Rhyme or reason: RNA-arginine interactions and the genetic code

Chemistry and Biology

Volumn 5, Issue 9, 1998, Pages

  Knight, Robin D ^a   Landweber, Laura F ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CODON; PROTEIN INTERACTION; PROTEIN RNA BINDING; STATISTICAL ANALYSIS;

EID: 0032169998     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(98)90001-1     Document Type: Note

References (41)

1. Woese, C.R. (1965). On the evolution of the genetic code. Proc. Natl Acad. Sci. USA, 54, 1546-1552.
2. Sonneborn, T.M. (1965). Degeneracy of the genetic code: extent, nature, and genetic implications. In Evolving Genes and Proteins. (Bryson, V. & Vogel, H.J, eds), pp. 377-297, Academic Press, New York.
3. Zuckerkandl, E. & Pauling, L. (1965). Evolutionary divergence and convergence in proteins. In Evolving Genes and Proteins. (Bryson, V. & Vogel, H.J, eds), pp. 97-166, Academic Press, New York.
4. Woese, C.R. (1967). The Genetic Code: The Molecular Basis for Genetic Expression. Harper & Row, New York.
5. Crick, F.H.C. (1968). The origin of the genetic code. J. Mol. Biol. 38, 367-379.
6. Wong, J.T.-F. (1975). A co-evolution theory of the genetic code. Proc. Natl Acad. Sci. USA, 72, 1909-1912.
7. Woese, C.R., Dugre, D.H., Saxinger, W.C. & Dugre, S.A. (1966). The molecular basis for the genetic code. Proc. Natl Acad. Sci. USA, 55, 966-974.
8. Pelc, S.R. & Welton, M.G.E. (1966). Stereochemical relationship between coding triplets and amino acids. Nature 209, 868-872.
9. Dunnill, P. (1966). Triplet nucleotide - amino acid pairing: a stereochemical basis for the division between protein and nonprotein amino acids. Nature 210, 1267-1268.
10. Alberti, S. (1997). The origin of the genetic code and protein synthesis. J. Mol. Evol. 45, 352-358.
11. Yarus, M. (1989). Specificity of arginine binding by the Tetrahymena intron. Biochemistry 28, 980-988.
12. Hopfield, J.J. (1978). Origin of the genetic code: a testable hypothesis based on tRNA structure, sequence, and kinetic proofreading. Proc. Natl Acad. Sci. USA 75, 4334-4338.
13. Shimizu, M. (1982). Molecular basis for the genetic code. J. Mol. Evol. 18, 297-303.
14. de Duve, C. (1988). The second genetic code. Nature 333, 117-118.
15. Noller, H.F. (1993), On the origin of the ribosome: coevolution of subdomains of tRNA and rRNA. In The RNA World. (Gesteland, R.F. & Atkins, J.F., eds), pp. 137-156, Cold Spring Harbor Laboratory Press, New York.
16. Schimmel, P., Giege, R., Moras, D. & Yokoyama, S. (1993). An operational genetic code for amino acids and possible relationship to genetic code. Proc. Natl Acad. Sci. USA 90, 8763-8768.
17. Maizels, N. & Weiner, A.M. (1994). Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc. Natl Acad. Sci. USA 91, 6729-6734.
18. Dick, T.P. & Schamel, W.W.A. (1995). Molecular evolution of transfer RNA from two precursor hairpins: Implications for the origin of protein synthesis. J. Mol. Evol. 41, 1-9.
19. Ellington, A.D. & Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
20. Tuerk, C. & Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
21. Robertson, D.L. & Joyce, G.F. (1990). Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344, 467-468.
22. Connell, G.J., Illangsekare, M. & Yarus, M. (1993). Three small ribooligonucleotides with specific arginine sites. Biochemistry 32, 5497-5502.
23. Connell, G.J. & Yarus, M. (1994). RNAs with dual specificity and dual RNAs with similar specificity. Science 264, 1137-1141.
24. Yarus, M. (1993), An RNA-amino acid affinity. In The RNA World. (Gesteland, R.F. & Atkins, J.F., eds), pp. 205-217, Cold Spring Harbor Laboratory Press, New York.
25. 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.
26. Tao, J. & Frankel, A.D. (1996). Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry 35, 2229-2238.
27. 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.
28. Tao, J. & Frankel, A.D. (1992). Specific binding of arginine to TAR RNA. Proc. Natl Acad. Sci. USA 89, 2723-2726.
29. Yang, Y., Kochoyan, M., Burgstaller, P., Westhof, E. & Famulok, F. (1996). Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 272, 1343-1346.
30. Sokal, R.R. & Rohlf, F.J. (1995). Biometry: the Principles and Practice of Statistics in Biological Research. (3rd edn). W.H. Freeman and Company, New York.
31. Jiang, F., Kumar, R.A., A, J.R. & Patel, D.J. (1996). Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382, 183-186.
32. Fan, P., Suri, A.K., Fiala, R., Live, D. & Patel, D.J. (1996). Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol. 258, 480-500.
33. 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.
34. Jiang, L., Suri, A.K., Fiala, R. & Patel, D.J. (1997). Saccharide - RNA recognition in an aminoglycoside antibiotic - RNA aptamer complex. Chem. Biol. 4, 35-50.
35. Zimmermann, G.R., Shields, T.P., Jenison, R.D., Wick, C.L. & Pardi, A. (1998). A semiconserved residue inhibits complex formation by stabilizing interactions in the free state of a theophylline-binding RNA. Biochemistry 37, 9186-9192.
36. Yarus, M. (1998). Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J. Mol. Evol. 47, 109-117.
37. Majerfeld, I. & Yarus, M. (1994). An RNA pocket for an aliphatic hydrophobe. Nat. Struct. Biol. 1, 287-292.
38. Majerfeld, I. & Yarus, M. (1998). Isoleucine:RNA sites with essential coding sequences. RNA 4, 471-478.
39. Zinnen, S. & Yarus, M. (1995). An RNA pocket for the planar aromatic sidechains of phenylalanine and tryptophane. Nucleic Acids Symp. Ser. 33, 148-151.
40. Jukes, T.H. (1973). Arginine as an evolutionary intruder into protein synthesis. Biochem. Biophy. Res. Commun. 53, 709-714.
41. Grantham, R. (1974). Amino acid difference formula to help explain protein evolution. Science 185, 862-865.