Predicting structures and stabilities for H-type pseudoknots with interhelix loops

RNA

Volumn 15, Issue 4, 2009, Pages 696-706

  Cao, S ^a   Chen, Shi Jie ^a  

^a UNIVERSITY OF MISSOURI   (United States)

Author keywords

Folding thermodynamics; Interhelix loop; RNA folding; RNA pseudoknot; Structural predictions

Indexed keywords

ARTICLE; CONFORMATION; ENTROPY; PRIORITY JOURNAL; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; ENTROPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RETROELEMENTS; RNA;

EID: 62549128665     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1429009     Document Type: Article

References (83)

1. Arnott, S. and Hukins, D.W.L. 1972. Optimized parameters for RNA double-helices. Biochem. Biophys. Res. Commun. 48: 1392-1399.
2. Bon, M., Vernizzi, G., Orland, H., and Zee, A. 2008. Topological classification of RNA structures. J. Mol. Biol. 379: 900-911.
3. Brierley, I., Digard, P., and Inglis, S.C. 1989. Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot. Cell 57: 537-547.
4. Brierley, I., Pennell, S., and Gilbert, R.J.C. 2007. Viral RNA pseudo- knots: Versatile motifs in gene expression and replication. Nat. Rev. Microbiol. 5: 598-610.
5. Brierley, I., Gilbert, R.J.C., and Pennell, S. 2008. RNA pseudoknots and the regulation of protein synthesis. Biochem. Soc. Trans. 36: 684-689.
6. Burke, D.H., Scates, L., Andrews, K., and Gold, L. 1996. Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. J. Mol. Biol. 264: 650-666.
7. Cao, S. and Chen, S.-J. 2005. Predicting RNA folding thermodynamics with a reduced chain representation model. RNA 11: 1884-1897.
8. Cao, S. and Chen, S.-J. 2006a. Free-energy landscapes of RNA/RNA complexes: With applications to snRNA complexes in spliceo-somes. J. Mol. Biol. 357: 292-312.
9. Cao, S. and Chen, S.-J. 2006b. Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res. 34: 2634-2652.
10. Cao, S. and Chen, S.-J. 2008. Predicting ribosomal frameshifting efficiency. Phys. Biol. 5: 016002. doi: 10.1088/1478-3975/5/1/ 016002.
11. Chen, S.-J. 2008. RNA folding: Conformational statistics, folding kinetics, and ion electrostatics. Annu. Rev. Biophys. 37: 197-214.
12. Chen, S.-J. and Dill, K.A. 2000. RNA folding energy landscapes. Proc. Natl. Acad. Sci. 97: 646-651.
13. Chen, X.Y., Kang, H.S., Shen, L.X., Chamorro, M., Varmus, H.E., and Tinoco Jr., I. 1996. A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA. J. Mol. Biol. 260: 479-483.
14. Chen, J.L., Blasco, M.A., and Greider, C.W. 2000. Secondary structure of vertebrate telomerase RNA. Cell 100: 503-514.
15. Chen, X., He, S., Zhang, F., Wang, Z., Chen, R., and Gao, W. 2008. FlexStem: Improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinformatics 24: 1994-2001.
16. Chu, V.B. and Herschlag, D. 2008. Unwinding RNA's secrets: Advances in the biology, physics, and modeling of complex RNAs. Curr. Opin. Struct. Biol. 18: 305-314.
17. Comolli, L.R., Smirnov, I., Xu, L., Blackburn, E.H., and James, T.L. 2002. A molecular switch underlies a human telomerase disease. Proc. Natl. Acad. Sci. 99: 16998-17003.
18. Cornish, P.V., Hennig, M., and Giedroc, D.P. 2005. A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc. Natl. Acad. Sci. 102: 12694-12699.
19. Christensen, S.M., Ye, J.Q., and Eickbush, T.H. 2006. RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site. Proc. Natl. Acad. Sci. 103:17602-17607.
20. Deiman, B.A., Kortlever, R.M., and Pleij, C.W. 1997. The role of the pseudoknot at the 3′end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA poly-merase. J. Virol. 71: 5990-5996.
21. Ding, Y. 2006. Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 12: 323-331.
22. Dirks, R.M. and Pierce, N.A. 2003. A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem. 24: 1664-1677.
23. Duarte, C.M. and Pyle, A.M. 1998. Stepping through an RNA structure: A novel approach to conformational analysis. J. Mol. Biol. 284: 1465-1478.
24. Ferré-D'Amaré, A.R., Zhou, K.H., and Doudna, J.A. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395: 567-574.
25. Flory, P.J. 1969. Statistical mechanics of chain molecules. Wiley, New York.
26. Giedroc, D.P. and Cornish, P.V. 2008. Frameshifting RNA pseudo- knots: Structure and mechanism. Virus Res. (in press). doi: 10.1016/j.virusres. 2008.06.008.
