Minimal primer and primer-free SELEX protocols for selection of aptamers from random DNA libraries

BioTechniques

Volumn 44, Issue 3, 2008, Pages 351-360

  Pan, Weihua ^a   Xin, Ping ^a   Clawson, Gary A ^a,b  

^a PENN STATE COLLEGE OF MEDICINE   (United States)

^b PENN STATE MILTON S HERSHEY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA;

ARTICLE; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; DNA BINDING; DNA FLANKING REGION; DNA LIBRARY; DNA MODIFICATION; DNA SEQUENCE; HUMAN; HUMAN CELL; MELANOMA CELL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

APTAMERS, NUCLEOTIDE; DNA PRIMERS; GENE LIBRARY; POLYMERASE CHAIN REACTION; SELEX APTAMER TECHNIQUE;

EID: 41849128549     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000112689     Document Type: Article

References (23)

1. Tuerk, C. and L. Gold. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-510.
2. Ellington, A.D. and J.W. Szostak. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822.
3. Pan, W., R.C. Craven, Q. Qiu, C.B. Wilson, J.W. Wills, S. Golovine, and J.F. Wang. 1995. Isolation of virus-neutralizing RNAs from a large pool of random sequences. Proc. Natl. Acad. Sci. USA 92:11509-11513.
4. Wang, J., H. Jiang, and F. Liu. 2000. In vitro selection of novel RNA ligands that bind human cytomegalovirus and block viral infection. RNA 6:571-583.
5. Blank, M., T. Weinschenk, M. Priemer, and H. Schluesener. 2001. Systematic evolution of a DNA aptamer binding to rat brain tumor microvessels: selective targeting of endothelial regulatory protein pigpen. J. Biol. Chem. 276:16464-16468.
6. Hicke, B.J., C. Marion, Y.F. Chang, T. Gould, C.K. Lynott, D. Parma, P.G. Schmidt, and S. Warren. 2001. Tenascin-C aptamers are generated using tumor cells and purified protein. J. Biol. Chem. 276:48644-48654.
7. Daniels, D.A., H. Chen, B.J. Hicke, K.M. Swiderek, and L. Gold. 2003. A tenascin-C aptamer identified by tumor cell SELEX: systematic evolution of ligands by exponential enrichment. Proc. Natl. Acad. Sci. USA 100:15416-15421.
8. Cerchia, L., F. Duconge, C. Pestourie, J. Boulay, Y. Aissouni, K. Gombert, B. Tavitian, V. de Franciscis, et al. 2005. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol. 3:e123.
9. Wang, C., M. Zhang, G. Yang, D. Zhang, H. Ding, H. Wang, M. Fan, B. Shen, et al. 2003. Single-stranded DNA aptamers that bind differentiated but not parental cells: subtractive systematic evolution of ligands by exponential enrichment. J. Biotechnol. 102:15-22.
10. Tang, Z., D. Shangguan, K. Wang, H. Shi, K. Sefah, P. Mallikratchy, H.W. Chen, Y. Li, et al. 2007. Selection of aptamers for molecular recognition and characterization of cancer cells. Anal. Chem. 79:4900-4907.
11. Perkins, A.C. and S. Missailidis. 2007. Radiolabeled aptamers for tumour imaging and therapy. Q. J. Nucl. Med. Mol. Imaging 51:292-296.
12. Sousa, R. 2000. Use of T7 RNA polymerase and its mutants for incorporation of nucleoside analogs into RNA. Methods Enzymol. 317:65-74.
13. Que-Gewirth, N.S. and B.A. Sullenger. 2007. Gene therapy progress and prospects: RNA aptamers. Gene Ther. 14:283-291.
14. Shtatland, T., S.C. Gill, B.E. Javornik, H.E. Johansson, B.S. Singer, O.C. Uhlenbeck, D.A. Zichi, and L. Gold. 2000. Interactions of Escherichia coli RNA with bacteriophage MS2 coat protein: genomic SELEX. Nucleic Acids Res. 28:e93.
15. Vater, A., F. Jarosch, K. Buchner, and S. Klussmann. 2003. Short bioactive Spiegelmers to migraine-associated calcitonin gene-related peptide rapidly identified by a novel approach: tailored-SELEX. Nucleic Acids Res. 31:e130.
16. Jarosch, F., K. Buchner, and S. Klussmann. 2006. In vitro selection using a dual RNA library that allows primerless selection. Nucleic Acids Res. 34:e86.
17. Wen, J.D. and D.M. Gray. 2004. Selection of genomic sequences that bind tightly to Ff gene 5 protein: primer-free genomic SELEX. Nucleic Acids Res. 32:e182.
18. Musheev, M.U. and S.N. Krylov. 2006. Selection of aptamers by systematic evolution of ligands by exponential enrichment: addressing the polymerase chain reaction issue. Anal. Chim. Acta 564:91-96.
19. Pan, W.H., P. Xin, V. Bui, and G.A. Clawson. 2003. Rapid identification of efficient target cleavage sites using a Hammerhead ribozyme library in an iterative manner. Mol. Ther. 7:128-139.
20. Pan, W.H. and G.A. Clawson. 2004. Identification of efficient cleavage sites in long-target RNAs. Methods Mol. Biol. 252:125-144.
21. Pan, W.H., P. Xin, J.D. Morrey, and G.A. Clawson. 2004. A self-processing ribozyme cassette: utility against human papillomavirus 11 E6/E7 mRNA and hepatitis B virus. Mol. Ther. 9:596-606.
22. Pan, W.-H., H. Devlin, C. Kelley, H. Isom, and G. Clawson. 2001. A selection system for identifying accessible sites in target RNAs. RNA 7:610-621.
23. Pan, W. and G. Clawson. 2003. Identification of efficient cleavage sites in long target RNAs, p. 125-144. In M. Sioud (Ed.), Methods in Molecular Biology, Catalytic Nucleic Acid Protocols, 2nd ed. Humana Press, Totowa, New Jersey.