Investigation of Mg2+- and temperature-dependent folding of the hairpin ribozyme by photo-crosslinking: Effects of photo-crosslinker tether length and chemistry

Nucleic Acids Research

Volumn 33, Issue 3, 2005, Pages 1058-1068

  Borda, Emily J ^a   Sigurdsson, Snorri Th ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF ICELAND   (Iceland)

Author keywords

[No Author keywords available]

Indexed keywords

AZIDE; MAGNESIUM; NUCLEOTIDE; RIBOZYME; CROSS LINKING REAGENT; DIVALENT CATION; HAIRPIN RIBOZYME; PHENYL AZIDE;

ARTICLE; CONCENTRATION RESPONSE; CONTROLLED STUDY; ENZYME ACTIVITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN CROSS LINKING; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN LOCALIZATION; RNA STRUCTURE; TEMPERATURE DEPENDENCE; CHEMISTRY; CONFORMATION; LIGHT; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SYNTHESIS; TEMPERATURE;

AZIDES; BASE SEQUENCE; CATIONS, DIVALENT; CROSS-LINKING REAGENTS; LIGHT; MAGNESIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, CATALYTIC; TEMPERATURE;

EID: 14844287055     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki237     Document Type: Article

References (39)

1. Hampel,K.J., Walter,N.G. and Burke,J.M. (1989) RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry, 28, 4929-4933.
2. Ferre-D'Amare,A.R. (2003) The hairpin ribozyme. Biopolymers, 73 71-78.
3. Fedor,M. (2000) Structure and function of the hairpin ribozyme. J. Mol. Biol., 297, 269-291.
4. Walter,F., Murchie,A.I.H. and Lilley,D.M.J. (1998) Folding of the four-way RNA junction of the hairpin ribozyme. Biochemistry, 37 17629-17636.
5. Siwkowski,A., Shippy,R. and Hampel,A. (1997) Analysis of hairpin ribozyme base mutations in loops 2 and 4 and their effects on cis-cleavage in vitro. Biochemistry, 36, 3930-3940.
6. Rupert,P.B. and Ferre-D'Amare,A. (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410, 780-786.
7. Hampel,A. and Cowan,J.A. (1997) A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem. Biol. 4, 513-517.
8. Nesbitt,S., Hegg,L.A. and Fedor,M. (1997) An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem. Biol., 4, 619-630.
9. Young,K.J., Gill,F. and Grasby,J.A. (1997) Metal ions play a passive role in the hairpin ribozyme catalysed reaction. Nucleic Acids Res. 25, 3760-3766.
10. Wilson,T.J. and Lilley,D.M.J. (2002) Metal ion binding and the folding of the hairpin ribozyme. RNA, 8, 587-600.
11. Tan,E., Wilson,T.J., Nahas,M., Clegg,R.M., Lilley,D.M.J. and Ha,T. (2003) A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate. Proc. Natl Acad. Sci. USA, 100, 9308-9313.
12. Hohng,S., Wilson,T.J., Tan,E., Clegg,R.M., Lilley,D.M.J. and Ha,T. (2004) Conformational flexibility of four-way junctions in RNA. J. Mol. Biol., 336, 69-79.
13. Pljevaljcic,G., Millar,D.P. and Deniz,A.A. (2004) Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding. Biophys. J., 87, 457-467.
14. Bokinsky,G., Rueda,D., Misra,V.K., Rhodes,M.M., Gordus,A., Babcock,H.P., Walter,N.G. and Zhuang,X. (2003) Single-molecule transition-state analysis of RNA folding. Proc. Natl Acad. Sci. USA, 100, 9302-9307.
15. Cai,Z. and Tinoco,J.Ignacio (1996) Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite. Biochemistry 35, 6026-6036.
16. Butcher,S.E., Allain,F.H.-T. and Feigon,J. (1999) Solution structure of the loop B domain from the hairpin ribozyme. Nature Struct. Biol., 6, 212-216.
17. Ryder,S.P. and Strobel,S.A. (2002) Comparative analysis of hairpin ribozyme structures and interference data. Nucleic Acids Res., 30, 1287-1291.
18. Earnshaw,D.J., Masquida,B., Muller,S., Sigurdsson,S.T., Eckstein,F., Westhof,E. and Gait,M.J. (1997) Inter-domain cross-linking and molecular modelling of the hairpin ribozyme. J. Mol. Biol., 274, 197-212.
19. Pinard,R., Heckman,J.E. and Burke,J.M. (1999) Alignment of the two domains of the hairpin ribozyme-substrate complex defined by interdomain photoaffinity crosslinking. J. Mol. Biol., 287, 239-251.
