Design of multistable RNA molecules

RNA

Volumn 7, Issue 2, 2001, Pages 254-265

  Flamm, Christoph ^a   Hofacker, Ivo L ^a   Maurer Stroh, Sebastian ^a   Stadler, Peter F ^a,b   Zehl, Martin ^a  

^a UNIVERSITY OF VIENNA   (Austria)

^b SANTA FE INSTITUTE   (United States)

Author keywords

RNA folding; RNA secondary structure prediction; RNA switches; Sequence design

Indexed keywords

RNA;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DRUG DESIGN; HEAT; MATHEMATICS; METABOLISM; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA STABILITY;

BASE PAIRING; BASE SEQUENCE; COMPUTER SIMULATION; DRUG DESIGN; HEAT; MATHEMATICS; MODELS, MOLECULAR; MUTATION; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA; RNA STABILITY;

EID: 0035257394     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838201000863     Document Type: Article

References (47)

1. Ancel LW, Fontana W. 2000. Plasticity, evolvability and modularity in RNA. J Exp Zool (Mol Dev Evol) 288:242-283.
2. Babitzke P, Yanofsky C. 1993. Reconstitution of Bacillus subtilis Trp attenuation in vitro with TRAP, the Trp RNA-binding attenuation protein. Proc Natl Acad Sci USA 90:133-137.
3. Baumstark T, Schroder AR, Riesner D. 1997. Viroid processing: Switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation. EMBO J 16:599-610.
4. Biebricher CK, Diekmann S, Luce R. 1982. Structural analysis of self-replicating RNA synthesized by Qβ replicase. J Mol Biol 754:629-648.
5. Biebricher CK, Luce R. 1992. In vitro recombination and terminal elongation of RNA by Qβ replicase. EMBO J 11:5129-5135.
6. Brion P, Westhof E. 1997. Hierarchy and dynamics of RNA folding. Annu Rev Biophys Biomol Struct 26:113-137.
7. Emerick VL, Woodson SA. 1993. Self-splicing of the Tetrahymena pre-rRNA is decreased by misfolding during transcription. Biochemistry 32:14062-14067.
8. Fayat G, Mayaux FJ, Sacerdot C, Fromant M, Springer M, Grunberg-Manago M, Blanquet S. 1983. Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20. J Mol Biol 171:239-261.
9. Flamm C, Fontana W, Hofacker I, Schuster P. 2000. RNA folding kinetics at elementary step resolution. RNA 6:325-338.
10. Fontana W, Konings DAM, Stadler PF, Schuster P. 1993a. Statistics of RNA secondary structures. Biopolymers 33:1389-1404.
11. Fontana W, Stadler PF, Bornberg-Bauer EG, Griesmacher T, Hofacker IL, Tacker M, Tarazona P, Weinberger ED, Schuster P. 1993b. RNA folding and combinatory landscapes. Phys Rev E 47:2083-2099.
12. Fresco JR, Adains A, Ascione R, Henley D, Lindahl T. 1966. Tertiary structure in transfer ribonucleic acids. Cold Spring Harbor Symp Quant Biol 37:527-539.
13. Giegerich R, Haase D, Rehmsmeier M. 1999. Prediction and visualization of structural switches in RNA. In: Altman RB, Dunker AK, Hunter L, Klein TE, eds. Proceedings of the Pacific Symposium on Biocomputing, vol 4. Singapore: World Scientific Press. pp 126-137.
14. Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler PF, Schuster P. 1996a. Analysis of RNA sequence structure maps by exhaustive enumeration. I. Neutral networks. Monath Chem 127:355-374.
15. Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadier PF,Schuster P. 1996b. Analysis of RNA sequence structure maps by exhaustive enumeration. II. Structures of neutral networks and shape space covering. Monath Chem 127:375-389.
16. Gultyaev AP, Batenburg FH, Pleij CW. 1998. Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm. J Mol Biol 276:43-55.
17. Hawkins ER, Chang SH, Mattice WL. 1977. Kinetics of the renaturation of yeast tRNALeu3. Biopolymers 76:1557-1566.
18. Hecker R, Wang ZM, Steger G, Riesner D. 1988. Analysis of RNA structures by temperature-gradient gel electrophoresis: Viroid replication and processing. Gene 72:59-74.
19. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P. 1994. Fast folding and comparison of RNA secondary structures. Monath Chem 125:167-188.
20. Jaeger JA, Turner DH, Zuker M. 1989. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA 86:7706-7710.
21. Lodmell JS, Dahlberg AE. 1997. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science 277:1262-1267.
22. Loss P, Schmitz M, Steger G, Riesner D. 1991. Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA. EMBO J 10:719-727.
23. Mathews D, Sabina J, Zucker M, Turner H. 1999. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J Mol Biol 288:911-940.
24. McCaskill JS. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105-1119.
25. Morgan SR, Higgs PG. 1998. Barrier heights between ground states in a model of RNA secondary structure. J Phys A 31:3153-3170.
26. Nagel JHA, Gultyaev AP, Derdes K, Pleij CWA. 1999. Metastable structures andrefolding kinetics in hok mRNA of plasmid R1. RNA 5:1408-1419.
27. Pan T, Fang X, Sosnick T. 1998. Pathway modulation, circular permutation and rapid RNA folding under kinetic control. J Mol Biol 256:721-731.
28. Pan T, Thirumalai D, Woodson SA. 1997. Folding of RNA involves parallel pathways. J Mol Biol 273:7-13.
29. Perrotta AT, Been MD. 1998. A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent proactive ribozyme conformation. J Mol Biol 279:361-373.
30. Putzer H, Gendron N, Grunberg-Manago M. 1992. Coordinate expression of the two threonyl-tRNA synthetase genes in Bacillus subtilis: Control by transcriptional antitermination involving a conserved regulatory sequence. EMBO J 11:3117-3127.
31. Reidys C, Stadler PF. 1996. Biomolecular shapes and algebraic structures. Computers & Chem 20:85-94.
32. Reidys CM. 1997. Random induced subgraphs of generalized n-cubes. Adv Appl Math 19:360-377.
33. Reidys CM, Stadler PF, Schuster P. 1997. Generic properties of combinatory maps: Neural networks of RNA secondary structures. Bull Math Biol 59:339-397.
34. Schultes EA, Bartel DP. 2000. One sequence, two ribozymes: Implications for the emergence of new ribozyme folds. Science 289:448-452.
35. Schuster P, Fontana W, Stadler PF, Hofacker IL. 1994. From sequences to shapes and back: A case study in RNA secondary structures. Proc Roy Soc (London) B 255:279-284.
36. Shapiro BA, Zhang K. 1990. Comparing multiple RNA secondary structures using tree comparisons. CABIOS 6:309-318.
37. Soukup GA, Breaker RR. 1999. Engineering precision RNA molecular switches. Proc Natl Acad Sci USA 96:3584-3589.
38. Tinoco I Jr, Bustamante C. 1999. How RNA folds. J Mol Biol 293:271-281.
39. Treiber DK, Rook MS, Zarrinkar PP, Williamson JR. 1998. Kinetic intermediate strapped by native interactions in RNA folding. Science 279:1943-1946.
40. Vertechi AM, Virasoro MA. 1989. Energy barriers in SK spin glass models. J Phys France 50:2325-2332.
41. von Ahsen U. 1998. Translational fidelity: Error-prone versus hyperaccurate ribosomes. Chem Biol 5:R3-R6.
42. Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M. 1994. Co-axial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA 91:9218-9222.
43. Wool IG, Glück A, Endo Y. 1992. Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. Trends Biochem 7:266-269.
44. Wuchty S, Fontana W, Hofacker IL, Schuster P. 1999. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49:145-165.
45. Zamora H, Luce R, Biebricher CK. 1995. Design of artificial short-chained RNA species that are replicated by Qβ replicase. Biochemistry 34:1261-1266.
46. Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.
47. Zuker M, Stiegler P. 1981. Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research 9:133-148.