Amino acids as RNA ligands: A direct-RNA-template theory for the code's origin

Journal of Molecular Evolution

Volumn 47, Issue 1, 1998, Pages 109-117

  Yarus, Michael ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Affinity selection; Genetic code; Internal loop; RNA structure; Selection amplification

Indexed keywords

AMINO ACID; ARGININE; DNA; LIGAND; RNA;

BINDING SITE; CATALYSIS; GENETIC CODE; HYDROPHOBICITY; INTRON; NONHUMAN; PEPTIDE SYNTHESIS; PROTEIN RNA BINDING; REVIEW; RNA SEQUENCE; RNA STRUCTURE;

AMINO ACIDS; ARGININE; BINDING SITES; EVOLUTION, MOLECULAR; GENETIC CODE; LIGANDS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PEPTIDE BIOSYNTHESIS; RNA; RNA, PROTOZOAN;

EID: 0031799551     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006357     Document Type: Review

References (49)

1. 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
2. Cedergren R, Miramontes P (1996) The puzzling origin of the genetic code. TIBS 21:199-200
3. Chen L, Frankel AD (1995) A peptide interaction in the major groove of RNA resembles interactions in the minor groove of DNA. Proc Natl Acad Sci USA 92:5077-5081
4. Conn MM, Prudent JR, Schultz PG (1996) Porphyrin metalation catalyzed by a small RNA molecule. J Am Chem Soc 118:7012-7013
5. Connell GJ, Yarus M (1994) RNAs with dual specificity and dual RNAs with similar specificity. Science 264:1137-1141
6. Connell GJ, Illangasekare M, Yarus M (1993) Three small ribooligonucleotides with specific arginine sites. Biochemistry 32:5497-5502
7. Crick FHC (1968) The origin of the genetic code. J Mol Biol 38:367-379
8. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-822
9. 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
10. Famulok M, Szostak W (1992) Stereospecific recognition of tryptophan agarose by in vitro selected RNA. J Am Chem Soc 114:3990-3991
11. Ferris JP, Hill AR Jr, Liu R, Orgel LE (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381:59-61
12. Geiger A, Burgstaller P, Eltz Hvd, Roeder A, Famulok M (1996) RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioseleclivity. Nucleic Acids Res 24:1029-1036
13. Golden BL, Cech TR (1996) Conformational switches involved in orchestrating the successive steps of group I RNA splicing. Biochemistry 35:3754-3763
14. Harada K, Frankel AD (1995) Identification of two novel arginine binding DNAs. EMBO J 14:5798-5811
15. Hicke BJ, Christian EL, Yarus M (1989) Stereoselective arginine binding is a phylogenetically conserved property of group I self-splicing RNAs. EMBO J 8:3843-3851
16. Hirao I, Ellington AD (1995) Re-creating the RNA world. Curr Biol 5:1017-1022
17. Illangasekare M, Kovalchuke O, Yarus M (1997) Essential structures of a self-aminoacylating RNA. J Mol Biol 274:519-529
18. Kim JL, Nikolov DB, Burley SK (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520-527
19. Kim Y, Geiger JH, Hahn S, Sigler PB (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature 365:512-520
20. Lacey JC Jr, Hall LM, Mullins DW Jr (1985) Rationalization of some genetic anticodonic assignments. Origins Life 16:69-79
21. la Cour TF, Nyborg J, Thirup S, Clark BFC (1985) Structural details of the binding of GDP to elongation factor Tu from E coli as studied by X-ray crystallography. EMBO J 4:2385-2388
22. Li Y, Sen D (1996) A catalytic DNA for porphyrin metallation. Nature Struct Biol 3:743-747
23. Lohse PA, Szostak JW (1996) Ribozyme-catalyzed amino-acid transfer reactions. Nature 381:442-444
24. Majerfeld I, Yarus M (1994) An RNA pocket for an aliphatic hydrophobe. Nature Struct Biol 1:287-292
25. Majerfeld I, Yarus M (1998) Isoleucine binding sites with essential coding sequences. RNA 4:471-478
26. Michel F, Hanna M, Green R, Bartel DP, Szostak JW (1989) The guanosine binding site of the Tetrahymena intron. Nature 342:391-395
27. Noller HF, Hoffarth V, Zimniak L (1992) Unusual resistance of peptidyl transferase to protein extraction methods. Science 256:1416-1419
28. Orgel LE (1968) Evolution of the genetic apparatus. J Mol Biol 38: 381-393
29. Pai EF, Kabsh W, Krengel U, Holmes KC, John J, Wittinghofer A (1989) Structure of the guanine nucleotide binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. Nature 341:209-214
30. Pugilisi JD, Chen L, Blanchard S, Frankel AD (1995) Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science 270:1200-1203
31. Robertson DL, Joyce GF (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467-468
32. Shub DA (1991) The antiguity of group I introns. Curr Opin Genet Dev 1:478-484
33. Sundquist WI (1996) Tattle tales. Nature Struct Biol 3:8-11
34. Tan R, Frankel AD (1995) Structural variety of arginine-rich RNA-binding peptides. Proc Natl Acad Sci USA 92:5282-5286
35. Tao J, Frankel AD (1996) Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry 35:2229-2238
36. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to T4 DNA polymerase. Science 249: 505-510
37. Welch M, Majerfeld I, Yarus M (1997) 23S rRNA similarity from selection for peptidyltransferase mimicry. Biochemistry 36:6614-6623
38. Werner MH, Huth JR, Gronenborn AM, Clore GM (1995) Molecular basis of human 46X,Y sex reversal revealed from the 3-dimensional solution structure of the human SRY-DNA complex. Cell 81:705-714
39. Woese CR, Dugre DH, Dugre AS, Kondo M, Saxinger WC (1967) On the fundamental nature and evolution of the genetic code. Cold Spring Harbor Symp Quant Biol 31:723-736
40. 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
41. Yarus M (1988) A specific amino acid binding site composed of RNA. Science 240:1751-1758
42. Yarns M (1991) An RNA-amino acid complex and the origin of the genetic code. New Biol 3:183-189
43. Yarus M (1993) An RNA-amino acid affinity. In: Gesteland RF, Atkins JF (eds) The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 205-217
44. Yarus M, Christian EL (1989) Genetic code origins. Nature 342:349-350
45. Yarus M, Majerfeld I (1992) Co-optimization of ribozyme substrate stacking and L-arginine binding. J Mol Biol 225:945-949
46. Yarus M, Illangasekare M, Christian EL (1991a) Selection of small molecules by the Tetrahymena catalytic center. EMBO J 19:1297-1304
47. Yarus M, Illangasekare M, Christian EL (1991b) An axial binding site in the Tetrahymena precursor RNA. J Mol Biol 222:995-1012
48. Ye X, Kumar RA, Patel DJ (1995) Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem Biol 2:827-840
49. Zinnen S, Yarus M (1995) An RNA pocket for the planar aromatic side chains of phenylalanine and tryptophan. Nucleic Acids Symp Ser 33:148-151