An examination of coaxial stacking of helical stems in a pseudoknot motif: The gene 32 messenger RNA pseudoknot of bacteriophage T2

RNA

Volumn 5, Issue 2, 1999, Pages 257-271

  Holland, Jason A ^a   Hansen, Mark R ^a,b   Du, Zhihua ^a   Hoffman, David W ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

NMR spectroscopy; RNA pseudoknot; RNA structure

Indexed keywords

ADENOSINE TRIPHOSPHATE; GUANOSINE TRIPHOSPHATE; MESSENGER RNA;

ARTICLE; BACTERIOPHAGE; CARBON NUCLEAR MAGNETIC RESONANCE; CONTROLLED STUDY; ISOTOPE LABELING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; RNA STRUCTURE;

CARBON ISOTOPES; DNA-BINDING PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MYOVIRIDAE; NITROGEN ISOTOPES; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; VIRAL PROTEINS;

UNIDENTIFIED BACTERIOPHAGE;

EID: 0033061281     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299981360     Document Type: Article

References (64)

1. Aboul-ela F, Karn J, Varani G. 1995. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J Mol Biol 253:313-332.
2. Addess K, Basilion JP, Klausner RD, Rouault TA, Pardi A. 1997. Structure and dynamics of the iron responsive element RNA: Implications for binding of the RNA by iron regulatory proteins. J Mol Biol 274:72-83.
3. Allain FH-T, Varani G. 1995. Structure of the P1 helix from group 1 self-splicing introns. J Mol Biol 250:333-353.
4. Arnott S, Hukins DWL, Dover SD. 1972. Optimized parameters for RNA double-helices. Biochem Biophys Res Commun 48:1392-1398.
5. Batey RT, Inada M, Kujawinski E, Puglisi JD, Williamson, JR. 1992. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy. Nucleic Acids Res 20:4515-4523.
6. 1H-detected heteronuclear multiple-bond correlation spectroscopy. J Mag Reson 78:185-191.
7. Benard L, Philippe C, Dondon L, Grunberg-Manago M, Ehresmann B, Ehresmann C, Portier C. 1994. Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli. Mol Microbiol 14:31-40.
8. Brünger AT. 1993. X-PLOR version 3.1: A system for X-ray crystallography and NMR. New Haven, Connecticut: Yale University Press.
9. 15N-labeled nucleotides. J Mag Reson 29:45-63.
10. Chen X, Chamorro M, Lee SI, Shen LX, Hines JV, Tinoco I, Varmus HE. 1995. Structural and functional studies of retroviral RNA pseudoknots involved in ribosomal frameshifting: Nucleotides at the junction of the two stems are important for efficient ribosomal frameshifting. EMBO J 14:842-852.
11. Chen X, Kang H, Shen LX, Chamorro M, Varmus HE, Tinoco I. 1996. A characteristic bent conformation of RNA pseudoknots promotes -1 frameshifting during translation of retroviral RNA. J Mol Biol 260:479-483.
12. Deckman IC, Draper DE. 1987. S4-alpha mRNA translation regulation complex. II. Secondary structures of the RNA regulatory site in the presence and absence of S4. J Mol Biol 196:323-332.
13. Dieckmann T, Feigon J. 1997. Assignment methodology for larger RNA oligonucleotides: Application to an ATP-binding RNA aptamer. J Biomol NMR 9:259-72.
14. Du Z, Giedroc DP, Hoffman DW. 1996. Structure of the autoregulatory pseudoknot within the gene 32 messenger RNA of bacteriophages T2 and T6: A model for a family of structurally related RNA pseudoknots. Biochemistry 35:4187-4198.
15. Du Z, Hoffman DW. 1997. An NMR and mutational study of the pseudoknot within the gene 32 mRNA of bacteriophage T2: Insights into a family of structurally related RNA pseudoknots. Nucleic Acids Res 25:1130-1135.
