Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain

Nature

Volumn 429, Issue 6989, 2004, Pages 318-322

  Ma, Jin Biao ^a   Ye, Keqiong ^a   Patel, Dinshaw J ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; CRYSTAL STRUCTURE; PROTEINS; RNA; VIRUSES;

BINDING POCKETS; COMPLEMENTARY STRANDS; EUKARYOTES; SILENCING PATHWAYS;

GENETIC ENGINEERING;

DOUBLE STRANDED RNA; ESTER; NUCLEOTIDE; PROTEIN; SMALL INTERFERING RNA; EIF2C1 PROTEIN, HUMAN; INITIATION FACTOR;

BIOLOGY; RNA;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; DISSOCIATION CONSTANT; GEL PERMEATION CHROMATOGRAPHY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; RNA TRANSPORT; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ELECTRICITY; ENZYME SPECIFICITY; GENETICS; HUMAN; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SURFACE PLASMON RESONANCE; X RAY CRYSTALLOGRAPHY;

EUKARYOTA; RNA VIRUSES;

AMINO ACID MOTIFS; BASE SEQUENCE; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ELECTROSTATICS; EUKARYOTIC INITIATION FACTORS; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RNA, SMALL INTERFERING; SUBSTRATE SPECIFICITY; SURFACE PLASMON RESONANCE;

EID: 2442679207     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02519     Document Type: Article

References (30)

1. Denli, A.M. & Hannon, G. J. RNAi: an ever-growing puzzle. Trends Biochem. Sci. 28, 196-201 (2003).
2. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
3. Voinnet, O. RNA silencing as a plant immune system against viruses. Trends Genet. 17, 449-459 (2001).
4. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833-1837 (2002).
5. Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232-2237 (2002).
6. Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363-366 (2001).
7. Elbashir, S. M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188-200 (2001).
8. Hammond, S. M., Bernstein, E., Beach, D. & Hannon, G. J. An RNA-directed nuclease mediates posttranscriptional gene silencing in Drosophila cells. Nature 404, 293-296 (2000).
9. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146-1150 (2001).
10. Nykanen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309-321 (2001).
11. Martinez, J., Patkaniowska, A., Urlaub, H., Luhrmann, R. & Tuschl, T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563-574 (2002).
12. Yan, K. S. et al. Structure and conserved RNA binding of the PAZ domain. Nature 426, 468-474 (2003).
13. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain. Nature 426, 465-469 (2003).
14. Song, J. J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nature Struct. Biol. 10, 1026-1032 (2003).
15. Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877-6888 (2001).
16. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998).
17. Chiu, Y. L. & Rana, T. M. siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034-1048 (2003).
18. Theobald, D. L., Mitton-Fry, R. M. & Wuttke, D. S. Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct. 32, 115-133 (2003).
19. Liu, Q. et al. R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway. Science 301, 1921-1925 (2003).
20. Hohjoh, H. RNA interference (RNAi) induction with various types of synthetic oligonucleotide duplexes in cultured human cells. FEBS Lett. 521, 195-199 (2002).
21. Harborth, J. et al. Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev. 13, 83-105 (2003).
22. Chiu, Y. L. & Rana, T. M. RNAi in human cells: basic structural and functional features of small interfering RNA. Mol. Cell 10, 549-561 (2002).
23. Holen, T., Amarzguioui, M., Wiiger, M. T., Babaie, E. & Prydz, H. Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res. 30, 1757-1766 (2002).
24. Amarzguioui, M., Holen, T., Babaie, E. & Prydz, H. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res. 31, 589-595 (2003).
25. Czaudema, F. et al. Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res. 31, 2705-2716 (2003).
26. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
27. Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
28. Jones, T. & Kjeldgaard, M. Electron-density map interpretation. Methods Enzymol. 227, 174-208 (1997).
29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296 (1991).
30. Katsamba, P. S., Park, S. & Laird-Offringa, I. A. Kinetic studies of RNA-protein interactions using surface plasmon resonance. Methods 26, 95-104 (2002).