Related Content
Search Google Scholar for:
More Information
Related Jobs from ScienceCareers
|
|
Science 13 January 2006: Vol. 311. no. 5758, pp. 195 - 198 DOI: 10.1126/science.1121638
|
|
Research Articles
Structural Basis for Double-Stranded RNA Processing by Dicer
Ian J. MacRae,1,3
Kaihong Zhou,1,3
Fei Li,1
Adrian Repic,1
Angela N. Brooks,1
W. Zacheus Cande,1
Paul D. Adams,4
Jennifer A. Doudna1,2,3,4*
The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.
1 Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
2 Department of Chemistry, University of California, Berkeley, CA 94720, USA.
3 Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
4 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
* To whom correspondence should be addressed: E-mail: doudna{at}berkeley.edu
Read the Full Text
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
- Rejoice--RNAi for Yeast.
- D. Moazed (2009)
Science
326, 533-534
| Abstract »
| Full Text »
| PDF »
- Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei.
- K. L. Patrick, H. Shi, N. G. Kolev, K. Ersfeld, C. Tschudi, and E. Ullu (2009)
PNAS
106, 17933-17938
| Abstract »
| Full Text »
| PDF »
- Structural and biochemical insights into 2'-O-methylation at the 3'-terminal nucleotide of RNA by Hen1.
- C. Mui Chan, C. Zhou, J. S. Brunzelle, and R. H. Huang (2009)
PNAS
106, 17699-17704
| Abstract »
| Full Text »
| PDF »
- A Single dicer Gene Is Required for Efficient Gene Silencing Associated with Two Classes of Small Antisense RNAs in Mucor circinelloides.
- J. P. de Haro, S. Calo, M. Cervantes, F. E. Nicolas, S. Torres-Martinez, and R. M. Ruiz-Vazquez (2009)
Eukaryot. Cell
8, 1486-1497
| Abstract »
| Full Text »
| PDF »
- Gene silencing in the marine diatom Phaeodactylum tricornutum.
- V. De Riso, R. Raniello, F. Maumus, A. Rogato, C. Bowler, and A. Falciatore (2009)
Nucleic Acids Res.
37, e96
| Abstract »
| Full Text »
| PDF »
- High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis.
- X. Chen, L. J. Collins, P. J. Biggs, and D. Penny (2009)
Gen Biol Evol
2009, 165-175
| Abstract »
| Full Text »
| PDF »
- Suppression of RNA silencing by Flock house virus B2 protein is mediated through its interaction with the PAZ domain of Dicer.
- G. Singh, S. Popli, Y. Hari, P. Malhotra, S. Mukherjee, and R. K. Bhatnagar (2009)
FASEB J
23, 1845-1857
| Abstract »
| Full Text »
| PDF »
- Multiple Dicer Genes in the Early-Diverging Metazoa.
- D. de Jong, M. Eitel, W. Jakob, H.-J. Osigus, H. Hadrys, R. DeSalle, and B. Schierwater (2009)
Mol. Biol. Evol.
26, 1333-1340
| Abstract »
| Full Text »
| PDF »
- Epigenetic and microRNA-mediated regulation in diabetes.
- P. Muhonen and H. Holthofer (2009)
Nephrol. Dial. Transplant.
24, 1088-1096
| Full Text »
| PDF »
- A dominant mutation in DCL1 suppresses the hyl1 mutant phenotype by promoting the processing of miRNA.
- Y. Tagami, H. Motose, and Y. Watanabe (2009)
RNA
15, 450-458
| Abstract »
| Full Text »
| PDF »
- Human Dicer Binds Short Single-strand and Double-strand RNA with High Affinity and Interacts with Different Regions of the Nucleic Acids.
- W. F. Lima, H. Murray, J. G. Nichols, H. Wu, H. Sun, T. P. Prakash, A. R. Berdeja, H. J. Gaus, and S. T. Crooke (2009)
J. Biol. Chem.
284, 2535-2548
| Abstract »
| Full Text »
| PDF »
- A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs.
- H. S. Soifer, M. Sano, K. Sakurai, P. Chomchan, P. Saetrom, M. A. Sherman, M. A. Collingwood, M. A. Behlke, and J. J. Rossi (2008)
Nucleic Acids Res.
36, 6511-6522
| Abstract »
| Full Text »
| PDF »
- Dicer Cuts the Kidney.
- J.J. D. Ho and P. A. Marsden (2008)
J. Am. Soc. Nephrol.
19, 2043-2046
| Full Text »
| PDF »
- Conifers have a unique small RNA silencing signature.
- E. V. Dolgosheina, R. D. Morin, G. Aksay, S. C. Sahinalp, V. Magrini, E. R. Mardis, J. Mattsson, and P. J. Unrau (2008)
RNA
14, 1508-1515
| Abstract »
| Full Text »
| PDF »
- From the Cover: The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1.
- Z. Dong, M.-H. Han, and N. Fedoroff (2008)
PNAS
105, 9970-9975
| Abstract »
| Full Text »
| PDF »
- The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members.
- T. A. Farazi, S. A. Juranek, and T. Tuschl (2008)
Development
135, 1201-1214
| Abstract »
| Full Text »
| PDF »
- Structural and biochemical insights into the dicing mechanism of mouse Dicer: A conserved lysine is critical for dsRNA cleavage.
