The importance of internal loops within RNA substrates of ADAR1

Journal of Molecular Biology

Volumn 291, Issue 1, 1999, Pages 1-13

  Lehmann, Katrina A ^a   Bass, Brenda L ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Deaminase; Double stranded RNA; Inosine; RNA editing

Indexed keywords

ADENOSINE; ADENOSINE DEAMINASE; DOUBLE STRANDED RNA; INOSINE;

ARTICLE; BASE MISPAIRING; BASE PAIRING; DEAMINATION; ENZYME SUBSTRATE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA EDITING; RNA STRUCTURE;

EID: 0344035669     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2914     Document Type: Article

References (43)

1. Bass B. L. RNA editing and hypermutation by adenosine deamination. Trends Biochem. Sci. 22:1997;157-162.
2. Bass B. L., Weintraub H. A developmentally regulated activity that unwinds RNA duplexes. Cell. 48:1987;607-613.
3. Bass B. L., Weintraub H. An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell. 55:1988;1089-1098.
4. Bevilacqua P. C., Cech T. R. Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR. Biochemistry. 35:1996;9983-9994.
5. Burns C. M., Chu H., Rueter S. M., Hutchinson L. K., Canton H., Sanders-Bush E., Emeson R. B. Regulation of serotonin-2C receptor G-protein coupling by RNA editing. Nature. 387:1997;303-308.
6. Cai Z., Tinoco I. Jr. Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite. Biochemistry. 35:1996;6026-6036.
7. Chelladurai B., Li H., Zhang K., Nicholson A. W. Mutational analysis of a ribonuclease III processing signal. Biochemistry. 32:1993;7549-7558.
8. Clemens M. J., Elia A. The double-stranded RNA-dependent protein kinase PKR: structure and function. J. Interferon Cytokine Res. 17:1997;503-524.
9. Correll C. C., Freeborn B., Moore P. B., Steitz T. A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell. 91:1997;705-712.
10. Court D. RNA processing and degradation by RNase III. Belasco J. G., Braverman G. Control of Messenger RNA Stability. 1993;71-116 Academic Press, San Diego.
11. Dabiri G. A., Lai F., Drakas R. A., Nishikura K. Editing of the GluR-B ion channel RNA in vitro by recombinant double-stranded RNA adenosine deaminase. EMBO J. 15:1996;34-45.
12. 2+permeability of unedited and edited versions of the kainate selective glutamate receptor GluR6. Proc. Natl Acad. Sci. USA. 90:1993;755-759.
13. Herb A., Higuchi M., Sprengel R., Seeburg P. H. Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences. Proc. Natl Acad. Sci. USA. 93:1996;1875-1880.
14. Higuchi M., Single F. N., Kohler M., Sommer B., Sprengel R., Seeburg P. H. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell. 75:1993;1361-1370.
15. Holbrook S. R., Cheong C., Tinoco I. Jr, Kim S. H. Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature. 353:1991;579-581.
16. Hough R. F., Bass B. L. Purification of the Xenopus laevis double-stranded RNA adenosine deaminase. J. Biol. Chem. 269:1994;9933-9939.
17. Hurst S. R., Hough R. F., Aruscavage P. J., Bass B. L. Deamination of mammalian glutamate receptor RNA by Xenopus dsRNA adenosine deaminase: similarities to in vivo RNA editing. RNA. 1:1995;1051-1060.
18. Inoue T., Cech T. R. Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: a technique for RNA structure analysis using chemical probes and reverse transcriptase. Biochemistry. 82:1985;648-652.
19. Jang S. B., Hung L. W., Chi Y. I., Holbrook E. L., Carter R. J., Holbrook S. R. Structure of an RNA internal loop consisting of tandem C-A+ base pairs. Biochemistry. 37:1998;11726-11731.
20. Lomeli H., Mosbacher J., Melcher T., Hoger T., Geiger J. R., Kuner T., Monyer H., Higuchi M., Bach A., Seeburg P. H. Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science. 266:1994;1709-1713.
21. Maas S., Melcher T., Seeburg P. H. Mammalian RNA-dependent deaminases and edited mRNAs. Curr. Opin. Cell Biol. 9:1997;343-349.
22. Mathews M. B., Shenk T. Adenovirus virus-associated RNA and translation control. J. Virol. 65:1991;5657-5662.
23. McGhee J. D., von Hippel P. H. Theoretical aspects of DNA-protein interactions: co-operative and non- co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol. 86:1974;469-489.
24. Melcher T., Maas S., Herb A., Sprengel R., Seeburg P. H., Higuchi M. A mammalian RNA editing enzyme. Nature. 379:1996;460-464.
25. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15:1987;8783-8798.
26. Nicholson A. W. Structure, reactivity, and biology of double-stranded RNA. Prog. Nucl. Acid Res. Mol. Biol. 52:1996;1-65.
27. Nishikura K., Yoo C., Kim U., Murray J. M., Estes P. A., Cash F. E., Liebhaber S. A. Substrate specificity of the dsRNA unwinding/modifying activity. EMBO J. 10:1991;3523-3532.
28. O'Connell M. A. RNA editing: rewriting receptors. Curr. Biol. 7:1997;R437-439.
29. Paul M. S., Bass B. L. Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA. EMBO J. 17:1998;1120-1127.
30. Peritz A. E., Kierzek R., Sugimoto N., Turner D. H. Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops. Biochemistry. 30:1991;6428-6436.
31. Polson A. G., Bass B. L. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J. 13:1994;5701-5711.
32. Polson A. G., Bass B. L., Casey J. L. RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase. Nature. 380:1996;454-456.
33. Robertson H. D. Escherichia coli ribonuclease III cleavage sites. Cell. 30:1982;669-672.
34. Saccomanno L., Bass B. L. The cytoplasm of Xenopus oocytes contains a factor that protects double-stranded RNA from adenosine-to-inosine modification. Mol. Cell. Biol. 14:1994;5425-5432.
35. SantaLucia J. Jr, Kierzek R., Turner D. H. Stabilities of consecutive A. C, C. C, G. G, U. C, and U. U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U.U and C.C.+ pairs. Biochemistry. 30:1991;8242-8251.
36. 1. Biochemistry. 30:1991;494-499.
37. Stroebel S. A., Cech T. R., Usman N., Beigelman L. The 2,6-diaminopurine riboside-5-methylisocytidine wobble base pair: an isoenergetic substitution for the study of G-U pairs in RNA. Biochemistry. 33:1994;13824-13835.
38. Wagner R. W., Nishikura K. Cell cycle expression of RNA duplex unwindase activity in mammalian cells. Mol. Cell. Biol. 8:1988;770-777.
39. Weeks K. M., Crothers D. M. Major groove accessibility of RNA. Science. 261:1993;1574-1577.
40. Wimberly B., Varani G., Tinoco I. Jr. The conformation of loop E of eukaryotic 5S ribosomal RNA. Biochemistry. 32:1993;1078-1087.
41. Xia T., McDowell J. A., Turner D. H. Thermodynamics of nonsymmetric tandem mismatches adjacent to G.C base pairs in RNA. Biochemistry. 36:1997;12486-12497.
42. Yang J.-H., Sklar P., Axel R., Maniatis T. Editing of glutamate receptor subunit B pre-mRNA in vitro by site-specific deamination of adenosine. Nature. 374:1995;77-81.
43. Zacharias M., Hagerman P. J. The influence of symmetric internal loops on the flexibility of RNA. J. Mol. Biol. 257:1996;276-289.