Aptamer base: A collaborative knowledge base to describe aptamers and SELEX experiments

Database

Volumn 2012, Issue , 2012, Pages

  Cruz Toledo, Jose ^a   McKeague, Maureen ^a   Zhang, Xueru ^a   Giamberardino, Amanda ^a   McConnell, Erin ^a   Francis, Tariq ^a   DeRosa, Maria C ^a   Dumontier, Michel ^a  

^a CARLETON UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; PEPTIDE APTAMER;

ARTICLE; COMBINATORIAL CHEMISTRY; DATA BASE; FACTUAL DATABASE; METHODOLOGY;

APTAMERS, NUCLEOTIDE; APTAMERS, PEPTIDE; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; RESEARCH DESIGN; SELEX APTAMER TECHNIQUE;

EID: 84862257625     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bas006     Document Type: Article

References (39)

1. Böhm, H.-J. and Schneider, G (eds). (2003) Protein-Ligand Interactions: From Molecular Recognition to Drug Design. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
2. Vant-Hull, B., Gold, L. and Zichi, D.A. (2000) Theoretical principles of in vitro selection using combinatorial nucleic acid libraries. Curr. Protoc. Nucleic Acid Chem., Chapter 9, Unit 9 1.
3. Pirogova, E., Istivan, T., Gan, E. et al. (2011) Advances in methods for therapeutic peptide discovery, design and development. Curr. Pharm. Biotechnol., 12, 1117-1127.
4. Vodnik, M., Zager, U., Strukelj, B. et al. (2011) Phage display: Selecting straws instead of a needle from a haystack. Molecules, 16, 790-817.
5. Bradbury, A.R., Sidhu, S., Dubel, S. and McCafferty, J. (2011) Beyond natural antibodies: The power of in vitro display technologies. Nat. Biotechnol., 29, 245-254.
6. Laing, C. and Schlick, T. (2011) Computational approaches to RNA structure prediction, analysis, and design. Curr. Opin. Struct. Biol., 21, 306-318.
7. Zhou, X., Ren, L., Meng, Q. et al. (2010) The next-generation sequencing technology and application. Protein Cell, 1, 520-536.
8. Field, D., Garrity, G., Gray, T. et al. (2008) The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol., 26, 541-547. (Pubitemid 351668038)
9. Campbell, D. (2008) Don't forget people and specimens that make the database. Nature, 455, 590.
10. Hammami, R., Zouhir, A., Naghmouchi, K., Ben Hamida, J. and Fliss, I. (2008) SciDBMaker: New software for computer-aided design of specialized biological databases. BMC Bioinformatics, 9, 121.
11. Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818-822.
12. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
13. Jayasena, S.D. (1999) Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clin. Chem., 45, 1628-1650. (Pubitemid 29419030)
14. Sinha, J., Reyes, S.J. and Gallivan, J.P. (2010) Reprogramming bacteria to seek and destroy an herbicide. Nat. Chem. Biol., 6, 464-470.
15. Stead, S.L., Ashwin, H., Johnston, B. et al. (2010) An RNA-aptamerbased assay for the detection and analysis of malachite green and leucomalachite green residues in fish tissue. Anal. Chem., 82, 2652-2660.
16. McKeague, M., Bradley, C.R., De Girolamo, A. et al. (2010) Screening and initial binding assessment of fumonisin b(1) aptamers. Int. J. Mol. Sci., 11, 4864-4881.
17. Kim, Y.H., Sung, H.J., Kim, S. et al. (2011) An RNA aptamer that specifically binds pancreatic adenocarcinoma up-regulated factor inhibits migration and growth of pancreatic cancer cells. Cancer Lett., 313, 76-83.
18. Ramalingam, D., Duclair, S., Datta, S.A. et al. (2011) RNA aptamers directed to human immunodeficiency virus type 1 Gag polyprotein bind to the matrix and nucleocapsid domains and inhibit virus production. J. Virol., 85, 305-314.
19. Bayrac, A.T., Sefah, K., Parekh, P. et al. (2011) In vitro selection of DNA aptamers to glioblastoma multiforme. ACS Chem. Neurosci., 2, 175-181.
20. Nimjee, S.M., Rusconi, C.P. and Sullenger, B.A. (2005) Aptamers: An emerging class of therapeutics. Annu. Rev. Med., 56, 555-583. (Pubitemid 40299797)
21. White, R.R., Sullenger, B.A. and Rusconi, C.P. (2000) Developing aptamers into therapeutics. J. Clin. Invest., 106, 929-934.
22. Brody, E.N. and Gold, L. (2000) Aptamers as therapeutic and diagnostic agents. J. Biotechnol., 74, 5-13.
23. McKeague, M., Giamberardino, A. and DeRosa, M.C. (2011) Advances in Aptamer-Based Biosensors for Food Safety. In: Somerset, V. (ed.). Environmental BioSensors. InTech, http://www.intechopen.com/ articles/show/title/advances-in- aptamer-based-biosensors-for-foodsafety.
24. Lee, J.F., Hesselberth, J.R., Meyers, L.A. et al. (2004) Aptamer database. Nucleic Acids Res., 32, D95-100.
25. Ponomarenko, J.V., Orlova, G.V., Frolov, A.S. et al. (2002) SELEXDB: A database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data. Nucleic Acids Res., 30, 195-199. (Pubitemid 34679540)
26. Thodima, V., Pirooznia, M. and Deng, Y. (2006) RiboaptDB: A comprehensive database of ribozymes and aptamers. BMC Bioinformatics, 7 (Suppl 2), S6.
27. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J. et al. (2011) GenBank. Nucleic Acids Res., 39, D32-37.
28. Cochrane, G., Akhtar, R., Bonfield, J. et al. (2009) Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res., 37, D19-25.
29. Kaminuma, E., Mashima, J., Kodama, Y. et al. (2010) DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res., 38, D33-38.
30. Chen, P.P. (1976) The entity-relationship model-toward a unified view of data. ACM Transactions on database systems, 1, 9-36.
31. Silverman, S.K. (2009) Artificial functional nucleic acids: Aptamers, ribozymes, and deoxyribozymes identified by in vitro selection. In: Li, Y. and Lu, Y. (eds). Functional Nucleic Acids for Analytical Applications. Springer, New York, pp. 47-108.
32. Hofacker, I.L. and Stadler, P.F. (2006) Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics, 22, 1172-1176. (Pubitemid 43779007)
33. Mathews, D.H., Disney, M.D., Childs, J.L. et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA, 101, 7287-7292. (Pubitemid 38638025)
34. Mathews, D.H., Sabina, J., Zuker, M. et al. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940. (Pubitemid 29248642)
35. Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55. (Pubitemid 351355097)
36. SweoIG/TaskForces/CommunityProjects/LinkingOpenData (2011), W3C http://www.w3.org/wiki/SweoIG/TaskForces/CommunityPro jects/LinkingOpenData (1 July 2011, date last accessed).
37. RDF Primer (2004), W3C http://www.w3.org/TR/rdf-primer/ (1 July 2011, date last accessed).
38. Cho, E.J., Lee, J.W. and Ellington, A.D. (2009) Applications of aptamers as sensors. Annu. Rev. Anal. Chem. (Palo Alto Calif), 2, 241-264.
39. de Matos, P., Alcantara, R., Dekker, A. et al. (2010) Chemical entities of biological interest: An update. Nucleic Acids Res., 38, D249-254.