- Z. Du, J. K. Lee, R. Tjhen, R. M. Stroud, and T. L. James (2008)
PNAS
105, 2391-2396
| Abstract »
| Full Text »
| PDF »
- P68 RNA Helicase Unwinds the Human let-7 MicroRNA Precursor Duplex and Is Required for let-7-directed Silencing of Gene Expression.
- D. W. Salzman, J. Shubert-Coleman, and H. Furneaux (2007)
J. Biol. Chem.
282, 32773-32779
| Abstract »
| Full Text »
| PDF »
- Functional Anatomy of the Drosophila MicroRNA-generating Enzyme.
- X. Ye, Z. Paroo, and Q. Liu (2007)
J. Biol. Chem.
282, 28373-28378
| Abstract »
| Full Text »
| PDF »
- Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis.
- X. Chen, T. S. Rozhdestvensky, L. J. Collins, J. Schmitz, and D. Penny (2007)
Nucleic Acids Res.
35, 4619-4628
| Abstract »
| Full Text »
| PDF »
- Human TRBP and PACT Directly Interact with Each Other and Associate with Dicer to Facilitate the Production of Small Interfering RNA.
- K. H. Kok, M.-H. J. Ng, Y.-P. Ching, and D.-Y. Jin (2007)
J. Biol. Chem.
282, 17649-17657
| Abstract »
| Full Text »
| PDF »
- Structure of Aquifex aeolicus Argonaute Highlights Conformational Flexibility of the PAZ Domain as a Potential Regulator of RNA-induced Silencing Complex Function.
- U. J. Rashid, D. Paterok, A. Koglin, H. Gohlke, J. Piehler, and J. C.-H. Chen (2007)
J. Biol. Chem.
282, 13824-13832
| Abstract »
| Full Text »
| PDF »
- RNA stem-loops: To be or not to be cleaved by RNAse III.
- W. Ritchie, M. Legendre, and D. Gautheret (2007)
RNA
13, 457-462
| Abstract »
| Full Text »
| PDF »
- Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 Pathway in Arabidopsis Reveals Dependency on miRNA- and tasiRNA-Directed Targeting.
- M. D. Howell, N. Fahlgren, E. J. Chapman, J. S. Cumbie, C. M. Sullivan, S. A. Givan, K. D. Kasschau, and J. C. Carrington (2007)
PLANT CELL
19, 926-942
| Abstract »
| Full Text »
| PDF »
- Specific residues at every third position of siRNA shape its efficient RNAi activity.
- T. Katoh and T. Suzuki (2007)
Nucleic Acids Res.
35, e27
| Abstract »
| Full Text »
| PDF »
- Selenium derivatization of nucleic acids for crystallography.
- J. Jiang, J. Sheng, N. Carrasco, and Z. Huang (2007)
Nucleic Acids Res.
35, 477-485
| Abstract »
| Full Text »
| PDF »
- An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei.
- H. Shi, C. Tschudi, and E. Ullu (2006)
RNA
12, 2063-2072
| Abstract »
| Full Text »
| PDF »
- DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold.
- M. Dlakic (2006)
Bioinformatics
22, 2711-2714
| Abstract »
| Full Text »
| PDF »
- Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III.
- A. V. Pertzev and A. W. Nicholson (2006)
Nucleic Acids Res.
34, 3708-3721
| Abstract »
| Full Text »
| PDF »
- A novel class of small RNAs in mouse spermatogenic cells.
- S. T. Grivna, E. Beyret, Z. Wang, and H. Lin (2006)
Genes & Dev.
20, 1709-1714
| Abstract »
| Full Text »
| PDF »
- Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction.
- C.-I. An, V. B. Trinh, and Y. Yokobayashi (2006)
RNA
12, 710-716
| Abstract »
| Full Text »
| PDF »
- Drosha in Primary MicroRNA Processing.
- Y. LEE, J. HAN, K.-H. YEOM, H. JIN, and V.N. KIM (2006)
Cold Spring Harb Symp Quant Biol
71, 51-57
| Abstract »
| PDF »
- Substrate Selectivity of Exportin 5 and Dicer in the Biogenesis of MicroRNAs.
- E. LUND and J.E. DAHLBERG (2006)
Cold Spring Harb Symp Quant Biol
71, 59-66
| Abstract »
| PDF »
- Structure of Dicer and Mechanistic Implications for RNAi.
- I.J. MacRAE, F. LI, K. ZHOU, W.Z. CANDE, and J.A. DOUDNA (2006)
Cold Spring Harb Symp Quant Biol
71, 73-80
| Abstract »
| PDF »
- Structural Biology of RNA Silencing and Its Functional Implications.
- D.J. PATEL, J.-B. MA, Y.-R. YUAN, K. YE, Y. PEI, V. KURYAVYI, L. MALININA, G. MEISTER, and T. TUSCHL (2006)
Cold Spring Harb Symp Quant Biol
71, 81-93
| Abstract »
| PDF »
- The Expanding Universe of Noncoding RNAs.
- G.J. HANNON, F.V. RIVAS, E.P. MURCHISON, and J.A. STEITZ (2006)
Cold Spring Harb Symp Quant Biol
71, 551-564
| Abstract »
| PDF »
|
|