Nucleotide analog interference mapping of the hairpin ribozyme: Implications for secondary and tertiary structure formation

Journal of Molecular Biology

Volumn 291, Issue 2, 1999, Pages 295-311

  Ryder, Sean P ^a   Strobel, Scott A ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Catalytic RNA; Helix packing; Modification interference; Phosphorothioate

Indexed keywords

DEOXYRIBONUCLEOTIDE; HYDROXYL GROUP; NUCLEOTIDE DERIVATIVE; PHOSPHOROTHIOIC ACID; PURINE NUCLEOTIDE; RIBOSE; RIBOZYME;

ARTICLE; CATALYSIS; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; RNA STRUCTURE;

NON-A, NON-B HEPATITIS VIRUS;

EID: 0032808217     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2959     Document Type: Article

References (48)

1. Anderson P., Monforte J., Tritz R., Nesbitt S., Hearst J., Hampel A. Mutagenesis of the hairpin ribozyme. Nucl. Acids Res. 22:1994;1096-1100.
2. Berzal-Herranz A., Joseph S., Burke J. In vitro selection of active hairpin ribozymes by sequential RNA-catalyzed cleavage and ligation reactions. Genes Dev. 6:1992;129-134.
3. Berzal-Herranz A., Joseph S., Chowrira B. M., Butcher S. E., Burke J. M. Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme. EMBO J. 2:1993;2567-2574.
4. Boudvillain M., Pyle A. M. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. EMBO J. 17:1998;7091-7104.
5. Butcher S. E., Burke J. M. A photo-cross-linkable tertiary structure motif found in functionally distinct RNA molecules is essential for catalytic function of the hairpin ribozyme. Biochemistry. 33:1994a;992-999.
6. Butcher S. E., Burke J. M. Structure-mapping of the hairpin ribozyme. J. Mol. Biol. 244:1994b;52-63.
7. Butcher S. E., Allain F. H.-T., Feigon J. Solution structure of the loop B domain form the hairpin ribozyme. Nature Struct. Biol. 6:1999;212-216.
8. Cai Z., Tinoco I. Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite. Biochemistry. 35:1996;6026-6036.
9. Chowrira B. M., Burke J. M. Extensive phosporothioate substitution yields highly active and nuclease-resistant hairpin ribozymes. Nucl. Acids Res. 20:1992;2835-2840.
10. Chowrira B. M., Berzal-Herranz A., Keller C. F., Burke J. M. Four ribose 2′-hydroxyl groups essential for catalytic function of the hairpin ribozyme. J. Biol. Chem. 268:1993;19458-19462.
11. Christian E. L., Yarus M. Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena. J. Mol. Biol. 228:1992;743-758.
12. Conrad F., Hanne A., Gaur R. K., Krupp G. Enzymatic synthesis of 2′-modified nucleic acids: identification of important phosphate and ribose moieties in RNase P substrates. Nucl. Acids Res. 23:1995;1845-1853.
13. Earnshaw D. J., Gait M. J. Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucl. Acids Res. 26:1998;5551-5561.
14. Earnshaw D. J., Masquida B., Muller S., Sigurdsson S. T., Eckstein F., Westhof E., Gait M. J. Inter-domain cross-linking and molecular modelling of the hairpin ribozyme. J. Mol. Biol. 274:1997;197-212.
15. Estaban J. A., Walter N. G., Kotzorek G., Heckman J., Burke J. M. Structural basis for heterogenous kinetics: reengineering the hairpin ribozyme. Proc. Natl Acad. Sci. USA. 95:1998;6091-6096.
16. Feldstein P., Bruening G. Catalytically active geometry in the reversible circularization of 'mini-monomer' RNAs derived from the complementary strand of tobacco ringspot virus satellite RNA. Nucl. Acids Res. 21:1993;1991-1998.
17. Feldstein P., Buzayan J., Bruening G. Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA. Gene. 82:1989;53-61.
18. Gaur R. K., Krupp G. Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme. Nucl. Acids Res. 21:1993;21-26.
19. Grasby J., Gait M. Synthetic oligoribonucleotides carrying site-specific modifications for RNA structure-function analysis. Biochimie. 76:1994;1123-1134.
20. Grasby J. A., Mersmann K., Singh M., Gait M. J. Purine functional groups in the essential residues of the hairpin ribozyme required for catalytic cleavage of RNA. Biochemistry. 34:1995;4068-4076.
21. Hampel A., Tritz R. RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry. 28:1989;4929-4933.