16. Du Z, Holland JA, Hansen MR, Giedroc DP, Hoffman DW. 1997. Base-pairings within the RNA pseudoknot associated with the Simian Retrovirus-1 gag-pro frameshift site. J Mol Biol 271:463-470.
17. 13C magnetization transfer by isotropic mixing. Spin system identification in large proteins. J Amer Chem Soc 112:885-888.
18. 6MeG•C base pair. J Amer Chem Soc 115:12607-12608.
19. 1-labeled deoxyadenosine. J Amer Chem Soc 109:3169-3171.
20. Gluick TC, Wills NM, Gesteland R, Draper DE. 1997. Folding of an mRNA pseudoknot required for stop codon readthrough: Effects of mono-and divalent cations on stability. Biochemistry 36:16173-16186.
21. Phe. J Mol Biol 124:523-534.
22. Hoffman DW, Holland JA. 1995. Preparation of carbon-13 labeled ribonucleotides using acetate as an isotope source. Nucleic Acids Res 23:3361-3362.
23. Hoffman DW, White SW. 1995. The RNA stem-loop of the transactivation response (TAR) element of equine infectious anemia virus. Nucleic Acids Res 23:4058-4065.
24. James TL, James JL, Lapidot A. 1981. Structure and dynamic information about double-stranded DNA from nitrogen-15 NMR spectroscopy. J Amer Chem Soc 103:6748-6750.
25. Jiang F, Kumar RA, Jones RA, Patel DJ. 1996. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382:183-186.
26. Kay LE, Ikura M, Bax A. 1990. Proton-proton correlation via carbon-carbon couplings: A three-dimensional NMR approach for the assignment of aliphatic resonances in proteins labeled with carbon-13. J Amer Chem Soc 112:888-889.
27. Kolk MH, van der Graaf M, Wijmenga SS, Pleij CWA, Heus HA, Hilbers CW. 1998. NMR structure of a classical pseudoknot: Interplay of single-and double-stranded RNA. Science 280:433-438.
28. 15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: Application to interleukin-1 beta. Biochemistry 23:6150-6156.
29. Markowski V, Sullivan GR, Roberts JD. 1977. Nitrogen-15 nuclear magnetic resonance spectroscopy of some nucleosides and nucleotides. J Amer Chem Soc 99:713-718.
30. McPheeters DS, Stormo GD, Gold L. 1988. Autogenous regulatory site on the bacteriophage T4 gene 32 messenger RNA. J Mol Biol 201:517-535.
31. Michnicka MJ, Harper JW, King GC. 1993. Selective isotopic enrichment of synthetic RNA: Application to the HIV-1 TAR element. Biochemistry 32:395-400.
32. 15N labelled RNAs for heteronuclear multi-dimensional NMR studies. Nucleic Acids Res 20:4507-4513.
33. Pardi A. 1995. Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA. Methods Enzymol 261:350-80.
34. Philippe C, Bénard L, Portier C, Westhof E, Ehresmann B, Ehresmann C. 1995. Molecular dissection of the pseudoknot governing the translational regulation of E. coli ribosomal protein S15. Nucleic Acids Res 23:18-28.
35. Plateau P, Guéron M. 1982. Exchangeable proton NMR without line distortion. J Am Chem Soc 104:7310-7311.
36. Pleij CWA. 1994. RNA pseudoknots. Curr Opin Struc Biol 4:337-344.
37. Pleij CWA, Rietveld K, Bosch L. 1985. A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res 13:1717-1731.
38. Pley HW, Flaherty KM, McKay DB. 1994. Three dimensional structure of a hammerhead ribozyme. Nature 372:68-74.
39. Portier C, Philippe C, Dondon L, Grunberg-Manago M, Ebel JP, Ehresmann B, Ehresmann C. 1990. Translational control of ribosomal protein S15. Biochim Biophys Acta 1050:328-336.
40. Puglisi JD, Wyatt JR, Tinoco I. 1990. Conformation of an RNA pseudoknot. J Mol Biol 214:437-453.
