On the structural repertoire of pools of short, random RNA sequences

Journal of Theoretical Biology

Volumn 252, Issue 4, 2008, Pages 750-763

  Stich, Michael ^a   Briones, Carlos ^a   Manrubia, Susanna C ^a  

^a INSTITUTO NACIONAL DE TÉCNICA AEROESPACIAL   (Spain)

Author keywords

Genotype phenotype map; RNA folding; RNA motif; RNA world; Structural family

Indexed keywords

NUCLEOTIDE; SINGLE STRANDED RNA;

EVOLUTION; GENE EXPRESSION; GENOTYPE; PHENOTYPE; RNA;

ARTICLE; BIOLOGY; IN VITRO STUDY; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE;

EID: 44449168461     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.02.018     Document Type: Article

References (43)

1. Anderson P.C., and Mecozzi S. Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques. J. Comp. Chem. 27 (2006) 1631-1640
2. Backofen R., Bernhart S.H., Flamm C., Fried C., Fritzsch G., Hackermüller J., Hertel J., Hofacker I.L., Missal K., Mosig A., Prohaska S.J., Rose D., Stadler P.F., Tanzer A., Washietl S., and Will S. RNAs everywhere: genome-wide annotation of structured RNAs. J. Exp. Zool. (Mol. Dev. Evol.) 308B (2007) 1-25
3. Bartel D.P., and Szostak J.W. Isolation of new ribozymes from a large pool of random sequences. Science 261 (1993) 1411-1418
4. Carothers J.M., Oestreich S.C., Davis J.H., and Szostak J.W. Informational complexity and functional activity of RNA structures. J. Am. Chem. Soc. 126 (2004) 5130-5137
5. Fontana W., Konings D.A.M., Stadler P.F., and Schuster P. Statistics of RNA secondary structures. Biopolymers 33 (1993) 1389-1404
6. Gan H.H., Pasquali S., and Schlick T. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res. 31 (2003) 2926-2943
7. Gevertz J., Gan H.H., and Schlick T. In vitro RNA random pools are not structurally diverse: a computational analysis. RNA 11 (2005) 853-863
8. Grüner W., Giegerich R., Strothmann D., Reidys C., Weber J., Hofacker I.L., Stadler P.F., and Schuster P. Analysis of RNA sequence structure maps by exhaustive enumeration. I. Neutral networks. Monatsh. Chem. 127 (1996) 355-374
9. Grüner W., Giegerich R., Strothmann D., Reidys C., Weber J., Hofacker I.L., Stadler P.F., and Schuster P. Analysis of RNA sequence structure maps by exhaustive enumeration. II Structures of neutral networks and shape space covering. Monatsh. Chem. 127 (1996) 375-389
10. Gutell R.R., Cannone J.J., Shang Z., Du Y., and Serra M.J. A story: unpaired adenosine bases in ribosomal RNAs. J. Mol. Biol. 304 (2000) 335-354
11. Hackermüller J., Meisner N.-C., Auer M., Jaritz M., and Stadler P.F. The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene 345 (2005) 3-12
12. Hendrix D.K., Brenner S.E., and Holbrook S.R. RNA structural motifs: building blocks of a modular biomolecule. Quart. Rev. Biophys. 38 (2005) 221-243
13. Hiller M., Pudimat R., Busch A., and Backofen R. Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res. 34 (2006) e117
14. Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer L.S., Tacker M., and Schuster P. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125 (1994) 167-188
15. Hofacker I.L., Schuster P., and Stadler P.F. Combinatorics of RNA secondary structures. Discrete Appl. Math. 88 (1998) 207-237
16. Jaeger J.A., Turner D.H., and Zuker M. Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA 86 (1989) 7706-7710
17. Joyce G.F. Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73 (2004) 791-836
18. Khanam T., Muddashetty R.S., Kahvejian A., Sonenberg N., and Brosius J. Poly(a)-binding protein binds to a-rich sequences via RNA-binding domains 1 + 2 and 3 + 4. RNA Biol. 3 (2006) 170-177
