Exploring the Connection Between Synthetic and Natural RNAs in Genomes: A Novel Computational Approach

Lecture Notes in Computational Science and Engineering

Volumn 49, Issue , 2006, Pages 35-56

  Laserson, Uri ^a,b   Gan, Hin Hark ^a   Schlick, Tamar ^a,b  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; METABOLITES; PROTEINS; STABILITY; TRANSCRIPTION;

CANDIDATE SEQUENCES; COMPUTATIONAL APPROACH; FUNCTIONAL DIVERSITY; HEREDITARY MATERIALS; REGULATORY FUNCTIONS; STRUCTURAL INFORMATION; STRUCTURAL STABILITIES; TRANSCRIPTION REGULATIONS;

RNA;

EID: 79958075342     PISSN: 14397358     EISSN: None     Source Type: Book Series    
DOI: 10.1007/3-540-31618-3_3     Document Type: Article

References (56)

1. D. P. Arya, R. L. Coffee, I. Charles. Neomycin-induced hybrid triplex formation. J. Amer. Chem. Soc., 123:11093-11094, 2001.
2. D. P. Arya, R. L. Coffee, B. Willis, and A. I. Abramovitch. Aminoglycosidenucleic acid interactions: Remarkable stabilization of DNA and RNA triple helices by neomycin. J. Amer. Chem. Soc., 123:5385-5395, 2001.
3. J. P. Bachellerie, J. Cavaille, and A. Huttenhofer. The expanding snoRNA world. Biochimie, 84:775-90, 2002.
4. A. L. Barabási and E. Bonabeau. Scale-free networks. Sci. Amer., 288:60-69, 2003.
5. G. Benedetti and S. Morosetti. A graph-topological approach to recognition of pattern and similarity in RNA secondary structures. Biol. Chem., 59:179-184, 1996.
6. D. H. Burke, D. C. Hoffman, A. Brown, M. Hansen, A. Pardi, and L. Gold. RNA aptamers to the peptidyl transferase inhibitor chloramphenicol. Chem. Biol., 4:833-843, 1997.
7. J. H. Chen, S. Y. Le, and J. V. Maizel. Prediction of common secondary structures of RNAs: a genetic algorithm approach. Nucl. Acids Res., 28:991-999, 2000.
8. K. J. Devlin. Mathematics: the New Golden Age. Penguin, London, 1988.
9. J. A. Doudna and T. R. Cech. The chemical repertoire of natural ribozymes. Nature, 418:222-228, 2002.
10. A. D. Ellington and J. W. Szostak. In vitro selection of RNA molecules that bind specific ligands. Nature, 346: 818-822, 1990.
11. D. Fera, N. Kim, N. Shiffeldrim, J. Zorn, U. Laserson, H. H. Gan, and T. Schlick. RAG: RNA-As-Graphs web resource. BMC Bioinformatics, 5:88, 2004.
12. W. Fontana, D. A. Konings, P. F. Stadler, and P. Schuster. Statistics of RNA secondary structures. Biopolymers, 33:1389-1404, 1993.
13. W. Fontana, P. F. Stadler, E. G. Bornberg-Bauer, T. Griesmacher, I. L. Hofacker, M. Tacker, P. Tarazona, E. D. Weinberger, and P. Schuster. RNA folding and combinatory landscapes. Phys. Rev. E, 47:2083-2099, 1993.
14. H. H. Gan, S. Pasquali, and T. Schlick. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucl. Acids Res., 31:2926-2943, 2003.
15. C. Gaspin and E. Westhof. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J. Mol. Biol., 254:163-174, 1995.
16. W. W. Gibbs. The unseen genome: Gems among the junk. Sci. Amer., 289:46-53, 2003.
17. S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. R. Eddy. Rfam: an RNA family database. Nucl. Acids Res., 31:439-441, 2003.
18. J. Gross and J. Yellen. Graph Theory and its Applications. CRC Press, Boca Raton, FL, 1999.
19. F. Harary. The number of homeomorphically irreducible trees and other species. Acta Math., 101:141-162, 1959.
20. F. Harary. Graph Theory. Addison-Wesley, Reading, MA, 1969.
21. T. Hermann and D. J. Patel. Adaptive recognition by nucleic acid aptamers. Science, 287:820-825, 2000.
22. I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P. Schuster. Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125:167-188, 1994. www.tbi.univie.ac.-at/ivo/RNA/
23. A. Huttenhofer, J. Brosius, and J. P. Bachellerie. RNomics: Identification and function of small, non-messenger RNAs. Curr. Opin. Chem. Biol., 6:835-843, 2002.
24. A. Huttenhofer, M. Kiefmann, S. Meier-Ewert, J. O'Brien, H. Lehrach, J. P. Bachellerie, and J. Brosius. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J., 20:2943-2953, 2001.
25. L. Jiang, A. Majumdar, W. Hu, T. J. Jaishree, W. Xu, and D. J. Patel. Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer. Structure Fold Des., 7:817-827, 1999.
