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PDBsum entry 2ffl

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protein metals Protein-protein interface(s) links
Translation,hydrolase PDB id
2ffl
Jmol
Contents
Protein chains
732 a.a.
Metals
_MN ×39
Waters ×54
PDB id:
2ffl
Name: Translation,hydrolase
Title: Crystal structure of dicer from giardia intestinalis
Structure: Dicer. Chain: a, b, c, d. Synonym: ribonuclease iii. Engineered: yes. Mutation: yes
Source: Giardia intestinalis. Organism_taxid: 5741. Strain: portland-1. Atcc: 50803. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.
Resolution:
3.33Å     R-factor:   0.245     R-free:   0.275
Authors: J.A.Doudna,I.J.Macrae,P.D.Adams
Key ref:
I.J.Macrae et al. (2006). Structural basis for double-stranded RNA processing by Dicer. Science, 311, 195-198. PubMed id: 16410517 DOI: 10.1126/science.1121638
Date:
19-Dec-05     Release date:   24-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
A8BQJ3  (DCL_GIAIC) -  Endoribonuclease Dicer-like
Seq:
Struc:
 
Seq:
Struc:
754 a.a.
732 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   6 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
DOI no: 10.1126/science.1121638 Science 311:195-198 (2006)
PubMed id: 16410517  
 
 
Structural basis for double-stranded RNA processing by Dicer.
I.J.Macrae, K.Zhou, F.Li, A.Repic, A.N.Brooks, W.Z.Cande, P.D.Adams, J.A.Doudna.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Structural features of the Dicer PAZ domain. (A) Superposition of the C[ ]atoms of PAZ domains from Giardia Dicer (orange) and human Argonaute1 (white). Amino acids forming the 3' overhang-binding pocket are shown as sticks. (B) Electrostatic surface representation of the PAZ domains of Giardia Dicer and Argonaute1 (hAGO1). Asterisks denote 3' overhang-binding pockets. The RNA in Argonaute1 PAZ structure is drawn as green sticks.
Figure 4.
Fig. 4. A model for dsRNA processing by Dicer. Front and side views of a surface representation of Giardia Dicer with modeled dsRNA. Red and blue represent acidic and basic protein surface charge, respectively. Electrostatic surface potentials do not include contributions from bound metal ions. Putative catalytic metal ions are shown as green spheres. White arrows point to scissile phosphates. Asterisk denotes PAZ domain 3' overhang-binding pocket.
 
