Nucleotide bias observed with a short SELEX RNA aptamer library

Nucleic Acid Therapeutics

Volumn 21, Issue 4, 2011, Pages 253-263

  Thiel, William H ^a   Bair, Thomas ^b   Wyatt Thiel, Kristina ^a   Dassie, Justin P ^a,c   Rockey, William M ^d   Howell, Craig A ^a   Liu, Xiuying Y ^a   Dupuy, Adam J ^a   Huang, Lingyan ^e   Owczarzy, Richard ^e   Behlke, Mark A ^e   McNamara, James O ^a   Giangrande, Paloma H ^a,c,d  

^a UNIVERSITY OF IOWA   (United States)

^b DNA Facility   (United States)

^c Molecular and Cellular Biology Program   (United States)

^d Department of Radiation Oncology ^*  (United States)

^e INTEGRATED DNA TECHNOLOGIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; APTAMER; NUCLEOTIDE; PYRIMIDINE; RNA; RNA POLYMERASE;

ABBREVIATED VARIABLE REGION; ANIMAL CELL; ARTICLE; BINDING AFFINITY; BIOINFORMATICS; CHEMICAL COMPOSITION; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; DNA TEMPLATE; ENERGY YIELD; EXTERNAL BIAS; FEMALE; GENE AMPLIFICATION; GENE LIBRARY; GENE POOL; GENE TARGETING; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; MOUSE; NONHUMAN; NUCLEOTIDE BIAS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN TARGETING; RNA APTAMER LIBRARY; RNA SEQUENCE;

ANIMALS; APTAMERS, NUCLEOTIDE; BASE COMPOSITION; BASE SEQUENCE; CELL LINE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; PYRIMIDINES; RECEPTOR, EPHA2; RECOMBINANT PROTEINS; SELEX APTAMER TECHNIQUE; SEQUENCE ANALYSIS, RNA; THERMODYNAMICS; TRANSCRIPTION, GENETIC;

EID: 80052234755     PISSN: 21593337     EISSN: None     Source Type: Journal    
DOI: 10.1089/nat.2011.0288     Document Type: Article

References (37)

