Selection and characterization of anti-NF-κB p65 RNA aptamers

RNA

Volumn 14, Issue 6, 2008, Pages 1037-1047

  Wurster, Susan E ^a   Maher III, L James ^a  

^a MAYO GRADUATE SCHOOL   (United States)

Author keywords

Aptamer; In vitro selection; NF B; p65

Indexed keywords

APTAMER; DNA; DNA BINDING PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PROTEIN P50; RNA; SYNAPTOTAGMIN I;

ARTICLE; IN VITRO SELECTION; MOLECULAR LIBRARY; NONHUMAN; PRIORITY JOURNAL; RNA ANALYSIS; RNA LIBRARY; RNA SEQUENCE; RNA STRUCTURE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; DIMERIZATION; HUMANS; LIGANDS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; RNA; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTOR RELA;

HUMAN IMMUNODEFICIENCY VIRUS 1; MAMMALIA;

EID: 44149087131     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.878908     Document Type: Article

References (46)

1. Baeuerle, P.A. and Baltimore, D. 1996. NF-κB: Ten years after. Cell 87: 13-20.
2. Baldwin Jr., A.S. 1996. The NF-κB and IκB proteins: New discoveries and insights. Annu. Rev. Immunol. 14: 649-683.
3. Beg, A.A. and Baltimore, D. 1996. An essential role for NF-κB in preventing TNF-α-induced cell death. Science 274: 782-784.
4. Brown, T.S. and Bevilacqua, P.C. 2005. Method for assigning double-stranded RNA structures. Biotechniques 38: 368-372.
5. Burke, J.M. and Berzal-Herranz, A. 1993. In vitro selection and evolution of RNA: Applications for catalytic RNA, molecular recognition, and drug discovery. FASEB J. 7: 106-112.
6. Burke, D.H., Scates, L., Andrews, K., and Gold, L. 1996. Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. J. Mol. Biol. 264: 650-666.
7. Carmody, R.J., Ruan, Q., Palmer, S., Hilliard, B., and Chen, Y.H. 2007. Negative regulation of toll-like receptor signaling by NF-κB p50 ubiquitination blockade. Science 317: 675-678.
8. Cassiday, L.A. and Maher III, L.J. 2001. In vivo recognition of an RNA aptamer by its transcription factor target. Biochemistry 40: 2433-2438.
9. Cassiday, L.A. and Maher III, L.J. 2002. Having it both ways: Transcription factors that bind DNA and RNA. Nucleic Acids Res. 30: 4118-4126. doi: 10.1093/nar/gkf512.
10. Cassiday, L.A. and Maher III, L.J. 2003. Yeast genetic selections to optimize RNA decoys for transcription factor NF-κB. Proc. Natl. Acad. Sci. 100: 3930-3935.
11. Cassiday, L.A., Lebruska, L.L., Benson, L.M., Naylor, S., Owen, W.G., and Maher III, L.J. 2002. Binding stoichiometry of an RNA aptamer and its transcription factor target. Anal. Biochem. 306: 290-297.
12. Chen, F.E. and Ghosh, G. 1999. Regulation of DNA binding by Rel/NF-κB transcription factors: Structural views. Oncogene 18: 6845-6852.
13. Chen, Y.Q., Ghosh, S., and Ghosh, G. 1998. A novel DNA recognition mode by the NF-κB p65 homodimer. Nat. Struct. Biol. 5: 67-73.
14. Choi, K.H., Park, M.W., Lee, S.Y., Jeon, M.Y., Kim, M.Y., Lee, H.K., Yu, J., Kim, H.J., Han, K., Lee, H., et al. 2006. Intracellular expression of the T-cell factor-1 RNA aptamer as an intramer. Mol. Cancer Ther. 5: 2428-2434.
15. Dobrovolskaia, M.A. and Kozlov, S.V. 2005. Inflammation and cancer: When NF-κB amalgamates the perilous partnership. Curr. Cancer Drug Targets 5: 325-344.
16. Dutta, J., Fan, Y., Gupta, N., Fan, G., and Gelinas, C. 2006. Current insights into the regulation of programmed cell death by NF-κB. Oncogene 25: 6800-6816.
17. Ellington, A.D. and Szostak, J.W. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
18. Escarcega, R.O., Fuentes-Alexandro, S., Garcia-Carrasco, M., Gatica, A., and Zamora, A. 2007. The transcription factor nuclear factor-κB and cancer. Clin. Oncol. (R Coll Radiol) 19: 154-161.
19. Fujita, T., Nolan, G., Ghosh, S., and Baltimore, D. 1992. Independent modes of transcriptional activation by the p50 and p65 subunits of NF-κB. Genes & Dev. 6: 775-781.
20. Garg, A. and Aggarwal, B.B. 2002. Nuclear transcription factor-κB as a target for cancer drug development. Leukemia 16: 1053-1068.
