RNA pseudoknots: Folding and finding

F1000 Biology Reports

Volumn 2, Issue 1, 2010, Pages

  Liu, Biao ^a   Mathews, David H ^b   Turner, Douglas H ^a,b  

^a UNIVERSITY OF ROCHESTER   (United States)

^b UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

COMPUTER PROGRAM; CRYOELECTRON MICROSCOPY; RETROVIRUS; REVIEW; RNA SEQUENCE; RNA STABILITY;

EID: 77955062966     PISSN: 17404118     EISSN: 1757594X     Source Type: Journal    
DOI: 10.3410/B2-8     Document Type: Review

References (61)

1. Brierley I, Pennell S, Gilbert RJ: Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nat Rev Microbiol 2007, 5:598-610. (Pubitemid 47074115)
2. Cornish PV, Hennig M, Giedroc DP: A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc Natl Acad Sci U S A 2005, 102:12694-9. (Pubitemid 41279428)
3. Theimer CA, Blois CA, Feigon J: Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol Cell 2005, 17:671-82.
4. Taufer M, Licon A, Araiza R, Mireles D, van Batenburg FH, Gultyaev AP, Leung MY: PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. Nucleic Acids Res 2009, 37:D127-35.
5. Su L, Chen L, Egli M, Berger JM, Rich A: Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat Struct Biol 1999, 6:285-92. (Pubitemid 29107232)
6. Nixon PL, Rangan A, Kim YG, Rich A, Hoffman DW, Hennig M, Giedroc DP: Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot. J Mol Biol 2002, 322:621-33.
7. Pallan PS, Marshall WS, Harp J, Jewett FC 3rd, Wawrzak Z, Brown BA, 2nd, Rich A, Egli M: Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif. Biochemistry 2005, 44:11315-22. (Pubitemid 41209067)
8. Cornish PV, Stammler SN, Giedroc DP: The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical. RNA 2006, 12:1959-69.
9. Egli M, Minasov G, Su L, Rich A: Metal ions and flexibility in a viral RNA pseudoknot at atomic resolution. Proc Natl Acad Sci U S A 2002, 99:4302-7. (Pubitemid 34285980)
10. Chen G, Chang KY, Chou MY, Bustamante C, Tinoco I Jr: Triplex structures in an RNA pseudoknot enhance mechanical stability and increase efficiency of -1 ribosomal frameshifting. Proc Natl Acad Sci U S A 2009, 106:12706-11.
11. Gilbert SD, Rambo RP, Van Tyne D, Batey RT: Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 2008, 15:177-82.
12. Klein DJ, Edwards TE, Ferre-D'Amare AR: Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobase. Nat Struct Mol Biol 2009, 16:343-4.
13. Spitale RC, Torelli AT, Krucinska J, Bandarian V, Wedekind JE: The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J Biol Chem 2009, 284:11012-6.
14. Klein DJ, Ferre-D'Amare AR: Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 2006, 313:1752-6.
15. Toor N, Keating KS, Taylor SD, Pyle AM: Crystal structure of a self-spliced group II intron. Science 2008, 320:77-82.
16. Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA: Crystal structure of a self-splicing group I intron with both exons. Nature 2004, 430:45-50.
17. Golden BL, Kim H, Chase E: Crystal structure of a phage Twort group I ribozyme-product complex. Nat Struct Mol Biol 2005, 12:82-9. (Pubitemid 40082921)
18. Pfingsten JS, Costantino DA, Kieft JS: Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science 2006, 314:1450-4.
19. Ferre-D'Amare AR, Zhou K, Doudna JA: Crystal structure of a hepatitis delta virus ribozyme. Nature 1998, 395:567-74. (Pubitemid 28475703)
20. Guo F, Gooding AR, Cech TR: Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. Mol Cell 2004, 16:351-62.
21. Cao S, Chen SJ: Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res 2006, 34:2634-52. (Pubitemid 43985627)
22. Cao S, Chen SJ: Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA 2009, 15:696-706.
23. Akutsu T: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Appl Math 2000, 104:45-62.
24. Lyngso RB, Pedersen CN: RNA pseudoknot prediction in energy-based models. J Comput Biol 2000, 7:409-27.
25. van Batenburg FH, Gultyaev AP, Pleij CW: An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J Theor Biol 1995, 174:269-80.
26. Isambert H, Siggia ED: Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Proc Natl Acad Sci U S A 2000, 97:6515-20. (Pubitemid 30412745)
27. Dawson WK, Fujiwara K, Kawai G: Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding. PLoS One 2007, 2:e905.
28. Rivas E, Eddy SR: A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol 1999, 285:2053-68. (Pubitemid 29078170)
29. Reeder J, Giegerich R: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 2004, 5:104.
30. Dirks RM, Pierce NA: A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem 2003, 24:1664-77.