19. Kim N., Gan H.H., and Schlick T. A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA 13 (2007) 478-492
20. Knight R., and Yarus M. Finding specific RNA motifs: function in a zeptomole world?. RNA 9 (2003) 218-230
21. Knight R., De Sterck H., Markel R., Smit S., Oshmyansky A., and Yarus M. Abundance of correctly folded RNA motifs in sequence space calculated on computational grids. Nucleic Acids Res. 33 (2005) 5924-5935
22. Lee J.F., Hesselberth J.R., Meyers L.A., and Ellington A.D. Aptamer database. Nucleic Acids Res. 32 (2004) D95-D100
23. Liao B., and Wang T. General combinatorics of RNA secondary structure. Math. Biosci. 191 (2004) 69-81
24. Lilley D.M.J. Structure, folding and mechanisms of ribozymes. Curr. Opin. Struct. Biol. 15 (2005) 313-323
25. Lorsch J.R., and Szostak J.W. In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature 371 (1994) 31-36
26. Majerfeld I., and Yarus M. A diminutive and specific RNA binding site for L-tryptophan. Nucleic Acids Res. 33 (2005) 5482-5493
27. Manrubia S.C., and Briones C. Modular evolution and increase of functional complexity in replicating RNA molecules. RNA 13 (2007) 97-107
28. Mathews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
29. Moore P.B. Structural motifs in RNA. Annu. Rev. Biochem. 68 (1999) 287-300
30. Ohmichi T., Nakano S.-I., Miyoshi D., and Sugimoto N. Long RNA dangling end has large energetic contribution to duplex stability. J. Am. Chem. Soc. 124 (2002) 10367-10372
31. Pedersen J.S., Bejerano G., Siepel A., Rosenbloom K., Lindblad-Toh K., Lander E.S., Kent J., Miller W., and Haussler D. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2 (2006) e33
32. Petrillo M., Silvestro G., Di Nocera P.-P., Boccia A., and Paolella G. Stem-loop structures in prokaryotic genomes. BMC Genomics 7 (2006) 170
33. Puerta-Fernández E., Romero-López C., Barroso-delJesús A., and Berzal-Herranz A. Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol. Rev. 27 (2003) 75-97
34. Sabeti P.C., Unrau P.J., and Bartel D.P. Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem. Biol. 4 (1997) 767-774
35. Schuster P., and Stadler P.F. Landscapes: complex optimization problems and biopolymer structures. Computers Chem. 18 (1994) 295-324
36. Schuster P., Fontana W., Stadler P.F., and Hofacker I.L. From sequences to shapes and back: a case study in RNA secondary structures. Proc. Roy. Soc. London B 255 (1994) 279-284
37. Shapiro B.A. An algorithm for comparing multiple RNA secondary structures. Comput. Appl. Biosci. 4 (1988) 387-393
38. Stein P.R., and Waterman M.S. On some new sequences generalizing the Catalan and Motzkin numbers. Discrete Math. 26 (1978) 261-272
39. Svoboda P., and Di Cara A. Hairpin RNA: a secondary structure of primary importance. Cell. Mol. Life Sci. 63 (2006) 901-918
40. Tacker M., Stadler P.F., Bornberg-Bauer E.G., Hofacker I.L., and Schuster P. Algorithm independent properties of RNA secondary structure predictions. Eur. Biophys. J. 25 (1996) 115-130
41. Waterman, M.S., 1978. Secondary structure of single-stranded nucleic acids. In Studies in Foundation and Combinatorics, Advances in Mathematics Supplementary Studies, vol. 1, Academic Press, New York, pp. 167-212.
42. Wilson D.S., and Szostak J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68 (1999) 611-647
43. Zorn J., Gan H.H., Shiffeldrim N., and Schlick T. Structural motifs in ribosomal RNAs: implications for RNA design and genomics. Biopolymers 73 (2004) 340-347