20. Merrill,S.H. and Unruh,C.C. (1963) Photosensitive azide polymers. J. Appl. Polym. Sci., 7, 273-279.
21. Keana,J.F.W. and Cai,S.X. (1990) New reagents for photoaffinity labeling: Synthesis and photolysis of functionalized perfluorophenyl azides. J. Org. Chem., 55, 3640-3647.
22. Ferre-D'Amare,A.R. and Doudna,J.A. (1996) Use of cis- and trans ribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res., 24, 977-978.
23. Nikonowicz,E.P., Sirr,A., Legault,P., Jucker,F.M., Baer,L.M. and Pardi,A. (1992) Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies. Nucleic Acids Res., 20, 4507-4513.
24. He,B., Rong,M., Lyakhov,D., Gartenstein,H., Diaz,G., Castagna,R., McAllister,W.T. and Durbin,R.K. (1997) Rapid mutagenesis and purification of phage RNA polymerases. Protein Expr. Purif., 9 142-151.
25. Markley,J.C., Godde,F. and Sigurdsson,S.T. (2001) Identification and characterization of a divalent metal ion-dependent cleavage site in the hammerhead ribozyme. Biochemistry, 40, 13849-13856.
26. Sigurdsson,S.T. and Eckstein,F. (1996) Site specific labelling of sugar residues in oligoribonucleotides: Reactions of aliphatic isocyanates with 2′ amino groups. Nucleic Acids Res., 24, 3129-3133.
27. Buchmueller,K.L., Hill,B.T., Platz,M.S. and Weeks,K.M. (2003) RNA-tethered phenyl azide photocrosslinking via a short-lived indiscriminant electrophile. J. Am. Chem. Soc., 125, 10850-10861.
28. Schrock,A.K. and Schuster,G.B. (1984) Photochemistry of phenyl azide: chemical properties of the transient intermediates. J. Am. Chem. Soc. 106, 5228-5234.
29. Gritsan,N.P., Gudmundsdottir,A.D., Tigelaar,D., Zhu,Z., Karney,W.L., Hadad,C.M. and Platz,M.S. (2001) A laser flash photolysis and quantum chemical study of the fluorinated derivatives of singlet phenylnitrene. J. Am. Chem. Soc., 123, 1951-1962.
30. Schnapp,K.A. and Platz,M.S. (1993) A laser flash photolysis study of di-, tri- and tetrafluorinated phenylnitrenes; implications for photoaffinity labeling. Bioconjug. Chem., 4, 178-183.
31. Schnapp,K.A., Poe,R., Leyva,E., Soundararajan,N. and Platz,M.S. (1993) Exploratory photochemistry of fluorinated aryl azides. Implications for the design of photoaffinity labeling reagents. Bioconjug. Chem., 4, 172-177.
32. Sigurdsson,S.T., Seeger,B., Kutzke,U. and Eckstein,F. (1996) A mild and simple method for the preparation of isocyanates from aliphatic amines using trichloromethyl chloroformate. Synthesis of an isocyanate containing an activated disulfide. J. Org. Chem., 61, 3883-3884.
33. Fedor,M.J. (1999) Tertiary structure stabilization promotes hairpin ribozyme ligation. Biochemistry, 38, 11040-11050.
34. Poe,R., Schnapp,K.A., Young,M.J.T., Grayzar,J. and Platz,M.S. (1992) Chemistry and kinetics of singlet (pentafluorophenyl)nitrene. J. Am. Chem. Soc., 114, 5054-5067.
35. Demeshkina,N., Repkova,M., Ven'Yaminova,A., Graifer,D. and Karpova,G. (2000) Nucleotides of 18S rRNA surrounding mRNA codons at the human ribosomal A, P, and E sites: A cross linking study with mRNA analogs carrying an aryl azide group at either the uracil or the guanine residue. RNA, 6, 1727-1736.
36. Favre,A. and Fourrey,J.L. (1995) Structural probing of small endonucleolytic ribozymes in solution using thio-substituted nucleobases as intrinsic photolabels. Acc. Chem. Res., 28, 375-382.
37. Bravo,C., Lescure,F., Laugaa,P., Fourrey,J.L. and Favre,A. (1996) Folding of the HDV antigenomic ribozyme pseudoknot structure deduced from long-range photocrosslinks. Nucleic Acids Res., 24, 1351-1359.
38. Bravo,C., Woisard,A., Fourrey,J.-L., Laugaa,P. and Favre,A. (1999) A Y form of hammerhead ribozyme trapped by photo-cross-links retains full cleavage activity. Biochimie, 81, 201-212.
39. Hiley,S.L., Sood,V.D., Fan,J. and Collins,R.A. (2002) 4-thio-U cross-linking identifies the active site of the VS ribozyme. EMBO J. 21, 4691-4698.