31. Condon A, Davy B, Rastegari B, Zhao S, Tarrant F: Classifying RNA pseudoknotted structures. Theor Comput Sci 2004, 320:35-50.
32. Hart JM, Kennedy SD, Mathews DH, Turner DH: NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc 2008, 130:10233-9.
33. Nixon PL, Giedroc DP: Energetics of a strongly pH dependent RNA tertiary structure in a frameshifting pseudoknot. J Mol Biol 2000, 296:659-71.
34. Theimer CA, Finger LD, Trantirek L, Feigon J: Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA. Proc Natl Acad Sci U S A 2003, 100:449-54.
35. Soto AM, Misra V, Draper DE: Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg2+ ions. Biochemistry 2007, 46:2973-83.
36. Liu B, Shankar N, Turner DH: Fluorescence competition assay measurements of free energy changes for RNA pseudoknots. Biochemistry 2009, [Epub ahead of print].
37. Xia T, SantaLucia J Jr., Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH: Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 1998, 37:14719-35. (Pubitemid 28487580)
38. Hansen TM, Reihani SN, Oddershede LB, Sorensen MA: Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting. Proc Natl Acad Sci U S A 2007, 104:5830-5.
39. Green L, Kim CH, Bustamante C, Tinoco I Jr: Characterization of the mechanical unfolding of RNA pseudoknots. J Mol Biol 2008, 375:511-28. (Pubitemid 350199660)
40. Namy O, Moran SJ, Stuart DI, Gilbert RJ, Brierley I: A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting. Nature 2006, 441:244-7.
41. Cao S, Chen SJ: Predicting ribosomal frameshifting efficiency. Phys Biol 2008, 5:16002.
42. Chen G, Wen JD, Tinoco I: Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA 2007, 13:2175-88. (Pubitemid 350127559)
43. Kim NK, Zhang Q, Zhou J, Theimer CA, Peterson RD, Feigon J: Solution structure and dynamics of the wild-type pseudoknot of human telomerase RNA. J Mol Biol 2008, 384:1249-61.
44. Meyer IM, Miklos I: SimulFold: Simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput Biol 2007, 3:1441-54.
45. Tabaska JE, Cary RB, Gabow HN, Stormo GD: An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics 1998, 14:691-9.
46. Witwer C, Hofacker IL, Stadler PF: Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans Comput Biol Bioinform 2004, 1:66-77.
47. Ren J, Rastegari B, Condon A, Hoos HH: HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA 2005, 11:1494-504. (Pubitemid 41396919)
48. Ruan J, Stormo GD, Zhang W: An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics 2004, 20:58-66. (Pubitemid 38088341)
49. ten Dam E, Brierley I, Inglis S, Pleij C: Identification and analysis of the pseudoknot-containing gag-pro ribosomal frameshift signal of simian retrovirus-1. Nucleic Acids Res 1994, 22:2304-10.
50. ten Dam EB, Verlaan PW, Pleij CW: Analysis of the role of the pseudoknot component in the SRV-1 gag-pro ribosomal frameshift signal: loop lengths and stability of the stem regions. RNA 1995, 1:146-54.
51. Michiels PJ, Versleijen AA, Verlaan PW, Pleij CW, Hilbers CW, Heus HA: Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J Mol Biol 2001, 310:1109-23.
52. Comolli LR, Smirnov I, Xu L, Blackburn EH, James TL: A molecular switch underlies a human telomerase disease. Proc Natl Acad Sci U S A 2002, 99:16998-7003.
53. Chen JL, Greider CW: Functional analysis of the pseudoknot structure in human telomerase RNA. Proc Natl Acad Sci U S A 2005, 102:8080-5; discussion 8077-89.
54. Chen JL, Greider CW: Telomerase RNA structure and function: implications for dyskeratosis congenita. Trends Biochem Sci 2004, 29:183-92.
55. Cao S, Chen SJ: Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity. J Mol Biol 2007, 367:909-24. (Pubitemid 46330371)
56. Kang H, Tinoco I Jr: A mutant RNA pseudoknot that promotes ribosomal frameshifting in mouse mammary tumor virus. Nucleic Acids Res 1997, 25:1943-9. (Pubitemid 27303389)
57. Kang H, Hines JV, Tinoco I Jr: Conformation of a non-frameshifting RNA pseudoknot from mouse mammary tumor virus. J Mol Biol 1996, 259:135-47.
58. Shen LX, Tinoco I Jr: The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus. J Mol Biol 1995, 247:963-78.
59. Kolk MH, van der Graaf M, Fransen CT, Wijmenga SS, Pleij CW, Heus HA, Hilbers CW: Structure of the 30-hairpin of the TYMV pseudoknot: preformation in RNA folding. EMBO J 1998, 17:7498-504.
60. Kolk MH, van der Graaf M, Wijmenga SS, Pleij CW, Heus HA, Hilbers CW: NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA. Science 1998, 280:434-8.
61. Nonin-Lecomte S, Felden B, Dardel F: NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation. Nucleic Acids Res 2006, 34:1847-53.