Aptamers to Small Molecules

The Aptamer Handbook: Functional Oligonucleotides and Their Applications

Volumn , Issue , 2006, Pages 94-115

  Fickert, Heiko ^a   Fransson, Iris G ^a   Hahn, Ulrich ^a  

^a UNIVERSITY OF HAMBURG   (Germany)

Author keywords

Aptamer handbook; Aptamers to amino acids; Aptamers to carbohydrates; Aptamers to cofactors; Aptamers to natural products; Aptamers to nucleotides nucleosides nucleobases; Aptamers to organic or fluorescent dyes; Aptamers to small molecules; Chimeric approach for aptamer selection; in vitro selection of target binding oligonucleotides

Indexed keywords

EID: 84879840775     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/3527608192.ch4     Document Type: Chapter

References (70)

1. Anderson, P. C., Mecozzi, S. (2005). Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline. J Am Chem Soc 127, 5290-5291.
2. Araki, M., Okuno, Y., Hara, Y., Sugiura, Y. (1998). Allosteric regulation of a ribozyme activity through ligand-induced conformational change. Nucleic Acids Res 26, 3379-3384.
3. Babendure, J. R., Adams, S. R., Tsien, R. Y. (2003). Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc 125, 14716-14717.
4. Baugh, C., Grate, D., and Wilson, C. (2000). 2.8 A crystal structure of the malachite green aptamer. J Mol Biol 301, 117-128.
5. Burgstaller, P., Famulok, M. (1994). Isolation of RNA aptamers for biological cofactors by in vitro selection. Angew Chem, Int Ed Engl 33, 1084-1087.
6. Burgstaller, P., Kochoyan, M., Famulok, M. (1995). Structural probing and damage selection of citrulline-and arginine-specific RNA aptamers identify base positions required for binding. Nucleic Acids Res 23, 4769-4776.
7. Burke, D. H., Gold, L. (1997). RNA aptamers to the adenosine moiety of S-adenosyl methionine: structural inferences from variations on a theme and the reproducibility of SELEX. Nucleic Acids Res 25, 2020-2024.
8. Burke, D. H., Hoffman, D. C. (1998). A novel acidophilic RNA motif that recognizes coenzyme A. Biochemistry 37, 4653-4663.
9. Connell, G. J., Illangesekare, M., Yarus, M. (1993). Three small ribooligonucleotides with specific arginine sites. Biochemistry 32, 5497-5502.
10. Desai, S. K., Gallivan, J. P. (2004). Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 126, 13247-13254.
11. Ellington, A. D., Szostak, J. W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
12. Ellington, A. D., Szostak, J. W. (1992). Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 355, 850-852.
13. Famulok, M. (1994). Molecular recognition of amino acids by RNA-aptamers: An L-citrulline binding RNA motif and its evolution into an L-arginine binder. J Am Chem Soc 116, 1698-1706.
14. Flinders, J., DeFina, S.C., Brackett, D.M., Baugh, C., Wilson, C., and Dieckmann, T. (2004). Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex. Chembiochem 5, 62-72.
15. Frauendorf, C., Jaschke, A. (2001). Detection of small organic analytes by fluorescing molecular switches. Bioorg Med Chem 9, 2521-2524.
16. Gebhardt, K., Shokraei, A., Babaie, E., Lindqvist, B. H. (2000). RNA aptamers to Sadenosylhomocysteine: kinetic properties, divalent cation dependency, and comparison with anti-S-adenosylhomocysteine antibody. Biochemistry 39, 7255-7265.
17. Geiger, A., Burgstaller, P., von der Eltz, H., Roeder, A., Famulok, M. (1996). RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res 24, 1029-1036.
18. Gold, L., Polisky, B., Uhlenbeck, O., Yarus, M. (1995). Diversity of oligonucleotide functions. Annu Rev Biochem 64, 763-797.
19. Grate, D., Wilson, C. (1999). Laser-mediated, site-specific inactivation of RNA transcripts. Proc Natl Acad Sci USA 96, 6131-6136.
