Oligonucleotide aptamers that recognize small molecules

Current Opinion in Structural Biology

Volumn 9, Issue 3, 1999, Pages 324-329

  Famulok, Michael ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ANTIBIOTIC AGENT; DNA; DYE; FLUORESCENT DYE; KANAMYCIN; NUCLEIC ACID; OLIGONUCLEOTIDE; RECEPTOR; RNA; STREPTOMYCIN DERIVATIVE; TOBRAMYCIN; VIOMYCIN;

BIOSENSOR; MOLECULAR RECOGNITION; PRIORITY JOURNAL; RECEPTOR BINDING; REVIEW;

EID: 0033150948     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)80043-8     Document Type: Article

References (75)

1. Ellington AD: RNA selection. Aptamers achieve the desired recognition. Curr Biol 1994, 4:427-429.
2. Uphoff KW, Bell SD, Ellington AD: In vitro selection of aptamers: The dearth of pure reason. Curr Opin Struct Biol 1996, 6:281-288.
3. Gold L, Polisky B, Uhlenbeck O, Yarus M: Diversity of oligonucleotide functions. Annu Rev Biochem 1995, 64:763-797.
4. Osborne SE, Ellington AD: Nucleic acid selection and the challenge of combinatorial chemistry. Chem Rev 1997, 97:349-370.
5. Cech TR, Szewczak AA: Selecting apt RNAs for NMR. RNA 1996, 2:625-627.
6. Egli M: Wie in vitro selektierte RNA-aptamere funktionieren-die räumlichen strukturen von substrat-RNA-aptamer-komplexen. Angew Chem Int Ed 1997, 36:480-482. [Title translation: In vitro selected receptors rationalized: the first 3D structures of RNA aptamer/substrate complexes.]
7. Feigon J, Dieckmann T, Smith FW: Aptamer structures from A to ζ. Chem Biol 1996, 3:611-617.
8. Heus HA: RNA aptamers. Nat Struct Biol 1997, 4:597-600.
9. Patel DJ: Structural analysis of nucleic acid aptamers. Curr Opin Chem Biol 1997, 1:32-46.
10. Patel DJ, Suri AK, Jiang F, Liang L, Fan P, Kumar RA, Nonin S: Structure, recognition and adaptive binding in RNA aptamer complexes. J Mol Biol 1997, 272:645-664.
11. Westhof E, Masquida B, Jaeger L: RNA tectonics: Towards RNA design. Fold Des 1996, 1:R78-R88.
12. Batey RT, Rambo RP, Doudna JA: Tertiary motifs in RNA structure and folding. Angew Chem Int Ed 1999, 38:in press.
13. Holeman LA, Robinson SL, Szostak JW, Wilson C: Isolation and characterization of fluorophore-binding RNA aptamers. Fold Des 1998, 3:423-431.
14. Wilson C, Szostak JW: Isolation of a fluorophore-specific DNA aptamer with weak redox activity. Chem Biol 1998, 5:609-617. This paper describes one of only a few examples in which an aptamer that was selected merely to bind a certain small molecule ligand was later shown to exhibit catalytic activity.
15. Werstuck G, Green MR: Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998, 282:296-298. This was one of the first papers to show that aptamers exhibit their function even when-integrated into a large mRNA inside a cellular context. In this case, an aptamer for a small dye or antibiotic molecule was inserted into the 5′ untranslated region of a reporter gene. In the presence of the small molecule, the expression of the reporter gene was drastically reduced in an aptamer/ligand-dependent fashion in higher eukaryotic cells.
16. Yang Q, Goldstein IJ, Mei HY, Engelke DR: DNA ligands that bind tightly and selectively to cellobiose. Proc Natl Acad Sci USA 1998, 95:5462-5467. An interesting example of the isolation of an aptamer that binds to a small molecule in solution using an insoluble matrix composed of the polymerized ligand.
17. Wang Y, Killian J, Hamasaki K, Rando RR: RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry 1996, 35:12338-12346.
18. Wallis MG, Von Ahsen U, Schroeder R, Famulok M: A novel RNA motif for neomycin recognition. Chem Biol 1995, 2:543-552.
19. Famulok M, Hüttenhofer A: In vitro selection analysis of neomycin binding RNAs with a mutagenized pool of variants of the 16S rRNA decoding region. Biochemistry 1996, 35:4265-4270.
20. Wallis MG, Streicher B, Wank H, Von Ahsen U, Clodi E, Wallace ST, Famulok M, Schroeder R: In vitro selection of a viomycin-binding RNA pseudoknot. Chem Biol 1997, 4:357-366. The aptamer described is the second example of a pseudoknot structure for an in vitro selected RNA that binds to a small molecule (the first one was the aptamer for cyanocobalamine [70]). The characteristics of this structure led to the interesting observation that viomycin recognition by many biologically relevant natural RNAs may also occur via pseudoknot structures. This, in turn, may help to explain the mechanism by which viomycin modulates the dimerization of RNAs.
21. Wallace ST, Schroeder R: In vitro selection and characterization of streptomycin-binding RNAs: Recognition discrimination between antibiotics. RNA 1998, 4:112-123.