26. N. Kim, N. Shiffeldrim, H. H. Gan, and T. Schlick. Candidates for novel RNA topologies. J. Mol. Biol., 341:1129-1144, 2004.
27. J. Kitagawa, Y. Futamura, and K. Yamamoto. Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures. Nucl. Acids Res., 31:2006-2013, 2004.
28. S. Y. Le, R. Nussinov, and J. V. Maizel. Tree graphs of RNA secondary structures and their comparisons. Comput. Biomed. Res., 22:461-473, 1989.
29. T. J. Macke, D. J. Ecker, R. R. Gutell, D. Gautheret, D. A. Case, and R. Sampath. RNAMotif, an RNA secondary structure definition and search algorithm. Nucl. Acids Res., 29:4724-4735, 2001.
30. H. Margalit, B. A. Shapiro, A. B. Oppenheim, and J. V. Maizel, Detection of common motifs in RNA secondary structure. Nucl. Acids Res., 17:4829-4845, 1989.
31. J. S. Mattick. Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep., 2:986-991, 2001.
32. J. S. Mattick and M. J. Gagen. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms. Mol. Biol. Evol., 18:1611-1630, 2001.
33. A. Nahvi, N. Sudarsan, M. S. Ebert, X. Zou, K. L. Brown, and R. R. Breaker. Genetic control by a metabolite binding mRNA. Chem. Biol., 9:1043-1049, 2002.
34. Y. Okazaki, M. Furuno, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420:563-573, 2002.
35. S. Pasquali, H. H. Gan, and T. Schlick. Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nucl. Acids Res., 2005. In Press.
36. N. Piganeau and R. Schroeder. Aptamer structures: A preview into regulatory pathways? Chem. Biol., 10:103-104, 2003.
37. E. Rivas and S. R. Eddy. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285:2053-2068, 1999.
38. E. Rivas and S. R. Eddy. Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. Bioinformatics, 16:583-605, 2000.
39. K. Salehi-Ashtiani and J. W. Szostak. In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature, 414:82-84, 2001.
40. M. Sassanfar and J. W. Szostak. An RNA motif that binds ATP. Nature, 364:550-553, 1993.
41. T. Schlick. Molecular Modeling: An Interdisciplinary Guide. Springer-Verlag, New York, NY, 2002.
42. P. Schuster, W. Fontana, P. F. Stadler, and I. L. Hofacker. From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B. Biol. Sci., 255:279-284, 1994.
43. B. A. Shapiro and K. Z. Zhang. Comparing multiple RNA secondary structures using tree comparisons. Comput. Appl. Biosci., 6:309-318, 1990.
44. G. A. Soukup and R. R. Breaker. Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA, 96:3584-3589, 1999.
45. G. A. Soukup and R. R. Breaker. Nucleic acid molecular switches. Trends Biotechnol., 17:469-476, 1999.
46. G. A. Soukup and R. R. Breaker. Allosteric nucleic acid catalysts. Curr. Opin. Struct. Biol., 10:318-325, 2000.
47. S. Spiegelman. An approach to the experimental analysis of precellular evolution. Q. Rev. Biophys., 4:213-253, 1971.
48. G. Storz. An expanding universe of noncoding RNAs. Science, 296:1260-1263, 2002.
49. V. Tereshko, E. Skripkin, and D. J. Patel. Encapsulating streptomycin within a small 40-mer RNA. Chem. Biol., 10:175-187, 2003.
50. I. Tinoco, C. Bustamante. How RNA folds. J. Mol. Biol., 293:271-281, 1999.
51. C. Tuerk and L. Gold. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249:505-510, 1990.
52. S. T. Wallace and R. Schroeder. In vitro selection and characterization of streptomycin-binding RNAs: Recognition discrimination between antibiotics. RNA, 4:112-123, 1998.
53. D. S. Wilson and J. W. Szostak. In vitro selection of functional nucleic acids. Ann. Rev. Biochem., 68:611-647, 1999.
54. W. Winkler, A. Nahvi, and R. R. Breaker. Thiamine derivatives bind messenger RNAs directly to regulate bacterial expression. Nature, 419:952-956, 2002.
55. W. C. Winkler, S. Cohen-Chalamish, and R. R. Breaker. An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. USA, 99:15908-15913, 2002.
56. M. Zuker, D. H. Mathews, and D. H. Turner. Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In J. Barciszewski and B. F. C. Clark, editors, RNA Biochemistry and Biotechnology, NATO ASI Series, pages 11-43. Klewer Academic Publishers, Dordrecht, NL, 1999.