In vitro selection of aptamers: The dearth of pure reason

Current Opinion in Structural Biology

Volumn 6, Issue 3, 1996, Pages 281-288

  Uphoff, Kyle W ^a   Bell, Sabine D ^a   Ellington, Andrew D ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; DNA BINDING PROTEIN; NUCLEIC ACID; REV PROTEIN; UNCLASSIFIED DRUG;

CONSENSUS SEQUENCE; CROSS LINKING; DNA BINDING; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; RNA BINDING;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0029891450     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80045-5     Document Type: Article

References (51)

1. Kramer FR, Mills DR, Cole PE, Nishihara T, Spiegelman S: Evolution of in vitro sequence and phenotype of a mutant RNA resistant to ethidium bromide. J Mol Biol 1974, 89:719-736.
2. Orgel L: Selection in vitro. Proc R Soc Lond B Biol Sci 1979, 205:435-442.
3. Szostak JW: Structure and activity of ribozymes. In Redesigning the Molecules of Life. Edited by Benner S. Berlin: Springer-Verlag; 1988:87-113.
4. Gold L, Polisky B, Uhlenbeck O, Yarus M: Diversity of oligonucleotide functions. Annu Rev Biochem 1995, 64:763-797. This review provides a comprehensive summary of work carried out at NeXstar, but lacks detailed descriptions of many other contributions.
5. Gold L: Oligonucleotides as research, diagnostic, and therapeutic agents. J Biol Chem 1995, 270:13581-13584.
6. Ellington AD, Conrad R: Aptamers as potential nucleic acid pharmaceuticals. In Biotechnology Annual Review, vol 1. Edited by El-Gewely MR. Amsterdam: Elsevier Science; 1995:185-214.
7. Kenan DJ, Tsai DE, Keene JD: Exploring molecular diversity with combinatorial shape libraries. Trends Biochem Sci 1994, 19:57-64.
8. Klug SJ, Famulok M: All you wanted to know about SELEX. Mol Biol Rep 1994, 20:97-107.
9. Conrad RC, Giver L, Tian Y, Ellington AD: In vitro selection methodologies to probe RNA function and structure. Mol Div 1995, 1:69-78. This paper constitutes a concise 'how to' manual for selection experiments.
10. Hirao I, Ellington AD: Re-creating the RNA world. Curr Biol 1995, 9:1017-1022. This paper constitutes an example of how the results of selection experiments can be used to interpret the course of molecular evolution.
11. Ellington AD: Aptamers achieve the desired recognition. Curr Biol 1994, 4:427-429.
12. 2+. RNA 1995, 1:538-550.
13. Wang Y, Rando RR: Specific binding of aminoglycoside antibiotics to RNA. Chem Biol 1995, 2:281-290.
14. 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.
15. Wallis MG, Von Ahsen U, Schroeder R, Famulok M: A novel RNA motif for neomycin recognition. Chem Biol 1995, 2:543-552. This paper gives a very thorough selection and characterization of an ap-tamer that targets a small organic ligand.
16. Lu M, Draper D: On the role of rRNA tertiary structure in recognition of ribosomal protein L11 and thiostrepton. Nucleic Acids Res 1995, 23:3426-3433.
17. Famulok FM: 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.
18. Burgstaller P, Kochoyan M, Famulok M: Structural probing and damage selection of citrulline- and arginine-specific RNA aptamers identify base positions required for binding. Nucleic Acids Res 1995, 23:4769-4776.
19. Huizenga DE, Szostak JW: A DNA aptamer that binds adenosine and ATP. Biochemistry 1995, 34:656-665.
20. Lauhon CT, Szostak JW: RNA aptamers that bind flavin and nicotinamide redox cofactors. J Am Chem Soc 1995, 117:1246-1257.
21. Swanson HI, Chan WK, Bradfield CA: DNA binding specificities and pairing rules of the Ah receptor, ARNT, and SIM proteins. J Biol Chem 1995, 270:26292-26302. This paper constitutes an extremely interesting example of how selection can be used to delineate the information content of DMA-binding sites.
22. Brown D, Gold L: Template recognition by an RNA-dependent RNA polymerase: identification and characterization of two RNA binding sites on Qβ replicase. Biochemistry 1995, 34:14765-14774.
23. Brown D, Gold L: Selection and characterization of RNAs replicated by Qβ replicase. Biochemistry 1995, 34:14775-14782. This report investigates the molecular mechanism by which the polymerase replicates specific RNA templates. It gives examples of selection for function as opposed to selection for binding.
24. Rieger A, Nassal M: Distinct requirements for primary sequence in the 5′- and 3′-part of a bulge in the hepatitis B virus RNA encapsidation signal revealed by a combined in vivo selection/in vitro amplification system. Nucleic Acids Res 1995, 23:3909-3925.
25. Baskerville S, Zapp M, Ellington AD: High-resolution mapping of the human T-cell leukemia virus type I Rex-binding element by in vitro selection. J Virol 1995, 69:7559-7569.
26. Leclerc F, Cedergren R, Ellington AD: A three-dimensional model of the Rev-binding element of HIV-1 derived from analyses of aptamers. Nat Struct Biol 1994, 1:301-310. This paper constitutes an example of how selection data can be used to develop reasonably detailed three-dimensional structural models.
27. Jensen KB, Green L, MacDougal-Waugh S, Tuerk C: Characterization of an in vitro-selected RNA ligand to the HIV-1 Rev protein. J Mol Biol 1994, 235:237-247.
28. Nazrenko IA, Uhlenbeck OC: Defining a smaller RNA substrate for elongation factor Tu. Biochemistry 1995, 34:2545-2552.