22. Haller AA, Sarnow P: In vitro selection of a 7-methyl-guanosine binding RNA that inhibits translation of capped mRNA molecules. Proc Natl Acad Sci USA 1997, 94:8521-8526. An impressive example of a small-molecule-binding RNA aptamer that selectively blocks a biological process - the translation of capped mRNAs.
23. Kiga D, Futamura Y, Sakamoto K, Yokoyama S: An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition. Nucleic Acids Res 1998, 26:1755-1760.
24. Rink SM, Shen J-C, Loeb LA: Creation of RNA molecules that recognize the oxidative lesion 7,8-dihydro-8-hydroxy-2′-deoxyguanosine (8-oxodg) in DNA. Proc Natl Acad Sci USA 1998, 95:11619-11624. This paper shows that aptamers can potentially be used in examining very demanding problems of molecular recognition. Having been selected for its specific recognition of a monomeric guanosine derivative, this aptamer also is capable of recognizing the derivative with remarkable specificity and selectivity when embedded in single-stranded DNA. It will be interesting to see how this aptamer performs in 8-oxo-dG-derivatized double-stranded DNA.
25. Schroeder R, Von Ahsen U: Interaction of aminoglycoside antibiotics with RNA. In Nucleic Acids and Molecular Biology. Edited by Eckstein F, Lilley DMJ. Heidelberg: Springer-Verlag; 1996:53-74.
26. Olive JE, De Abreu DM, Rastogi T, Andersen AA, Mittermaier AK, Beattie TL, Collins RA: Enhancement of neurospora VS ribozyme cleavage by tuberactinomycin antibiotics. EMBO J 1995, 14:3247-3251.
27. Earnshaw DJ, Gait MJ: Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucleic Acids Res 1998, 26:5551-5561. In this paper, Earnshaw and Gait describe the interesting observation that neomycin B acts as an inhibitor of phosphodiester cleavage by the hairpin ribozyme, but only when divalent metal ions are present. In the absence of divalent metal ions, however, both neomycin B and spermidine stimulate the cleavage reaction. This phenomenon will be of great interest for understanding ribozymal cleavage mechanisms. This is one of very few examples of a nonmetal cofactor requirement for a ribozyme-catalyzed cleavage reaction.
28. Lato SM, Boles AR, Ellington AD: In vitro selection of RNA lectins: Using combinatorial chemistry to interpret ribozyme evolution. Chem Biol 1995, 2:291-303.
29. Burke DH, Hoffman DC, Brown A, Hansen M, Pardi A, Gold L: RNA aptamers to the peptidyl transferase inhibitor chloramphenicol. Chem Biol 1997, 4:833-843.
30. Knight RD, Landweber LF: Rhyme or reason: RNA-arginine interactions and the genetic code. Chem Biol 1998, 5:R215-R220.
31. Famulok M: 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 1994, 116:1698-1706.
32. Geiger A, Burgstaller P, Von der Eltz H, Roeder A, Famulok M: RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res 1996, 24:1029-1036.
33. Tao J, Frankel AD: Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry 1996, 35:2229-2238.
34. Connell GJ, Yarus M: RNAs with dual specificity and dual RNAs with similar specificity. Science 1994, 264:1137-1141.
35. Zimmerman GR, Jenison RD, Wick CL, Simorre J-P, Pardi A: Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat Struct Biol 1997, 4:644-649.
36. Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M: Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 1996, 272:1343-1347.
37. Jiang F, Kumar RA, Jones RA, Patel DJ: Structural basis of RNA folding and recognition in an AMP-RNA complex. Nature 1996, 382:183-186.
38. Fan P, Suri AK, Fiala R, Live D, Patel DJ: Molecular recognition in the FMN-RNA aptamer complex. J Mol Biol 1996, 258:480-500.
39. Jiang L, Suri AK, Fiala R, Patel DJ: Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chem Biol 1997, 4:35-50.
40. Yarus M: Amino acids as RNA ligands: A direct-RNA-template theory for the code's origin. J Mol Evol 1998, 47:109-117.
41. Majerfeld I, Yarus M: Isoleucine:RNA sites with associated coding sequences. RNA 1998, 4:471-478.
42. Majerfeld I, Yarus M: An RNA pocket for an aliphatic hydrophobe. Nat Struct Biol 1994, 1:287-292.
43. Eigen M, Lindemann BF, Tietze M, Winkler-Oswatitsch R, Dress A, Von Haeseler A: How old is the genetic code? Statistical geometry of tRNA provides an answer. Science 1989, 244:673-679.
44. Wong JT-F: A co-evolution theory of the genetic code. Proc Natl Acad Sci USA 1975, 72:1909-1912.
45. Tang J, Breaker RR: Rational design of allosteric ribozymes. Chem Biol 1997, 4:453-459. See annotation to [49•].
46. Soukup GA, Breaker RR: Engineering precision RNA molecular switches. Proc Natl Acad Sci USA 1999, 96:3584-3589. See annotation to [49•].
