A geometrical approach in folding a pseudoknot motif within the e. coli 16s-rna

Journal of Biomolecular Structure and Dynamics

Volumn 14, Issue 2, 1996, Pages 153-161

  Tung, Chang Shung ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARTICLE; BASE PAIRING; ESCHERICHIA COLI; GEOMETRY; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; STEREOCHEMISTRY; STRUCTURE ANALYSIS;

ESCHERICHIA COLI;

EID: 0029907278     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1996.10508104     Document Type: Article

References (31)

1. Cech, T. R., 1993. Biochemical Society Transactions, 21:229–234. Catalytic RNA:Structure and mechanism
2. Zaug, A. J., and Cech, T. R., 1986. Science, 231:470–475. The intervening sequence RNA of tetrahymena is an enzyme
3. Zaug, A. J., Been, M. D., and Cech, T. R., 1986. Nature, 324:429–433. The tetrahymena ribozyme acts like an RNA restriction endonuclease
4. Zaug, A. J., Grosshans, C. A., and Cech, T. R., 1988. Biochem., 27 Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme-enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme substrate complexes., 8924–8931
5. Jenison, R. D., Gill, S. C., Pardi, A., and Polisky, B., 1994. Science, 263:1425–1429. High-resolution molecular discrimination by RNA
6. Jellinek, D., Lynott, C. K., Bifkin, D. B., and Janjic, N., 1993. Proc. Natl. Acad. Sci. USA, 90:11227–11231. High-affinity RNA ligands to basic fibroblast growth factor inhibit receptor binding
7. Tuerk, C., MacDougal, S., and Gold, L., 1992. Proc. Natl. Acad. Sci. USA, 89:6988–6992. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase
8. Schneider, D., Tuerk, C., and Gold, L., 1992. Selection of high affinity RNA igands to the bac teriophage R17 coat protein. J. Mol. Biol., 225:862–869.
9. Connell, G. J., Illangesekare, M., and Yarns, M., 1993. Biochem., 32:5497–5502. 3 small ribooligonucleotides with specific arginine sites
10. Tuerk, C., and Gold, L., 1990. Science, 249:505–510. Systematic evolution of ligands by exponential enrichment:RNA lig ands to bacteriophage T4 DNA Polymerase
11. Sussman, J. L., Holbrook, S. R., Warrant, R. W., Church, G. M., and Kim, S., 1978. J. Mol.Biol., 123:607–630. H. Crystal structure of yeast phenylalanine t-RNA. (I):Crystallographic refinement
12. Comarmond, M. B., Giege, R., Thierry, J. C., Moras, D., and Fischer, J., 1986. Acta Crystallogr., Sect.B, 42:272–280. 3-dimensionaI structure of yeast transfer RNAasp (I):Structure determination
13. Puglisi, J. D., Wyatt, J. R., and Tinoco, I., Jr. 1990. J. Mol. Biol., 214:437–453. a). Conformation of an RNA pseudoknot
14. Puglisi, J. D., Wyatt, J. R., and Tinoco, I., Jr. 1990. Biochem., 29:4215–4226. b). Solution Conformation of an RNA hairpin loop
15. Malhotra, A., and Harvey, S. C., 1994. J. Mol. Biol., 240:308–340. A quantitative model of the escherichia coli 16S RNA in the 30S ribosomal subunit
16. Major, F., Turcotte, M., Gautheret, D., Lapalme, G., Fillion, m. E., and Cedergren, R., 1991. Science, 253:1255–1260. The combination of Symbolic and Numerical Computation for Three-Dimensional Modeling of RNA
17. Erie, D. A., Suri, A. K., Breslauer, K. J., Jones, R. A., and Olson, W. K., 1993. Biochemistry, 32:436–454. Theoretical pre dictions of DNA hairpin loop conformation:correlations with thermodynamic and spectroscopic data
18. Westhof, E., 1993. J. Mol. Str., 286:203–210. Modelling the three-dimensional structure of ribonucleic acids
19. Gutell, R. R., Larsen, N., and Woese, C. R., 1994. Microbiological Reviews, Lessons from an evolving rRNA:16S and 23S rRNA structures from a comparative perspective. 10–26
20. Gutell, R. R., Weiser, B., Woese, C. R., and Noller, H. F., 1985. Mol. Biol., 32:155–216. Comparative anatomy of 16S-like ribosomal RNA. Prog. Nucleic Acid Res
21. Gutell, R. R., and Woese, C. R., 1990. Proc. Natl. Acad. Aci. USA, 87:663–667. Higher order structural elements in ribosomal RNAs:pseu do-knots and the use of non-canonical pairs
22. Moazed, D., and Noller, H. F., 1986. Cell, 47:985–994. Transfer-RNA shields specific nucleotides in 16S ribosomal- RNA from attack by chemical probes
23. Stern, S., Weiser, B., and Noller, H. F., 1988. J. Mol. Biol., 204:447–481. Model for the 3-dimensional folding of 16-S ribo somal-RNA
24. Arnott, S., and Hukins, D. W.L., 1972. Biochem. Biophys. Res. Commun., 47:4141–4155. Confromational parameters (with estimated standard deviations) for A- and B-DNA
25. Pleij, C. W.A., Rietveld, K., and Bosch, L., 1985. Nucleic Acids Res., 13:1717–1731. A new principle of RNA folding based on pseudoknotting
26. Tung, C.-S., 1993. Computation of Biomolecular Structures:Achievements, Problems, and Perspectives Edited by:Soumpasis, D. M., and Jovin, T. M., New York:Springer Verlag.
27. Goldstein, H., 1959. Classical Mechanics Reading, MA:Addison-Wesley.
28. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H., and Teller, E., 1953. Chem. Phys., 21:1087–1092. Equation of state calculations by fast computing machines. J
29. Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Profeta, S., Jr and Weiner, P., 1984. J. Am. Chem. Soc., 106:765–784. A new force field for molecular mechanical simulation of nucleic acids and proteins
30. Tung, C.-S., and Carter, E. S., II. 1994. CABIOS, 10:427–433. Nucleic acid modeling tool (NAMOT):an interactive graphic tool for modeling nucleic acid structures
31. Richmond, T. J., Finch, J. T., Klug, A., Rhodes, D., and Rushton, B., 1984. Nature, 311:532–537. Structure of the nucle osome core particle at 7A resolution