1. BEJERANO, G., HAUSSLER, D., and BLANCHETTE, M. (2004a). Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics 20, i40-i48. (Pubitemid 41296669)
2. BEJERANO, G., PHEASANT, M., MAKUNIN, I., STEPHEN, S., KENT, W.J., MATTICK, J.S., and HAUSSLER, D. (2004b). Ultraconserved elements in the human genome. Science 304, 1321-1325. (Pubitemid 38697428)
3. BIESECKER, G., DIHEL, L., ENNEY, K., and BENDELE, R.A. (1999). Derivation of RNA aptamer inhibitors of human complement C5. Immunopharmacology 42, 219-230. (Pubitemid 29322305)
4. B́ONNET, E., WUYTS, J., ROUZE P., and VAN DE PEER, Y. (2004). Evidence that microRNA precursors, unlike other non-coding RNAS, have lower folding free energies than random sequences. Bioinformatics 20, 2911-2917. (Pubitemid 39619182)
5. BORER, P.N., DENGLER, B., TINOCO, I., and UHLENBECK, O.C. (1974). Stability of ribonucleic acid double-stranded helices. J. Mol. Biol. 86, 843-853.
6. CHEN, J.H., LE, S.Y., SHAPIRO, B., CURREY, K.M., and MAI-ZEL, J.V. (1990). A computational procedure for assessing the significance of RNA secondary structure. Comput. Appl. Biosci. 6, 7-18. (Pubitemid 20104011)
7. CLOTE, P., FERRE, F., KRANAKIS E., and KRIZANC, D. (2005). Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11, 578-591. (Pubitemid 40594326)
8. 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., and GIANGRANDE, P.H. (2009). Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat. Biotech. 27, 839-846.
9. DOLLINS, C.M., NAIR, S., BOCZKOWSKI, D., LEE, J., LAY-ZER, J.M., GILBOA, E., and SULLENGER, B.A. (2008). Assembling OX40 aptamers on a molecular scaffold to create a receptor-activating aptamer. Chem. Biol. 15, 675-682. (Pubitemid 351957907)
10. ELLINGTON, A.D., and SZOSTAK, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
11. FREIER, S.M., KIERZEK, R., JAEGER, J.A., SUGIMOTO, N., CARUTHERS, M.H., NEILSON, T., and TURNER, D.H. (1986). Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. U. S. A 83, 9373-9377. (Pubitemid 17223363)
12. GIANGRANDE, P.H., ZHANG, J., TANNER, A., ECKHART, A.D., REMPEL, R.E., ANDRECHEK, E.R., LAYZER, J.M., KEYS, J.R., HAGEN, P.O., NEVINS, J.R., KOCH, W.J., and SULLENGER, B.A. (2007). Distinct roles of E2F proteins in vascular smooth muscle cell proliferation and intimal hyper-plasia. Proc. Natl. Acad. Sci. U. S. A. 104, 12988-12993. (Pubitemid 351737580)
13. GRAGOUDAS, E.S., ADAMIS, A.P., CUNNINGHAM, E.T., FEINSOD, M., and GUYER, D.R. (2004). Pegaptanib for neo-vascular age-related macular degeneration. N. Engl. J. Med. 351, 2805-2816. (Pubitemid 40051904)
14. HERMANN T, PATEL DJ. (2000). Adaptive recognition by nuoleic acid aptamers. Science 287, 820-825. (Pubitemid 30084318)
15. HOFACKER, I.L., FONTANA, W., STADLER, P.F., BON-HOEFFER, L.S., TACKER, M., and SCHUSTER, P. (1994). Fast folding and comparison of RNA secondary structures. Mon-atsh Chem Chem Mon 125, 167-188.
16. HUANG, Y., ECKSTEIN, F., PADILLA, R., and SOUSA, R. (1997). Mechanism of ribose 2'-group discrimination by an RNA polymerase. Biochemistry 36, 8231-8242. (Pubitemid 27297532)
17. LE, S.Y., CHEN, J.H., and MAIZEL, J.V. (1989). Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses. Nucl. Acids Res. 17, 6143-6152. (Pubitemid 19198594)
18. LUPOLD, S.E., HICKE, B.J., LIN, Y., and COFFEY, D.S. (2002). Identification and Characterization of nuclease-stabilized rna molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res. 62, 4029-4033. (Pubitemid 34791070)
19. MATHEWS, D.H., SABINA, J., ZUKER, M., and TURNER, D.H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940. (Pubitemid 29248642)
20. McNAMARA, J.O., KOLONIAS, D., PASTOR, F., MITTLER, R.S., CHEN, L., GIANGRANDE, P.H., SULLENGER, B., and GILBOA, E. (2008). Multivalent 4-1BB binding aptamers costimulate CD8\+ T cells and inhibit tumor growth in mice. J. Clin. Invest. 118, 376-386.
21. MEYERS, L.A., LEE, J.F., COWPERTHWAITE, M., and ELLINGTON, A.D. (2004). The robustness of naturally and artificially selected nucleic acid secondary structures. J. Mol. Evol. 58, 681-691. (Pubitemid 38781701)
22. MI, Z., GUO, H., RUSSELL, M.B., LIU, Y., SULLENGER, B.A., and KUO, P.C. (2009). RNA aptamer blockade of osteopontin inhibits growth and metastasis of MDA-MB231 breast cancer cells. Mol. Ther. 17, 153-161.
23. NIMJEE, S.M., RUSCONI, C.P., and SULLENGER, B.A. (2004). Aptamers: an emerging class of therapeutics. Annu. Rev. Med. 56, 555-583. (Pubitemid 40299797)
24. ONEY, S., NIMJEE, S.M., LAYZER, J., QUE-GEWIRTH, N., GINSBURG, D., BECKER, R.C., AREPALLY, G., and SUL-LENGER, B.A. (2007). Antidote-controlled platelet inhibition targeting von Willebrand factor with aptamers. Oligonucleo-tides 17, 265-274. (Pubitemid 47463359)
25. PADILLA, R., and SOUSA, R. (1999). Efficient synthesis of nucleic acids heavily modified with non-canonical ribose 2'-groups using a mutantT7 RNA polymerase (RNAP). Nucleic Acids Res. 27, 1561-1563. (Pubitemid 29206303)
26. REESE, C.B. (2005). Oligo-and poly-nucleotides: 50 years of chemical synthesis. Org. Biomol. Chem. 3, 3851-3868. (Pubitemid 41640794)
27. ROBERTS, J.D., BEBENEK, K., and KUNKEL, T.A. (1988). The accuracy of reverse transcriptase from HIV-1. Science 242, 1171-1173. (Pubitemid 19007043)
28. RUCKMAN, J., GREEN, L.S., BEESON, J., WAUGH, S., GILLETTE, W.L., HENNINGER, D.D., CLAESSON WELSH, L., and JANJIC, N. (1998). 2'-Fluoropyrimidine RNA-based apta-mers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain. J. Biol. Chem. 273, 20556-20567. (Pubitemid 28377626)
29. RUSCONI, C.P., SCARDINO, E., LAYZER, J., PITOC, G.A., ORTEL, T.L., MONROE, D., and SULLENGER, B.A. (2002). RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419, 90-94. (Pubitemid 34987876)
30. SASSANFAR, M., and SZOSTAK, J.W. (1993). An RNA motif that binds ATP. Nature 364, 550-553. (Pubitemid 23273104)
31. SOUSA, R., and PADILLA, R. (1995). A mutant T7 RNA poly-merase as a DNA polymerase. EMBO J. 14, 4609-4621.
32. THIEL, K.W., and GIANGRANDE, P.H. (2009). Therapeutic applications of DNA and RNA aptamers. Oligonucleotides 19, 209-222.
33. TUERK, C., and GOLD, L. (1990). Systematic evolution of li-gands by exponential enrichment: RNA ligands to bacterio-phage T4 DNA polymerase. Science 249, 505-510.
34. WASHIETL, S., HOFACKER, I.L., LUKASSER, M., HUTTEN-HOFER, A., and STADLER, P.F. (2005). Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat. Biotech. 23, 1383-1390. (Pubitemid 41679390)
35. YU, H., and GOODMAN, M.F. (1992). Comparison of HIV-1 and avian myeloblastosis virus reverse transcriptase fidelity on RNA and DNA templates. J. Biol. Chem. 267, 10888-10896.
36. ZHOU, J., SWIDERSKI, P., LI, H., ZHANG, J., NEFF, C.P., AKKINA, R., and ROSSI, J.J. (2009). Selection, characterization and application of new RNA HIV gp 120 aptamers for facile delivery of Dicer substrate siRNAs into HIV infected cells. Nucleic Acids Res. 37, 3094-3109.
37. ZIMMERMANN, B., GESELL, T., CHEN, D., LORENZ, C., and SCHROEDER, R.E. (2010). Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX. PLoS ONE 5, e9169.