabet. Nat Biotechnol 31: 453-457.
28. Schwarzer, A, Holtmann, H, Brugman, M, Meyer, J, Schauerte, C, Zuber, J et al. (2014). Hyperactivation of mTORC1 and mTORC2 by multiple oncogenic events causes addiction to eIF4E-dependent mRNA translation in T-cell leukemia. Oncogene (epub ahead of print).
29. Seow, Y, Sibley, CR and Wood, MJ (2012). Artificial mirtron-mediated gene knockdown: functional DMPK silencing in mammalian cells. RNA 18: 1328-1337.