20. Grate, D., Wilson, C. (2001). Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. Bioorg Med Chem 9, 2565-2570.
21. Harada, K., Frankel, A. D. (1995). Identification of two novel arginine binding DNAs. EMBO J 14, 5798-5811.
22. Harvey, I., Garneau, P., Pelletier, J. (2002). Inhibition of translation by RNA-small molecule interactions. RNA 8, 452-463.
23. Holeman, L. A., Robinson, S. L., Szostak, J. W., Wilson, C. (1998). Isolation and characterization of fluorophore-binding RNA aptamers. Fold Des 3, 423-431.
24. Huizenga, D. E., Szostak, J. W. (1995). A DNA aptamer that binds adenosine and ATP. Biochemistry 34, 656-665.
25. Jenison, R. D., Gill, S. C., Pardi, A., Polisky, B. (1994). High-resolution molecular discrimination by RNA. Science 263, 1425-1429.
26. Jeong, S., Eom, T., Kim, S., Lee, S., Yu, J. (2001). In vitro selection of the RNA aptamer against the Sialyl Lewis X and its inhibition of the cell adhesion. Biochem Biophys Res Commun 281, 237-243.
27. Kato, T., Takemura, T., Yano, K., Ikebukuro, K., Karube, I. (2000a). In vitro selection of DNA aptamers which bind to cholic acid. Biochim Biophys Acta 1493, 12-18.
28. Kato, T., Yano, K., Ikebukuro, K., Karube, I. (2000b). Interaction of three-way DNA junctions with steroids. Nucleic Acids Res 28, 1963-1968.
29. Kiga, D., Futamura, Y., Sakamoto, K., Yokoyama, S. (1998). An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition. Nucleic Acids Res 26, 1755-1760.
30. Knight, R. D., Landweber, L. F. (1998). Rhyme or reason: RNA-arginine interactions and the genetic code. Chem Biol 5, R215-220.
31. Knight, R. D., Freeland, S. J., Landweber, L. F. (1999). Selection, history and chemistry: the three faces of the genetic code. Trends Biochem Sci 24, 241-247.
32. Koizumi, M., Breaker, R. R. (2000). Molecular recognition of cAMP by an RNA aptamer. Biochemistry 39, 8983-8992.
33. Lauhon, C. T., Szostak, J. W. (1995). RNA aptamers that bind flavin and nicotinamide redox cofactors. J Am Chem Soc 117, 1246-1257.
34. Lin, C. H., Patel, D. J. (1996). Encapsulating an amino acid in a DNA fold. Nat Struct Biol 3, 1046-1050.
35. Lin, C. H., Patel, D. J. (1997). Structural basis of DNA folding and recognition in an AMPDNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP. Chem Biol 4, 817-832.
36. Lin, C. H., Wang, W., Jones, R. A., Patel, D. J. (1998). Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop. Chem Biol 5, 555-572.
37. Lorsch, J. R., Szostak, J. W. (1994). In vitro selection of RNA aptamers specific for cyanocobalamin. Biochemistry 33, 973-982.
38. Lozupone, C., Changayil, S., Majerfeld, I., Yarus, M. (2003). Selection of the simplest RNA that binds isoleucine. RNA 9, 1315-1322.
39. Majerfeld, I., Yarus, M. (1994). An RNA pocket for an aliphatic hydrophobe. Nat Struct Biol 1, 287-292.
40. Majerfeld, I., Yarus, M. (1998). Isoleucine: RNA sites with associated coding sequences. RNA 4, 471-478.
41. Manimala, J. C., Wiskur, S. L., Ellington, A. D., Anslyn, E. V. (2004). Tuning the specificity of a synthetic receptor using a selected nucleic acid receptor. J Am Chem Soc 126, 16515-16519.
42. Mannironi, C., Di Nardo, A., Fruscoloni, P., Tocchini-Valentini, G. P. (1997). In vitro selection of dopamine RNA ligands. Biochemistry 36, 9726-9734.
43. Mannironi, C., Scerch, C., Fruscoloni, P., Tocchini-Valentini, G. P. (2000). Molecular recognition of amino acids by RNA aptamers: the evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA 6, 520-527.
44. Masud, M. M., Kuwahara, M., Ozaki, H., Sawai, H. (2004). Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX. Bioorg Med Chem 12, 1111-1120.