47. Tang J, Breaker RR: Mechanism for allosteric inhibition of an ATP sensitive ribozyme. Nucleic Acids Res 1998, 26:4214-4221. This study suggests a possible mechanism for the inhibition of an engineered ATP-aptamer-containing hammerhead ribozyme by ATP. (See, also, annotation to [49•].)
48. Araki M, Okuno Y, Hara Y, Sugiura Y: Allosteric regulation of a ribozyme activity through ligand-induced conformational change. Nucleic Acids Res 1998, 26:3379-3384. See annotation to [49•].
49. Robertson MP, Ellington AD: In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol 1999, 17:62-66. Papers [45•-49•] are, together, very impressive examples of rational ribozyme engineering. The incorporation of aptamer sequences into the hammerhead ribozyme [45•-48•] or into an in vitro selected ligase ribozyme [49•] led to ribozyme variants that performed catalytic activity as a function of the presence or absence of the aptamer ligand.
50. Sassanfar M, Szostak JW: An RNA motif that binds ATP. Nature 1993, 364:550-553.
51. Ellington AD, Szostak JW: In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
52. Ellington AD, Szostak JW: Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 1992, 355:850-852.
53. Jenison RD, Gill SC, Pardi A, Polisky B: High-resolution molecular discrimination by RNA. Science 1994, 263:1425-1429.
54. Mannironi C, Di Nardo A, Fruscoloni P, Tocchini-Valentini GP: In vitro selection of dopamine RNA ligands. Biochemistry 1997, 36:9726-9734.
55. Famulok M, Szostak JW: Stereospecific recognition of tryptophan agarose by in vitro selected RNA. J Am Chem Soc 1992, 114:3990-3991.
56. Connell GJ, Illangesekare M, Yarus M: Three small ribooligonucleotides with specific arginine sites. Biochemistry 1993, 32:5497-5502.
57. Burgstaller P, Kochoyan M, Famulok M: Structural probing and damage selection of citrullin and arginine specific RNA aptamers identify base positions required for binding. Nucleic Acids Res 1995. 23:4769-4776.
58. Lin CH, Patel DJ: Encapsulating an amino acid in a DNA fold. Nat Struct Biol 1996, 3:1046-1050.
59. Lin CH, Wang W, Jones RA, Patel DJ: Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop. Chem Biol 1998, 5:555-572.
60. Harada K, Frankel AD: Identification of two novel arginine binding DNAs. EMBO J 1995, 14:5798-5811.
61. Nolte A, Klußmann S, Bald R, Erdmann VA, Fürste JP: Mirror-design of L-oligonucleotide ligands binding to L-arginine. Nat Biotechnol 1996, 14:1116-1119.
62. Dieckmann T, Suzuki E, Nakamura GK, Feigon J: Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA 1996, 2:628-640.
63. Nonin S, Jiang F, Patel DJ: Imino proton exchange and base pair kinetics in the AMP-RNA aptamer complex. J Mol Biol 1997, 268:359-374.
64. Burgstaller P, Famulok M: Isolation of RNA aptamers for biological cofactors by in vitro selection. Angew Chem Int Ed 1994, 33:1084-1087.
65. Burke DH, Gold L: 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 1997, 25:2020-2024.
66. Lin CH, Patel DJ: Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: Distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP. Chem Biol 1997, 4:817-832.
67. Huizenga DE, Szostak JW: A DNA aptamer that binds adenosine and ATP. Biochemistry 1995, 34:656-665.
68. Klußmann S, Nolte A, Bald R, Erdmann VA, Fürste JP: Mirror-image RNA that binds D-adenosine. Nat Biotechnol 1996, 14:1112-1115.
69. Lauhon CT, Szostak JW: RNA aptamers that bind flavin and nicotinamide redox cofactors. J Am Chem Soc 1995, 117:1246-1257.
70. Lorsch JR, Szostak JW: In vitro selection of RNA aptamers specific for cyanocobalamin. Biochemistry 1994, 33:973-982.
71. Jiang L, Patel DJ: Solution structure of the tobramycin-RNA aptamer complex. Nat Struct Biol 1998, 5:769-774.
72. Ye X, Gorin A, Ellington AD, Patel D: Deep penetration of an α-helix into the widened RNA major groove in the HIV-1 Rev peptide-RNA aptamer complex. Nat Struct Biol 1996, 3:1026-1033.
73. Giver L, Bartel DP, Zapp ML, Green MR, Ellington AD: Selective optimization of the Rev-binding element of HIV-1. Nucleic Acids Res 1993, 21:5509-5516.
74. Giver L, Bartel DP, Zapp ML, Green MR, Ellington AD: Selection and design of high-affinity RNA ligands for HIV-1 Rev. Gene 1993, 137:19-24.
75. Williams KP, Liu XH, Schumacher TN, Lin HY, Ausiello DA, Kim PS, Bartel DP: Bioactive and nuclease-resistant L-DNA ligand of vasopressin. Proc Natl Acad Sci USA 1997, 94:11285-11290. This paper, together with [61,68], shows that mirror-image RNAs of natural aptamers that were selected to bind to the mirror image of a certain target can stereospecifically recognize the target. The mirror-image RNAs are absolutely resistant to degradation by nucleases.