27. Giedroc, D.P., Theimer, C.A., and Nixon, P.L. 2000. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J. Mol. Biol. 298: 167-185.
28. Gultyaev, A.P., van Batenburg, F.H.D., and Pleij, C.W.A. 1995. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250: 37-51.
29. Gultyaev, A.P., Van Batenburg, F.H.D., and Pleij, C.W.A. 1999. An approximation of loop free-energy values of RNA H-pseudoknots. RNA 5: 609-617.
30. Hansen, T.M., Reihani, S.N.S., Oddershede, L.B., and Sørensen, M.A. 2007. Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting. Proc. Natl. Acad. Sci. 104: 5830-5835.
31. Hart, J.M., Kennedy, S.D., Mathews, D.H., and Turner, D.H. 2008. NMR-assisted prediction of RNA secondary structure: Identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J. Am. Chem. Soc. 130: 10233-10239.
32. Held, D.M., Kissel, J.D., Saran, D., Michalowski, D., and Burke, D.H. 2006a. Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication. J. Biol. Chem. 281: 25712-25722.
33. Held, D.M., Kissel, J.D., Patterson, J.T., Nickens, D.G., and Burke, D.H. 2006b. HIV-1 inactivation by nucleic acid aptamers. Front. Biosci. 11: 89-112.
34. Hofacker, I.L. 2003. Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429-3431.
35. Huang, X. and Ali, H. 2007. High sensitivity RNA pseudoknot prediction. Nucleic Acids Res. 35: 656-663.
36. Isambert, H. and Siggia, E.D. 2000. Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme. Proc. Natl. Acad. Sci. 97: 6515-6520.
37. Jabbari, H., Condon, A., and Zhao, S. 2008. Novel and efficient RNA secondary structure prediction using hierarchical folding. J. Comput. Biol. 15: 139-163.
38. Jossinet, F., Ludwig, T.E., and Westhof, E. 2007. RNA structure: Bioinformatic analysis. Curr. Opin. Microbiol. 10: 279-285.
39. Kopeikin, Z. and Chen, S.J. 2006. Folding thermodynamics of pseudoknotted chain conformations. J. Chem. Phys. 124: 154903. doi: 10.1063/1.2188940.
40. Li, P.T.X., Vieregg, J., and Tinoco Jr., I. 2008. How RNA unfolds and refolds. Annu. Rev. Biochem. 77: 77-100.
41. Mathews, D.H. and Turner, D.H. 2006. Prediction of RNA secondary structure by free-energy minimization. Curr. Opin. Struct. Biol. 16: 270-278.
42. Mathews, D.H., Sabina, J., Zuker, M., and Turner, D.H. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288: 911-940.
43. McCaskill, J.S. 1990. The equilibrium partition function and base-pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
44. Metzler, D. and Nebel, M.E. 2008. Predicting RNA secondary structures with pseudoknots by MCMC sampling. J. Math. Biol. 56: 161-181.
45. Michiels, P.J.A., Versleijen, A.A.M., Verlaan, P.W., Pleij, C.W.A., Hilbers, C.W., and Heus, H.A. 2001. Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol. 310: 1109-1123.
46. Murray, L.J., Arendall III., W.B., Richardson, D.C., and Richardson, J.S. 2003. RNA backbone is rotameric. Proc. Natl. Acad. Sci. 100: 13904-13909.
47. Murthy, V.L., Srinivasan, R., Draper, D.E., and Rose, G.D. 1999. A complete conformational map for RNA. J. Mol. Biol. 291: 313-327.
48. Namy, O., Moran, S.J., Stuart, D.I., Gilbert, R.J., and Brierley, I. 2006. A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting. Nature 441: 244-247.
49. Nussinov, R. and Jacobson, A.B. 1980. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc. Natl. Acad. Sci. 77: 6909-6913.
50. Nussinov, R., Pieczenik, G., Griggs, J., and Kleitman, D. 1978. Algorithms for loop matchings. SIAM Rev. Soc. Ind. Appl. Math. 35: 68-82.
51. Olson, W.K. 1980. Configurational statistics ofpolynucleotide chains: An updated virtual bond model to treat effects of base stacking. Macromolecules 13: 721-728.
52. Olson, W.K. and Flory, P.J. 1972. Spatial configurations of poly- nucleotide chains. I, Steric interactions in polyribonucleotides: A virtual bond model. Biopolymers 11: 1-23.
53. Pennell, S., Manktelow, E., Flatt, A., Kelly, G., Smerdon, S.J., and Brierley, I. 2008. The stimulatory RNA of the Visna-Maedi retrovirus ribosomal frameshifting signal is an unusual pseudo- knot with an interstem element. RNA 14: 1366-1377.
54. Perrotta, A.T. and Been, M.D. 1991. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta-virus RNA. Nature 350: 434-436.
55. Plant, E.P., Jacobs, K.L., Harger, J.W., Meskauskas, A., Jacobs, J.L., Baxter, J.L., Petrov, A.N., and Dinman, J.D. 2003. The 9 A solution: How mRNA pseudoknots promote efficient programmed - 1 ribosomal frameshifting. RNA 9: 168-174.
