Emergence of a code in the polymerization of amino acids along RNA templates

PLoS ONE

Volumn 4, Issue 6, 2009, Pages

  Lehmann, Jean ^a   Cibils, Michel ^b   Libchaber, Albert ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID; GLYCINE; TRANSFER RNA; PROTEIN; RNA;

AMINOACYLATION; ANTICODON; ARTICLE; BASE MISPAIRING; CATALYSIS; CODON; CONTROLLED STUDY; DISSOCIATION CONSTANT; GENETIC CODE; MICHAELIS MENTEN KINETICS; POLYMERIZATION; RIBOSOME; RNA SEQUENCE; RNA TRANSLATION; BIOCHEMISTRY; BIOLOGICAL MODEL; BIOPHYSICS; CHEMISTRY; KINETICS; METHODOLOGY; PROTEIN SYNTHESIS; STATISTICAL MODEL; THEORETICAL MODEL;

AMINO ACIDS; BIOCHEMISTRY; BIOPHYSICS; CODON; GENETIC CODE; KINETICS; MODELS, GENETIC; MODELS, STATISTICAL; MODELS, THEORETICAL; PROTEIN BIOSYNTHESIS; PROTEINS; RNA; RNA, TRANSFER;

EID: 66749191451     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005773     Document Type: Article

References (29)

1. Berg P, Bergmann FH, Ofengand EJ, Dieckmann M (1961) Enzymic synthesis of amino acyl derivatives of ribonucleic acid. J Biol Chem 236: 1726-1734.
2. Gromadski KB, Rodnina MV (2004) Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol Cell 13: 191-200.
3. Illangasekare M, Yarus M (1999) A tiny RNA that catalyzes both aminoacyl-RNA and peptidyl-RNA synthesis. RNA 5: 1482-1489.
4. Lehmann J, Reichel A, Buguin A, Libchaber A (2007) Efficiency of a self-aminoacylating ribozyme: Effect of the length and base-composition of its 3′ extension. RNA 13: 1191-1197.
5. Lehmann J (2000) Physico-chemical constraints connected with the coding properties of the genetic system. J theor Biol 202: 129-144.
6. Grosjean HJ, De Henau S, Crothers DM (1978) Physical basis for ambiguity in genetic coding interactions. Proc Natl Acad Sci U S A 75: 610-614.
7. Sievers A, Beringer M, Rodnina MV, Wolfenden R (2004) The ribosome as an entropy trap. Proc Natl Acad Sci U S A 101: 7897-7901.
8. Ledoux S, Uhlenbeck OC (2008) Different aa-tRNAs are selected uniformly on the ribosome. Mol Cell 31: 114-123.
9. Ogle JM, Brodersen DE, Clemons WM, Tarry MJ, Carter AP, et al. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292: 897-902.
10. Agmon F, Bashan A, Zarivach R, Yonath A (2005) Symmetry at the active site of the ribosome: structural and functional implications. Biol Chem 386: 833-844.
11. Miller SL (1987) Which organic compounds could have occurred on the prebiotic earth. Cold Spring Harbor Symposia on Quantitative Biology LII: 17-27.
12. 4-tetrahydrophthalate monophenyl esters. J Am Chem Soc 118: 2595-2605.
13. Armstrong AA, Amzel LM (2003) Role of entropy in increased rates of intramolecular reactions. J Am Chem Soc 125: 14596-14602.
14. Jung ME, Piizzi G (2005) Gem-Disubstituent effect: Theoretical basis and synthetic applications. Chem Rev 105: 1735-1766.
15. Agris PF (2004) Decoding the genome: a modified view. Nucl Ac Res 32: 223-238.
16. Olejniczak M, Dale T, Fahlman RP, Uhlenbeck OC (2005) Idiosyncratic tuning of tRNAs to achieve uniform ribosome binding. Nat Str Mol Biol 12: 788-793.
17. Auffinger P, Westhof E (2001) An extended structural signature for the tRNA anticodon loop. RNA 7: 334-342.
18. Eigen M, Schuster P (1978) Hypercycle - principle of natural self-organization. C. Realistic hypercycle. Naturwissenschaften 65: 341-369.
19. Ikehara K, Omori Y, Arai R, Hirose A (2002) A novel theory on the origin of the genetic code: A GNC-SNS hypothesis. J Mol Evol 54: 530-538.
20. Lehmann J, Riedo B, Dietler G (2004) Folding of small RNAs displaying the GNC base-pattern: implications for the self-organization of the genetic system. J theor Biol 227: 381-395.
21. Lacey JC, Wickramasinghe NSMD, Cook GW (1992) Experimental studies on the origin of the genetic code and the process of protein synthesis - a review update. Origins Life Evol Biosphere 22: 243-275.
22. Turner DH, Sugimoto N, Jaeger JA, Longfellow CE, Freier SM, et al. (1987) Improved parameters for prediction of RNA structure. Cold Spring Harbor Symposia on Quantitative Biology 52: 123-133.
23. Woese CR (1965) Order in the genetic code. Proc Natl Acad Sci U S A 54: 71-75.
24. Woese CR, Dugre DH, Saxinger WC, Dugre SA (1968) The molecular basis for the genetic code. Proc Natl Acad Sci U S A 55: 966-974.
25. Lacey JC, Mullins DW (1983) Experimental studies related to the origin of the genetic code and the process of protein synthesis - a review. Origins Life Evol Biosphere 13: 3-42.
26. Schimmel P, Giege R, Moras D, Yokoyama S (1993) An operational RNA code for amino acids and possible relation to genetic code. Proc Natl Acad Sci U S A 90: 8763-8768.
27. Delarue M (2007) An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13: 1-9.
28. Rodin SN, Rodin AS (2008) On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyltRNA synthetases. Heredity 100: 341-355.
29. Matthaei JH, Voigt HP, Heller G, Neth R, Schöch G, et al. (1966) Specific interactions of ribosomes in decoding. Cold Spring Harbor Symposia on Quantitative Biology 31: 25-38.