Chiral histidine selection by D-ribose RNA

RNA

Volumn 16, Issue 12, 2010, Pages 2370-2383

  Illangasekare, Mali ^a   Turk, Rebecca ^a   Peterson, G Colin ^a   Lladser, Manuel ^a   Yarus, Michael ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Amino acid; Aptamer; Ribose; Simultaneous successively squeezed selection; Stereoselection

Indexed keywords

HISTIDINE; NUCLEOTIDE; RIBOSE; RNA;

ARTICLE; ELUTION; PRIORITY JOURNAL; RNA BINDING; RNA SEQUENCE; RNA TRANSLATION;

BASE SEQUENCE; CATALYTIC DOMAIN; GENETIC CODE; HISTIDINE; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RANDOM ALLOCATION; RIBOSE; RNA; STEREOISOMERISM; SUBSTRATE SPECIFICITY;

EID: 78649667347     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2385310     Document Type: Article

References (40)

1. Anderson PC, Mecozzi S. 2005a. Identification of a 14mer RNA that recognizes and binds flavin mononucleotide with high affinity. Nucleic Acids Res 33: 6992-6999.
2. Anderson PC, Mecozzi S. 2005b. Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline. J Am Chem Soc 127: 5290-5291.
3. Batey RT, Gilbert SD, Montange RK. 2004. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432: 411-415.
4. Brown L, Cai T, DasGupta A. 2001. Interval estimation for a binomial proportion. Stat Sci 16: 101-117.
5. Carothers JM, Oestreich SC, Davis JH, Szostak JW. 2004. Informational complexity and functional activity of RNA structures. J Am Chem Soc 126: 5130-5137.
6. Ciesiolka J, Illangasekare M, Majerfeld I, Nickles T, Welch M, Yarus M, Zinnen S. 1996. Affinity selection-amplification from randomized ribooligonucleotide pools. Methods Enzymol 267: 315-335.
7. Coleman TM, Huang F. 2002. RNA-catalyzed thioester synthesis. Chem Biol 9: 1227-1236.
8. Coleman TM, Huang FH. 2005. Optimal random libraries for the isolation of catalytic RNA. RNA Biol 2: 129-136.
9. Devore JL. 2008. Probability and statistics for engineering and the sciences. Thomson Brooks/Cole, Belmont, CA.
10. Freeland SJ, Knight RD, Landweber LF. 1999. Do proteins predate DNA? Science 286: 690-692.
11. Illangasekare M, Yarus M. 2002. Phenylalanine-binding RNAs and genetic code evolution. J Mol Evol 54: 298-311.
12. Janas T, Widmann JJ, Knight R, Yarus M. 2010. Simple, recurring RNA binding sites for L-arginine. RNA 16: 805-816.
13. Johnson DB, Wang L. 2010. Imprints of the genetic code in the ribosome. Proc Natl Acad Sci 107: 8298-8303.
14. Joyce GF, Visser GM, van Boeckel CA, van Boom JH, Orgel LE, van Westrenen J. 1984. Chiral selection in poly(C)-directed synthesis of oligo(G). Nature 310: 602-604.
15. Klussmann S, Nolte A, Bald R, Erdmann VA, Furste JP. 1996. Mirror-image RNA that binds D-adenosine. Nat Biotechnol 14: 1112-1115.
16. Knight R, De Sterck H, Markel R, Smit S, Oshmyansky A, Yarus M. 2005. Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res 33: 5924-5935.
17. Legiewicz M, Yarus M. 2005. A more complex isoleucine aptamer with a cognate triplet. J Biol Chem 280: 19815-19822.
18. Legiewicz M, Lozupone C, Knight R, Yarus M. 2005. Size, constant sequences, and optimal selection. RNA 11: 1701-1709.
19. Lehman N. 2004. Assessing the likelihood of recurrence during RNA evolution in vitro. Artificial Life 10: 1-22.
20. Lozupone C, Changayil S, Majerfeld I, Yarus M. 2003. Selection of the simplest RNA that binds isoleucine. RNA 9: 1315-1322.
21. MacDermott AJ. 1995. Electroweak enantioselection and the origin of life. Orig Life Evol Biosph 25: 191-199.
22. Majerfeld I, Yarus M. 2005. A diminutive and specific RNA binding site for L-tryptophan. Nucleic Acids Res 33: 5482-5493.
23. Majerfeld I, Puthenvedu D, Yarus M. 2005. RNA affinity for molecular L-histidine; genetic code origins. J Mol Evol 61: 226-235.
24. Mason SF. 1987. Universal dissymmetry and the origin of biomolecular chirality. Biosystems 20: 27-35.
25. Nolte A, Klussmann S, Bald R, Erdmann VA, Furste JP. 1996. Mirrordesign of L-oligonucleotide ligands binding to L-arginine. Nat Biotechnol 14: 1116-1119. (Pubitemid 26299111)
26. Paul N, Springsteen G, Joyce GF. 2006. Conversion of a ribozyme to a deoxyribozyme through in vitro evolution. Chem Biol 13: 329-338.
27. Peterson GC. 2010. "Fairness Analysis via Poissonization." PhD thesis, University of Colorado, Boulder.
28. Profy AT, Usher DA. 1984. Stereoselective aminoacylation of polyribonucleotides. J Am Chem Soc 106: 5030-5031.
29. Ruta J, Ravelet C, Grosset C, Fize J, Ravel A, Villet A, Peyrin E. 2006. Enantiomeric separation using an l-RNA aptamer as chiral additive in partial-filling capillary electrophoresis. Anal Chem 78: 3032-3039. (Pubitemid 43726122)
30. Sandars PGH. 2005. Chirality in the RNA world and beyond. Int J Astrobiol 4: 49-61.
31. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. 1986. Information content of binding sites on nucleotide sequences. J Mol Biol 188: 415-431.
32. Tamura K, Schimmel P. 2004. Chiral-selective aminoacylation of an RNA minihelix. Science 305: 1253. doi: 10.1126/science.1099141.
33. Tamura K, Schimmel PR. 2006. Chiral-selective aminoacylation of an RNA minihelix: Mechanistic features and chiral suppression. Proc Natl Acad Sci 103: 13750-13752. (Pubitemid 44413979)
34. Vlassov A, Khvorova A, Yarus M. 2001. Binding and disruption of phospholipid bilayers by supramolecular RNA complexes. Proc Natl Acad Sci 98: 7706-7711. (Pubitemid 32642625)
35. Wickramasinghe NS, Lacey JC Jr. 1992. Esterification of all four monoribonucleotides with acetyl-D-L-valine proceeds with a preference for the D-isomer but the D/L ratio in the products declines as a function of the hydrophobicity of the nucleotide. Bioorg Chem 20: 265-268.
36. Yarus M. 2001. On translation by RNAs alone. Cold Spring Harb Symp Quant Biol 66: 207-215.
37. Yarus M, Knight RD. 2004. The scope of selection. In The genetic code and the origin of life (ed. LR Pouplana), pp 75-91. Landes Bioscience, Georgetown, TX.
38. Yarus M, Welch M. 2000. Peptidyl transferase: ancient and exiguous. Chem Biol 7: R187-R190.
39. Yarus M, Caporaso JG, Knight R. 2005. Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem 74: 179-198. (Pubitemid 40995505)
40. Yarus M, Widmann JJ, Knight R. 2009. RNA-amino acid binding: A stereochemical era for the Genetic Code. J Mol Evol 69: 406-429.