Structural prediction and binding analysis of hybridized aptamers

Journal of Molecular Recognition

Volumn 24, Issue 1, 2011, Pages 119-126

  Zhou, Jing ^a   Soontornworajit, Boonchoy ^a   Snipes, Matthew P ^a   Wang, Yong ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

aptamer discovery; aptamer truncation; intermolecular hybridization; intramolecular hybridization; molecular recognition; nucleic acid aptamer; secondary structure

Indexed keywords

APTAMER; OLIGONUCLEOTIDE;

ARTICLE; CHEMISTRY; GENETICS; HUMAN; HYBRIDIZATION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN SECONDARY STRUCTURE; TUMOR CELL LINE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CELL LINE, TUMOR; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; HYBRIDIZATION, GENETIC; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 78650917894     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.1034     Document Type: Article

References (28)

1. Brunel C, Romby P, 2000. Probing RNA structure and RNA-ligand complexes with chemical probes. Methods Enzymol. 318: 3-21.
2. Bruno JG, Carrillo MR, Cadieux CL, Lenz DE, Cerasoli DM, Phillips T, 2009. DNA aptamers developed against a soman derivative cross-react with the methylphosphonic acid core but not with flanking hydrophobic groups. J. Mol. Recognit. 22: 197-204.
3. Burmeister PE, Lewis SD, Silva RF, Preiss JR, Horwitz LR, Pendergrast PS, McCauley TG, Kurz JC, Epstein DM, Wilson C, Keefe AD, 2005. Direct in vitro selection of a 2′-O-methyl aptamer to VEGF. Chem. Biol. 12: 25-33.
4. Di Giusto DA, Knox SM, Lai YC, Tyrelle GD, Aung MT, King GC, 2006. Multitasking by multivalent circular DNA aptamers. ChemBioChem 7: 535-544.
5. Dittmer WU, Reuter A, Simmel FC, 2004. A DNA-based machine that can cyclically bind and release thrombin. Angew. Chem. Int. Ed. Engl. 43: 3550-3553.
6. Ellington AD, Szostak JW, 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
7. Gold L, Polisky B, Uhlenbeck O, Yarus M, 1995. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64: 763-797.
8. Jaeger L, Chworos A, 2006. The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol. 16: 531-543.
9. Jayasena SD, 1999. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45: 1628-1650.
10. Jenison RD, Gill SC, Pardi A, Polisky B, 1994. High-resolution molecular discrimination by RNA. Science 263: 1425-1429.
11. Lee JF, Stovall GM, Ellington AD, 2006. Aptamer therapeutics advance. Curr. Opin. Chem. Biol. 10: 282-289.
12. Liu XM, Zhang DJ, Cao GJ, Yang G, Ding HM, Liu G, Fan M, Shen BF, Shao NS, 2003. RNA aptamers specific for bovine thrombin. J. Mol. Recognit. 16: 23-27.
13. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH, 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101: 7287-7292.
14. Patel DJ, 1997. Structural analysis of nucleic acid aptamers. Curr. Opin. Chem. Biol. 1: 32-46.
15. Proske D, Blank M, Buhmann R, Resch A, 2005. Aptamers-basic research, drug development, and clinical applications. Appl. Microbiol. Biotechnol. 69: 367-374.
16. Rinker S, Ke Y, Liu Y, Chhabra R, Yan H, 2008. Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nat. Nanotechnol. 3: 418-422.
17. Shangguan D, Li Y, Tang Z, Cao ZC, Chen HW, Mallikaratchy P, Sefah K, Yang CJ, Tan W, 2006. Aptamers evolved from live cells as effective molecular probes for cancer study. Proc. Natl. Acad. Sci. USA 103: 11838-11843.
18. Shangguan D, Tang Z, Mallikaratchy P, Xiao Z, Tan W, 2007. Optimization and modifications of aptamers selected from live cancer cell lines. ChemBioChem 8: 603-606.
19. Tuerk C, Gold L, 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
20. Wakeman CA, Winkler WC, 2009. Structural probing techniques on natural aptamers. Methods Mol. Biol. 535: 115-133.
21. Wang JL, Xu DK, Chen HY, 2009. A novel protein analytical method based on hybrid-aptamer and DNA-arrayed electrodes. Electrochem. Commun. 11: 1627-1630.
22. Wei B, Cheng I, Luo KQ, Mi YL, 2008. Capture and release of protein by a reversible DNA-induced sol-gel transition system. Angew. Chem. Int. Ed. Engl. 47: 331-333.
23. Williamson JR, 2000. Induced fit in RNA-protein recognition. Nat. Struct. Biol. 7: 834-837.
24. Yan XL, Cao ZJ, Kai M, Lu JZ, 2009. Label-free aptamer-based chemiluminescence detection of adenosine. Talanta 79: 383-387.
25. Yang YS, Kochoyan M, Burgstaller P, Westhof E, Famulok M, 1996. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 272: 1343-1347.
26. Yang H, Liu H, Kang H, Tan W, 2008. Engineering target-responsive hydrogels based on aptamer-target interactions. J. Am. Chem. Soc. 130: 6320-6321.
27. Zhou J, Soontornworajit B, Snipes MP, Wang Y, 2009. Development of a novel pretargeting system with bifunctional nucleic acid molecules. Biochem. Biophys. Res. Commun. 386: 521-525.
28. Zuker M, 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic. Acids. Res. 31: 3406-3415.