22. Hampel A., Tritz R., Hicks M., Cruz P. 'Hairpin' catalytic RNA model: evidence for helices and sequence requirement for substrate RNA. Nucl. Acids Res. 18:1990;299-304.
23. Hampel K. J., Walter N. G., Burke J. M. The solvent-protected core of the hairpin ribozyme-substrate complex. Biochemistry. 37:1998;14672-14682.
24. Haseloff J., Gerlach W. Sequences required for self-catalyzed cleavage of the satellite RNA of tobacco ringspot virus. Gene. 82:1989;43-52.
25. Hegg L. A., Fedor M. A. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. Biochemistry. 34:1995;15813-15828.
26. Komatsu Y., Koizumi M., Nakamura H., Ohtsuka E. Loop-size variation to probe a bent structure of a hairpin ribozyme. J. Am. Chem. Soc. 116:1994;3692-3696.
27. Milligan J. F., Uhlenbeck O. C. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 180:1989;51-62.
28. Murchie A. I. H., Thomson J. B., Walter F., Lilley D. M. J. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol. Cell. 1:1998;873-881.
29. Murray J. B., Seyhan A. A., Walter N. G., Burke J. M., Scott W. G. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5:1998;587-595.
30. Nesbitt S. M., Erlacher H. A., Fedor M. J. The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects. J. Mol. Biol. 286:1999;1009-1024.
31. 2-methylguanosine. Biochemistry. 37:1998a;12933-12942.
32. Ortoleva-Donnelly L., Szewczak A. A., Gutell R. R., Strobel S. A. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA. 4:1998b;498-519.
33. Pinard R., Heckman J. E., Burke J. M. Alignment of the two domains of the hairpin ribozyme-substrate complex defined by interdomain photoaffinity crosslinking. J. Mol. Biol. 287:1999;239-251.
34. Rubino L., Tousignant M., Steger G., Kaper J. Nucleotide sequence and structural analysis of two satellite RNAs associated with chicory yellow mottle virus. J. Gen. Virol. 71:1990;1897-1903.
35. Ryder S. P., Strobel S. A. Nucleotide analog interference mapping. Methods, 18:1999;38-50.
36. Saenger W. Cantor C. Principles of Nucleic Acid Structure. 1984;Springer-Verlag, New York.
37. Schmidt S., Beigelman L., Karpeisky A., Usman N., Sorensen U. S., Gait M. Base and sugar requirements for RNA cleavage of essential nucleoside residues in internal loop B of the hairpin ribozyme: implications for secondary structure. Nucl. Acids Res. 24:1996;573-581.
38. Shippy R., Siwkowski A., Hampel A. Mutational analysis of loops 1 and 5 of the hairpin ribozyme. Biochemistry. 37:1998;564-570.
39. Siwkowski A., Shippy R., Hampel A. Analysis of hairpin ribozyme base mutations in loops 2 and 4 and their effects on cis-cleavage in vitro. Biochemistry. 36:1997;3930-3940.
40. Sousa R., Padilla R. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14:1995;4609-4621.
41. Strobel S. A., Ortoleva-Donnelly L. A hydrogen bonding triad stabilizes the chemical transition state of a group I ribozyme. Chem. Biol. 6:1999;153-165.
42. Strobel S. A., Shetty K. Defining the chemical groups essential for Tetrahymean group I intron function by nucleotide analog interference mapping. Proc. Natl Acad. Sci. USA. 94:1997;2903-2908.
43. Strobel S. A., Ortoleva-Donnelly L., Ryder S. P., Cate J. H., Moncoeur E. Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nature Struct. Biol. 5:1998;60-66.
44. Szewczak A. A., Ortoleva-Donnelly L., Ryder S. P., Strobel S. A. A minor groove triple helix in the active site of the Tetrahymena Group I intron. Nature Struct. Biol. 5:1998;1037-1042.
45. Uesugi S., Miki H., Ikehara M., Iwahashi H., Kyogoku Y. A linear relationship between electronegativity of 2′-substituents and conformation of adenine nucleosides. Tetrahedral Letters. 42:1979;4073-4076.
46. Walter N. G., Burke J. M. Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates. RNA. 3:1997;392-404.
47. Walter N. G., Burke J. M. The hairpin ribozyme: structure, assembly and catalysis. Curr. Opin. Chem. Biol. 2:1998;24-30.
48. Walter N. G., Hampel K. J., Brown K. M., Burke J. M. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J. 17:1998;2378-2391.