45. Meli, M., Vergne, J., Decout, J. L., Maurel, M. C. (2002). Adenine-aptamer complexes: a bipartite RNA site that binds the adenine nucleic base. J Biol Chem 277, 2104-2111.
46. Nix, J., Sussman, D., Wilson, C. (2000). The 1.3 A crystal structure of a biotin-binding pseudoknot and the basis for RNA molecular recognition. J Mol Biol 296, 1235-1244.
47. Robertson, M. P., Ellington, A. D. (2000). Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res 28, 1751-1759.
48. Robertson, S. A., Harada, K., Frankel, A. D., Wemmer, D. E. (2000). Structure determination and binding kinetics of a DNA aptamer-argininamide complex. Biochemistry 39, 946-954.
49. Roychowdhury-Saha, M., Lato, S. M., Shank, E. D., Burke, D. H. (2002). Flavin recognition by an RNA aptamer targeted toward FAD. Biochemistry 41, 2492-2499.
50. Saran, D., Frank, J., Burke, D. H. (2003). The tyranny of adenosine recognition among RNA aptamers to coenzyme A. BMC Evol Biol 3, 26.
51. Sassanfar, M., Szostak, J. W. (1993). An RNA motif that binds ATP. Nature 364, 550-553.
52. Sazani, P.L., Larralde, R., and Szostak, J.W. (2004). A small aptamer with strong and specific recognition of the triphosphate of ATP. J Am Chem Soc 126, 8370-8371.
53. Soukup, G. A., Emilsson, G. A., Breaker, R. R. (2000). Altering molecular recognition of RNA aptamers by allosteric selection. J Mol Biol 298, 623-632.
54. Srisawat, C., Goldstein, I. J., Engelke, D. R. (2001). Sephadex-binding RNA ligands: rapid affinity purification of RNA from complex RNA mixtures. Nucleic Acids Res 29, E4.
55. Stojanovic, M. N., Kolpashchikov, D. M. (2004). Modular aptameric sensors. J Am Chem Soc 126, 9266-9270.
56. Stojanovic, M. N., Landry, D. W. (2002). Aptamer-based colorimetric probe for cocaine. J Am Chem Soc 124, 9678-9679.
57. Stojanovic, M. N., de Prada, P., Landry, D. W. (2000). Fluorescent sensors based on aptamer self-assembly. J Am Chem Soc 122, 11547-11549.
58. Stojanovic, M. N., de Prada, P., Landry, D. W. (2001). Aptamer-based folding fluorescent sensor for cocaine. J Am Chem Soc 123, 4928-4931.
59. Stojanovic, M. N., Green, E. G., Semova, S., Nikic, D. B., Landry, D. W. (2003). Crossreactive arrays based on three-way junctions. J Am Chem Soc 125, 6085-6089.
60. Suess, B., Fink, B., Berens, C., Stentz, R., Hillen, W. (2004). A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res 32, 1610-1614.
61. Tao, J., Frankel, A. D. (1996). Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry 35, 2229-2238.
62. Vianini, E., Palumbo, M., Gatto, B. (2001). In vitro selection of DNA aptamers that bind L-tyrosinamide. Bioorg Med Chem 9, 2543-2548.
63. Werstuck, G., Green, M. R. (1998). Controlling gene expression in living cells through small molecule-RNA interactions. Science 282, 296-298.
64. Wilson, C., Szostak, J. W. (1995). In vitro evolution of a self-alkylating ribozyme. Nature 374, 777-782.
65. Wilson, C., Szostak, J. W. (1998). Isolation of a fluorophore-specific DNA aptamer with weak redox activity. Chem Biol 5, 609-617.
66. Yang, Q., Goldstein, I. J., Mei, H. Y., Engelke, D. R. (1998). DNA ligands that bind tightly and selectively to cellobiose. Proc Natl Acad Sci USA 95, 5462-5467.
67. Yang, Y., 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.
68. Yarus, M. (1998). Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J Mol Evol 47, 109-117.
69. Yarus, M. (2000). RNA-ligand chemistry: a testable source for the genetic code. RNA 6, 475-484.
70. Zimmermann, G. R., Jenison, R. D., Wick, C. L., Simorre, J. P., Pardi, A. (1997). Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat Struct Biol 4, 644-649.