21. Ghosh, G., van Duyne, G., Ghosh, S., and Sigler, P.B. 1995. Structure of NF-κB p50 homodimer bound to a κB site. Nature 373: 303-310.
22. Guo, J., Verma, U.N., Gaynor, R.B., Frenkel, E.P., and Becerra, C.R. 2004. Enhanced chemosensitivity to irinotecan by RNA interference-mediated down-regulation of the nuclear factor-κB p65 subunit. Clin. Cancer Res. 10: 3333-3341.
23. Hayden, M.S. and Ghosh, S. 2004. Signaling to NF-κB. Genes & Dev. 18: 2195-2224.
24. Huang, D.B., Vu, D., Cassiday, L.A., Zimmerman, J.M., Maher 3rd, L.J., and Ghosh, G. 2003. Crystal structure of NF-κB (p50)2 complexed to a high-affinity RNA aptamer. Proc. Natl. Acad. Sci. 100: 9268-9273.
25. Jaeger, J.A., Turner, D.H., and Zuker, M. 1989. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. 86: 7706-7710.
26. Jaeger, J.A., Turner, D.H., and Zuker, M. 1990. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183: 281-306.
27. Karin, M. 2006. Nuclear factor-κB in cancer development and progression. Nature 441: 431-436.
28. Karin, M. and Greten, F.R. 2005. NF-κB: Linking inflammation and immunity to cancer development and progression. Nat. Rev. Immunol. 5: 749-759.
29. Karin, M. and Lin, A. 2002. NF-κB at the crossroads of life and death. Nat. Immunol. 3: 221-227.
30. Karin, M., Cao, Y., Greten, F.R., and Li, Z.W. 2002. NF-κB in cancer: From innocent bystander to major culprit. Nat. Rev. Cancer 2: 301-310.
31. Kitajima, I., Shinohara, T., Bilakovics, J., Brown, D.A., Xu, X., and Nerenberg, M. 1992. Ablation of transplanted HTLV-I tax-transformed tumors in mice by antisense inhibition of NF-κB. Science 258: 1792-1795.
32. Lebruska, L.L. and Maher III., L.J. 1999. Selection and characterization of an RNA decoy for transcription factor NF-κB. Biochemistry 38: 3168-3174.
33. Lin, A. and Karin, M. 2003. NF-κB in cancer: A marked target. Semin. Cancer Biol. 13: 107-114.
34. Mayo, M.W., Wang, C.-Y., Cogswell, P.C., Rogers-Graham, K.S., Lowe, S.W., Der, C.J., and Baldwin, A.S. 1997. Requirement of NF-κB activation to suppress p53-independent apoptosis induced by oncogenic Ras. Science 278: 1812-1815.
35. McDonald, C.D. and Maher III., L.J. 1995. Recognition of duplex DNA by RNA polynucleotides. Nucleic Acids Res. 23: 500-506. doi: 10.1093/nar/23.3.500.
36. Mi, J., Zhang, X., Rabbani, Z.N., Liu, Y., Su, Z., Vujaskovic, Z., Kontos, C.D., Sullenger, B.A., and Clary, B.M. 2006. H1 RNA polymerase III promoter-driven expression of an RNA aptamer leads to high-level inhibition of intracellular protein activity. Nucleic Acids Res. 34: 3577-3584. doi: 10.1093/nar/gkl482.
37. Nakanishi, C. and Toi, M. 2005. Nuclear factor-κB inhibitors as sensitizers to anticancer drugs. Nat. Rev. Cancer 5: 297-309.
38. Perwez Hussain, S. and Harris, C.C. 2007. Inflammation and cancer: An ancient link with novel potentials. Int. J. Cancer 121: 2373-2380.
39. Reiter, N.J., Maher III, L.J., and Butcher, S.E. 2008. DNA mimicry by a high-affinity anti-NF-κB RNA aptamer. Nucleic Acids Res. 36: 1227-1236. doi: 10.1093/nar/gkm1141.
40. Soukup, G.A., Ellington, A.D., and Maher III., L.J. 1996. Selection of RNAs that bind to duplex DNA at neutral pH. J. Mol. Biol. 259: 216-228.
41. Suzan, M., Salaun, D., Neuveut, C., Spire, B., Hirsch, I., Le Bouteiller, P., Querat, G., and Sire, J. 1991. Induction of NF-KB during monocyte differentiation by HIV type 1 infection. J. Immunol. 146: 377-383.
42. Tuerk, C. and Gold, L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
43. Van Waes, C. 2007. Nuclear factor-κB in development, prevention, and therapy of cancer. Clin. Cancer Res. 13: 1076-1082.
44. Verma, I.M., Stevenson, J.K., Schwarz, E.M., Van Antwerp, D., and Miyamoto, S. 1995. Rel/NF-κB/IκB family: Intimate tales of association and dissociation. Genes & Dev. 9: 2723-2735.
45. Zhao, X., Shi, H., Sevilimedu, A., Liachko, N., Nelson, H.C., and Lis, J.T. 2006. An RNA aptamer that interferes with the DNA binding of the HSF transcription activator. Nucleic Acids Res. 34: 3755-3761. doi: 10.1093/nar/gkl470.
46. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.