29. Cui Y, Wang Q, Stormo GD, Calvo JM: A consensus sequence for binding of Lrp to DNA. J Bacteriol 1995, 177:4872-4880.
30. Ringquist S, Jones T, Snyder EE, Gibson T, Boni I, Gold L: High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites. Biochemistry 1995, 34:3640-3648.
31. Dobbelstein M, Shenk T: In vitro selection of RNA ligands for the ribosomal L22 protein associated with Epstein-Barr Virus expressed RNA by using randomized and cDNA-derived RNA libraries. J Virol 1995, 69:8027-8034.
32. Tacke R, Manley JL: The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J 1995, 14:3540-3551.
33. Heinrichs V, Baker BS: The Drosophila SR protein RBP1 contributes to the regulation of doublesex alternative splicing by recognizing RBP1 RNA target sequences. EMBO J 1995, 14:3987-4000.
34. Singh R, Valcarcel J, Green M: Distinct binding specificities and functions of higher eucaryotic polypyrimidine tract-binding proteins. Science 1995, 268:1173-1176. This paper constitutes an excellent example of the use of selection to define the biological role of nucleic acid binding proteins. The specificities of different RNA-binding proteins involved in splicing suggest models for competition and splicing regulation.
35. Schneider DJ, Feigon J, Hostomsky Z, Gold L: High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry 1995, 34:9599-9610. The authors describe a good example of how DNA as well as RNA aptamers can be selected.
36. Green L, Waugh S, Binkley JP, Hostomska Z, Hostomsky Z, Tuerk C: Comprehensive chemical modification interference and nucleotide substitution analysis of an RNA pseudoknot inhibitor to HIV-1 reverse transcriptase. J Mol Biol 1995, 247:60-68.
37. Allen P, Worland S, Gold L: Isolation of a high-affinity RNA ligands to HIV-1 integrase from a random pool. Virology 1995, 209:327-336.
38. Symensma TL, Giver L, Zapp M, Takle GB, Ellington AD: RNA aptamers selected to bind human immunodeficiency virus type 1 Rev in vitro are Rev responsive in vivo. J Virol 1996, 70:179-187. This paper describes an example of how aptamers selected in a test tube can be used within cells.
39. Tian Y, Adya N, Wagner S, Giam C, Green M, Ellington AD: Dissecting protein:protein interactions between transcription factors with an RNA aptamer. RNA 1995, 1:317-326.
40. Pan W, Craven RC, Qiu Q, Wilson CB, Wills JW, Golovine S, Wang J: Isolation of virus-neutralizing RNAs from a large pool of random sequences. Proc Natl Acad Sci USA 1995, 92:11509-11513. This paper constitutes an interesting demonstration that supramolecular ar-chitectures as well as simple proteins can be targets for in vitro selection experiments.
41. Conrad R, Keranen LM, Newton AC, Ellington AD: Isozyme-specific inhibition of protein kinase C by RNA aptamers. J Biol Chem 1994, 269:32051-32054.
42. Binkley J, Allen P, Brown D, Green L, Tuerk C, Gold L: RNA ligands to human nerve growth factor. Nucleic Acids Res 1995, 23:3198-3205.
43. Nieuwlandt D, Wecker M, Gold L: In vitro selection of RNA ligands to substance P. Biochemistry 1995, 34:5651-5659.
44. Jellinek D, Green LS, Bell C, Lynott CK, Gill N, Vargeese C, Kirschenheuter G, McGee DPC, Abesinghe P, Pieken WA et al.: Potent 2′-amino-2′-deoxypyrimidine RNA inhibitors of basic fibroblast growth factor. Biochemistry 1995, 34:11363-11372.
45. Green LS, Jellinek D, Bell C, Beebe LA, Feistner BD, Gill SC, Jucker FM, Janjic N: Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor. Chem Biol 1995, 2:683-695. This paper describes several nucleotide modifications that improve both the affinity and the stability of RNA aptamers. The characterization and analysis of selected sequences is a tour-de-force.
46. Smith D, Kirschenheuter GP, Charlton J, Guidot DM, Repine JE: In vitro selection of RNA-based irreversible inhibitors of human neutrophil elastase. Chem Biol 1995, 2:741-750. Coupling a small organic ligand to a RNA pool directs the selection of aptamers that bind to and covalently modify the active site of an enzyme.
47. Lin Y, Padmapriya A, Morden KM, Jayasena D: Peptide conjugation to an in vitro-selected DNA ligand improves enzyme inhibition. Proc Natl Acad Sci USA 1995, 92:11044-11048.
48. Jensen KB, Atkinson BL, Willis MC, Koch TH, Gold L: Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. Proc Natl Acad Sci USA 1995, 92:12220-12224. The authors generate aptamers that are high-affinity binders and able to photocrosslink to their target. One of the aptamers can crosslink without photons, using the surface chemistry of the protein.
49. Eaton BE, Gold L, Zichi DA: Let's get specific: the relationship between specificity and affinity. Chem Biol 1995, 2:633-638.
50. Macaya RF, Waldron JA, Beutel BA, Hetian G, Joesten ME, Yang M, Patel R, Bertelsen AH, Cook AF: Structural and functional characterization of potent antithrombotic oligonucleotides possessing both quadruplex and duplex motifs. Biochemistry 1995, 34:4478-4492.
51. Tsiang M, Gibbs CS, Griffin LC, Dunn KE, Leung LLK: Selection of a suppressor mutation that restores affinity of an oligonucleotide inhibitor for thrombin using in vitro genetics. J Biol Chem 1995, 270:19370-19376. Aptamers derived from a selection that targeted a suppressor mutation of thrombin were able to bind both the mutant and wild-type protein.