41. Qiu H, Kaluarachchi K, Du Z, Hoffman DW, Giedroc DP. 1996. Thermodynamics of folding of the RNA pseudoknot of the T4 gene 32 autoregulatory mRNA. Biochemistry 35:4175-4186.
42. Rietveld K, Pleij CWA, Bosch L. 1983. Three-dimensional models of the tRNA-like 3′ termini of some plant viral RNAs. EMBO J 2:1079-1085.
43. Saenger W. 1984. Principles of nucleic acid structure. New York: Springer-Verlag.
44. Santoro J, King G. 1992. A constant-time 2D Overbodenhausen experiment for inverse correlation of isotopically enriched species. J Mag Reson 97:202-207.
45. Shen LX, Tinoco I. 1995. The structure of an RNA pseudoknot that causes efficient frameshifting in mouse mammary tumor virus. J Mol Biol 247:963-978.
46. 15N HSQC experiments. J Biomol NMR 4:117-122.
47. Sussman JL, Holbrook SR, Warrant RW, Church GM, Kim S-H. 1978. Restrained refinement of the structure of yeast tRNAPhe. J Mol Biol 123:607-630.
48. Tang CK, Draper DE. 1989. Unusual mRNA pseudoknot structure is recognized by a protein translational repressor. Cell 57:531-536.
49. ten Dam EB, Brierley I, Inglis S, Pleij CWA. 1994. Identification and analysis of the pseudoknot-containing gag-pro ribosomal frameshift signal of simian retrovirus-1. Nucleic Acids Res 22:2303-2310.
50. ten Dam EB, Pleij CWA, Bosch L. 1990. RNA pseudoknots: Translational frameshifting and readthrough on viral RNAs. Viral Genes 4:121-136.
51. ten Dam EB, Pleij CWA, Draper, D. 1992. Structural and functional aspects of RNA pseudoknots. Biochemistry 37:11665-11676.
52. ten Dam EB, Verlaan PWG, Pleij CWA. 1995. Analysis of the role of the pseudoknot component in the SRV-1 gag-pol ribosomal frameshift signal: Loop lengths and stability of the stem regions. RNA 1:145-154.
53. Theimer CA, Wang Y, Hoffman DW, Krisch HM, Giedroc DP. 1998. Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot. J Mol Biol 279:545-564.
54. 1H correlated experiments. J Amer Chem Soc 113:9349-9352.
55. Varani G, Aboul-ela F, Allain FH. 1996. NMR investigations of RNA structure. Prog NMR Spectr 29:51-127.
56. Voet D, Rich A. 1970. The crystal structures of purines, pyrimidines, and their intermolecular complexes. Prog Nucleic Acid Res Mol Biol 10:183-265.
57. Vuister GW, Boelens R, Kaptein R. 1988. Non-selective three-dimensional NMR spectroscopy. The 3D NOE-HOHAHA experiment. J Mag Reson 80:175-185.
58. Wang C, Gao X, Jones RA. 1991. Nitrogen-15 labeled oligonucleotides. 2. Solvent isotope effects on the chemical shift of the adenine N1 in an A-T base pair. J Amer Chem Soc 113:1448-1450.
59. Westhof E, Dumas P, Moras D. 1988. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallogr A 44:112-123.
60. Wijmenga SS, van Buuren BNM. 1998. The use of NMR methods for conformational studies of nucleic acids. Prog NMR Spectr 32:287-387.
61. Wills NM, Gesteland RF, Atkins JF. 1991. Evidence that a downstream pseudoknot is required for translational read-through of the Moloney murine leukemia virus gag stop codon. Proc Natl Acad Sci USA 88:6991-6995.
62. Wills NM, Gesteland RF, Atkins JF. 1994. Pseudoknot-dependent read-through of retroviral gag termination codons: Importance of sequences in the spacer and loop 2. EMBO J 13:4137-4144.
63. 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6:135-140.
64. Zuiderweg ERP, Fesik SW. 1989. Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a. Biochemistry 28:2387-2391.