NMR structure of a classical pseudoknot: Interplay of single- and double-stranded RNA

Science

Volumn 280, Issue 5362, 1998, Pages 434-438

  Kolk, Michaël H ^a   Van Der Graaf, Marinette ^a,b   Wijmenga, Sybren S ^a,c   Pleij, Cornelis W A ^a,d   Heus, Hans A ^a   Hilbers, Cornelis W ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c UMEÅ UNIVERSITY   (Sweden)

^d LEIDEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; TRANSFER RNA;

ALPHA HELIX; ARTICLE; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; RNA CONFORMATION; TURNIP YELLOW MOSAIC VIRUS;

AMINO ACYL-TRNA SYNTHETASES; BINDING SITES; DIETHYL PYROCARBONATE; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MUTATION; NUCLEIC ACID CONFORMATION; RNA, DOUBLE-STRANDED; RNA, TRANSFER; RNA, VIRAL; TYMOVIRUS;

BRASSICA RAPA SUBSP. RAPA; TURNIP YELLOW MOSAIC VIRUS;

EID: 0032540504     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.280.5362.434     Document Type: Article

References (46)

1. E. ten Dam, C. W. A. Pleij, D. Draper, Biochemistry 31, 1665 (1992); C. W. A. Pleij, Curr. Opin. Struct. Biol. 4, 337 (1994).
2. E. ten Dam, C. W. A. Pleij, D. Draper, Biochemistry 31, 1665 (1992); C. W. A. Pleij, Curr. Opin. Struct. Biol. 4, 337 (1994).
3. J. D. Puglisi, J. R. Wyatt, I. Tinoco Jr., J. Mol. Biol. 214, 437 (1990).
4. L. X. Shen and I. Tinoco Jr., ibid. 247, 963 (1995).
5. Z. Du, D. Giedroc, D. Hoffman, Biochemistry 35, 4187 (1996).
6. M. Pinck, P. Yot, F. Chapeville, H. M. Duranton, Nature 226, 954 (1970); P. Yot, M. Pinck, A. L. Haenni, H. M. Duranton, F. Chapeville, Proc. Natl. Acad. Sci. U.S.A. 67, 1345 (1970).
7. M. Pinck, P. Yot, F. Chapeville, H. M. Duranton, Nature 226, 954 (1970); P. Yot, M. Pinck, A. L. Haenni, H. M. Duranton, F. Chapeville, Proc. Natl. Acad. Sci. U.S.A. 67, 1345 (1970).
8. K. Rietveld, R. Van Poelgeest, C. W. A. Pleij, J. H. Van Boom, L. Bosch, Nucleic Acids Res. 10, 1929 (1982).
9. R. M. W. Mans, C. W. A. Pleij, L. Bosch, Eur. J. Biochem. 201, 303 (1991).
10. C. Florentz et al., EMBO J. 2, 269 (1982).
11. T. C. Hall, Int. Rev. Cytol. 60, 1 (1979).
12. A. Van Belkum et al., Eur. J. Biochem. 183, 591 (1989).
13. Structure-probing experiments in which enzymatic digestion was done with RNase T1 and nuclease S1 {essentially as described [A. V. Van Belkum, P. Verlaan, J. B. Kun, C. W. A. Pleij, L. Bosch, Nucleic Acids Res. 16, 1931 (1988)]} confirmed the secondary structure presented in Fig. 1A. Fragments lacking the 5″ hairpin (residues 1 to 17) showed a different protection pattern for the pseudoknot, indicating an unstable structure under native conditions (M. H. Kolk et al., data not shown).
14. 2 solution at pH 6.7 and concentrated to 500 μl with a Centricon microconcentrator. Sample concentrations were between 1 and 2.5 mM.
15. 2 solution at pH 6.7 and concentrated to 500 μl with a Centricon microconcentrator. Sample concentrations were between 1 and 2.5 mM.
16. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
17. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
18. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
19. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
20. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
21. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
22. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
23. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
24. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
25. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
26. 31P} spin-echo difference experiments [G. W. Vuister, A. C. Wang, A. Bax, ibid. 115, 5334 (1993); P. Legault, F. M. Jucker, A. Pardi, FEBS Lett. 362, 156 (1995)]. Details of these experiments will be reported elsewhere.
27. -2 at the beginning of the cooling step. The average structure (〈SA〉) was determined from the 10 structures with the lowest energies and restraint violations out of the ensemble of 140 structures thus calculated and subjected to 6000 steps of restrained conjugate gradient energy minimization.
28. -2 at the beginning of the cooling step. The average structure (〈SA〉) was determined from the 10 structures with the lowest energies and restraint violations out of the ensemble of 140 structures thus calculated and subjected to 6000 steps of restrained conjugate gradient energy minimization.
29. S. S. Wijmenga, M. Kruithof, C. W. Hilbers, J. Biomol. NMR 10, 337 (1997).
30. D. C. Schweisguth and P. B. Moore, J. Mol. Biol. 267, 505 (1997).
31. L. J. Yao, T. L. James, J. T. Kealey, D. V. Santi, U. Schmitz, J. Biomol. NMR 9, 229 (1997).
32. P. Dumas et al., J. Biomol. Struct. Dyn. 4, 707 (1987).
33. To our knowledge, 17 pseudoknots have been described that are located at comparable positions in the valine-accepting tRNA-like structures found in tymo-, tobamo-, and furoviruses. All but one of these have an adenine at position 35. Hydrogen-bonding partners G30 and G31 are less strongly conserved throughout these species, being AG, GC, or AC in 7 out of 17 sequences. The anatomy of the possible tertiary interactions for these cases remains to be established.
34. M. Chastain and I. Tinoco Jr., Biochemistry 32, 14220 (1993); J. H. Cate et al., Science 273, 1678 (1996); H. W. Pley, K. M. Flaherty, D. B. McKay, Nature 372, 111 (1994).
35. M. Chastain and I. Tinoco Jr., Biochemistry 32, 14220 (1993); J. H. Cate et al., Science 273, 1678 (1996); H. W. Pley, K. M. Flaherty, D. B. McKay, Nature 372, 111 (1994).
36. M. Chastain and I. Tinoco Jr., Biochemistry 32, 14220 (1993); J. H. Cate et al., Science 273, 1678 (1996); H. W. Pley, K. M. Flaherty, D. B. McKay, Nature 372, 111 (1994).
37. Chemical shifts and NOEs pertaining to A35 remain unaffected in a temperature range from 5° to 40°. Imino proton resonances of the pseudoknot broaden considerably at temperatures above 50°.
38. M. A. Rould, J. J. Perona, T. A. Steitz, Nature 352, 213 (1991).
39. J. Rudinger, C. Florentz, T. Dreher, R. Giegé, Nucleic Acids Res. 20, 1865 (1992).
40. R. M. W. Mans, C. Guerrier-Takada, S. Altman, C. W. A. Pleij, ibid. 18, 3479 (1990).
41. B. A. L. M. Deiman, A. K. Koenen, P. W. G. Verlaan, C. W. A. Pleij, J. Virol., in press.
42. P. Schimmel, Cell 58, 9 (1989); I. Brierley, J. Gen. Virol. 76, 1885 (1995).
43. P. Schimmel, Cell 58, 9 (1989); I. Brierley, J. Gen. Virol. 76, 1885 (1995).
44. E. G. Stein, L. M. Rice, A. T. Brünger, J. Magn. Reson. 124, 154 (1997).
45. R. Koradi, M. Billeter, K. Wüthrich, J. Mol. Graphics 14, 51 (1996).
46. The NMR experiments were performed at the SON Large Scale NMR facility (Nijmegen and Utrecht, The Netherlands). This research was supported by the Netherlands Foundation of Chemical Research (SON) and the Dutch Life Science Foundation, with financial aid from the Netherlands Organization of Scientific Research. H.A.H. was supported by a grant from the Royal Netherlands Academy of Arts and Sciences. We wish to thank J. Joordens for technical assistance.