56. Reeder, J. and Giegerich, R. 2004. Design, implementation, and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5: 104. doi: 10.1186/1471-2105-5-104.
57. Reeder, J., Hochsmann, M., Rehmsmeier, M., Voss, B., and Giegerich, R. 2006. Beyond Mfold: Recent advances in RNA bioinformatics. J. Biotechnol. 124: 41-55.
58. Ren, J., Rastegari, B., Condon, A., and Hoos, H.H. 2005. HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. RNA 11: 1494-1504.
59. Richardson, J.S., Schneider, B., Murray, L.W., Kapral, G.J., Immormino, R.M., Headd, J.J., Richardson, D.C., Ham, D., Hershkovits, E., Williams, L.D., et al. 2008. RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA 14: 465-481.
60. Rivas, E. and Eddy, S.R. 1999. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285: 2053-2068.
61. Ruan, J., Stormo, G.D., and Zhang, W. 2004. An iterated loop matching approach to the prediction ofRNA secondary structures with pseudoknots. Bioinformatics 20: 58-66.
62. Schultes, E.A. and Bartel, D.P. 2000. One sequence, two ribozymes: Implications for the emergence of new ribozyme folds. Science 289: 448-452.
63. Schuster, P. 2006. Prediction of RNA secondary structures: From theory to models and real molecules. Rep. Prog. Phys. 69: 1419-1477.
64. Serra, M.J. and Turner, D.H. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol. 259: 242-261.
65. Shapiro, B.A., Yingling, Y.G., Kasprzak, W., and Bindewald, E. 2007. Bridging the gap in RNA structure prediction. Curr. Opin. Struct. Biol. 17: 157-165.
66. Somogyi, P., Jenner, A.J., Brierley, I., and Inglis, S.C. 1993. Ribosomal pausing during translation of an RNA pseudoknot. Mol. Cell. Biol. 13: 6931-6940.
67. Sperschneider, J. and Datta, A. 2008. KnotSeeker: Heuristic pseudo- knot detection in long RNA sequences. RNA 14: 630-640.
68. Staple, D.W. and Butcher, S.E. 2005. Pseudoknots: RNA structures with diverse functions. PLoS Biol. 3: e213. doi: 10.1371/journal.-pbio. 0030213.
69. Su, L., Chen, L., Egli, M., Berger, J.M., and Rich, A. 1999. Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat. Struct. Biol. 6: 285-292.
70. Tan, Z.J. and Chen, S.-J. 2008. Salt dependence ofnucleic acid hairpin stability. Biophys. J. 95: 738-752.
71. Tanner, N.K., Schaff, S., Thill, G., Petitkoskas, E., Craindenoyelle, A.M., and Westhof, E. 1994. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses. Curr. Biol. 4: 488-498.
72. ten Dam, E., Verlaan, P.W.G., and Pleij, C.W.A. 1995. Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribo- somal frameshift signal: Loop lengths and stability of the stem regions. RNA 1: 146-154.
73. Theimer, C.A., Blois, C.A., and Feigon, J. 2005. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol. Cell 17: 671-682.
74. Tuerk, C., MacDougal, S., and Gold, L. 1992. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcrip-tase. Proc. Natl. Acad. Sci. 89: 6988-6992.
75. van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A., Ng, J., and Oliehoek, J. 2000. Pseudobase: A database with RNA pseudoknots. Nucleic Acids Res. 28: 201-204.
76. van Belkum, A., Abrahams, J., Pleij, C., and Bosch, L. 1985. Five pseudoknots are present at the 204 nucleotides long 3' noncoding region of tobacco mosaic virus RNA. Nucleic Acids Res. 13: 7673-7686.
77. Wadley, L.M., Keating, K.S., Duarte, C.M., and Plye, A.M. 2007. Evaluating and learning from RNA pseudotorsional space: Quantitative validation of a reduced representation for RNA structure. J. Mol. Biol. 372: 942-957.
78. Walter, A.E. and Turner, D.H. 1994. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry 33: 12715-12719.
79. Williams Jr., A.L. and Tinoco Jr., I. 1986. A dynamic programming algorithm for finding alternative RNA secondary structures. Nucleic Acids Res. 14: 299-315.
80. Zhang, W.B. and Chen, S.J. 2001. A three-dimensional statistical mechanical model of folding double-stranded chain molecules. J. Chem. Phys. 114: 7669-7681.
81. Zhang, J., Lin, M., Chen, R., Wang, W., and Liang, J. 2008. Discrete state model and accurate estimation of loop entropy of RNA secondary structures. J. Chem. Phys. 128: 125107. doi: 10.1063/1.2895050.
82. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.
83. Zwieb, C., Wower, I., and Wower, J. 1999. Comparative sequence analysis of tmRNA. Nucleic Acids Res. 27: 2063-2071.