  The above figures are reprinted by permission from the AAAs: Science (2006, 311, 195-198) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22472616 A.N.Sawh, and T.F.Duchaine (2012).
Turning Dicer on its head.
  Nat Struct Mol Biol, 19, 365-366.  
22426548 P.W.Lau, K.Z.Guiley, N.De, C.S.Potter, B.Carragher, and I.J.MacRae (2012).
The molecular architecture of human Dicer.
  Nat Struct Mol Biol, 19, 436-440.  
21419681 E.S.Cenik, R.Fukunaga, G.Lu, R.Dutcher, Y.Wang, T.M.Tanaka Hall, and P.D.Zamore (2011).
Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease.
  Mol Cell, 42, 172-184.  
21753850 J.E.Park, I.Heo, Y.Tian, D.K.Simanshu, H.Chang, D.Jee, D.J.Patel, and V.N.Kim (2011).
Dicer recognizes the 5' end of RNA for efficient and accurate processing.
  Nature, 475, 201-205.  
20739353 J.Starega-Roslan, J.Krol, E.Koscianska, P.Kozlowski, W.J.Szlachcic, K.Sobczak, and W.J.Krzyzosiak (2011).
Structural basis of microRNA length variety.
  Nucleic Acids Res, 39, 257-268.  
21180718 N.Abe, H.Abe, T.Ohshiro, Y.Nakashima, M.Maeda, and Y.Ito (2011).
Synthesis and characterization of small circular double-stranded RNAs.
  Chem Commun (Camb), 47, 2125-2127.  
21362554 N.C.Welker, T.S.Maity, X.Ye, P.J.Aruscavage, A.A.Krauchuk, Q.Liu, and B.L.Bass (2011).
Dicer's helicase domain discriminates dsRNA termini to promote an altered reaction mode.
  Mol Cell, 41, 589-599.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
21306637 Y.Ando, Y.Maida, A.Morinaga, A.M.Burroughs, R.Kimura, J.Chiba, H.Suzuki, K.Masutomi, and Y.Hayashizaki (2011).
Two-step cleavage of hairpin RNA with 5' overhangs by human DICER.
  BMC Mol Biol, 12, 6.  
21193640 Y.Tian, D.K.Simanshu, J.B.Ma, and D.J.Patel (2011).
Inaugural article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains.
  Proc Natl Acad Sci U S A, 108, 903-910.
PDB codes: 3o3i 3o6e 3o7v 3o7x
20428234 A.N.Khachane, and P.M.Harrison (2010).
Mining mammalian transcript data for functional long non-coding RNAs.
  PLoS One, 5, e10316.  
20223951 A.Nakagawa, Y.Shi, E.Kage-Nakadai, S.Mitani, and D.Xue (2010).
Caspase-dependent conversion of Dicer ribonuclease into a death-promoting deoxyribonuclease.
  Science, 328, 327-334.  
20106953 H.Qin, F.Chen, X.Huan, S.Machida, J.Song, and Y.A.Yuan (2010).
Structure of the Arabidopsis thaliana DCL4 DUF283 domain reveals a noncanonical double-stranded RNA-binding fold for protein-protein interaction.
  RNA, 16, 474-481.
PDB code: 2kou
20400969 J.Ankarklev, J.Jerlström-Hultqvist, E.Ringqvist, K.Troell, and S.G.Svärd (2010).
Behind the smile: cell biology and disease mechanisms of Giardia species.
  Nat Rev Microbiol, 8, 413-422.  
20038112 J.P.Lu, S.C.Chai, and Q.Z.Ye (2010).
Catalysis and inhibition of Mycobacterium tuberculosis methionine aminopeptidase.
  J Med Chem, 53, 1329-1337.
PDB codes: 3iu7 3iu8 3iu9
20397215 J.Sheng, and Z.Huang (2010).
Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies.
  Chem Biodivers, 7, 753-785.  
20562854 J.T.Cuperus, A.Carbonell, N.Fahlgren, H.Garcia-Ruiz, R.T.Burke, A.Takeda, C.M.Sullivan, S.D.Gilbert, T.A.Montgomery, and J.C.Carrington (2010).
Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis.
  Nat Struct Mol Biol, 17, 997.  
20717561 J.W.Gaynor, B.J.Campbell, and R.Cosstick (2010).
RNA interference: a chemist's perspective.
  Chem Soc Rev, 39, 4169-4184.  
20523899 L.Braun, D.Cannella, P.Ortet, M.Barakat, C.F.Sautel, S.Kieffer, J.Garin, O.Bastien, O.Voinnet, and M.A.Hakimi (2010).
A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii.
  PLoS Pathog, 6, e1000920.  
20638269 M.Wieland, and M.Fussenegger (2010).
Ligand-dependent regulatory RNA parts for Synthetic Biology in eukaryotes.
  Curr Opin Biotechnol, 21, 760-765.  
20354150 N.C.Welker, D.M.Pavelec, D.A.Nix, T.F.Duchaine, S.Kennedy, and B.L.Bass (2010).
Dicer's helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs.
  RNA, 16, 893-903.  
20015091 P.Narayan, and M.Dragunow (2010).
Pharmacology of epigenetics in brain disorders.
  Br J Pharmacol, 159, 285-303.  
20395499 Q.Liu, and Z.Paroo (2010).
Molecular biology. Dicer's cut and switch.
  Science, 328, 314-315.  
20205586 Q.Liu, and Z.Paroo (2010).
Biochemical principles of small RNA pathways.
  Annu Rev Biochem, 79, 295-319.  
20849617 R.Luo, X.Xue, Z.Wang, J.Sun, Y.Zou, and W.Pan (2010).
Analysis and characterization of the genes encoding the Dicer and Argonaute proteins of Schistosoma japonicum.
  Parasit Vectors, 3, 90.  
  20230614 S.L.Ameres, and R.Fukunaga (2010).
Riding in silence: a little snowboarding, a lot of small RNAs.
  Silence, 1, 8.  
20132544 T.Cavalier-Smith (2010).
Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution.
  Biol Direct, 5, 7.  
19968858 W.M.Li, T.Barnes, and C.H.Lee (2010).
Endoribonucleases--enzymes gaining spotlight in mRNA metabolism.
  FEBS J, 277, 627-641.  
20660014 X.Zhang, and Y.Zeng (2010).
The terminal loop region controls microRNA processing by Drosha and Dicer.
  Nucleic Acids Res, 38, 7689-7697.  
20454920 X.Zhou, H.Guo, K.Chen, H.Cheng, and R.Zhou (2010).
Identification, chromosomal mapping and conserved synteny of porcine Argonaute family of genes.
  Genetica, 138, 805-812.  
20528154 Y.Okamitsu, T.Yamamoto, T.Fujii, H.Ochiai, and N.Sakamoto (2010).
Dicer is Required for the Normal Development of Sea Urchin, Hemicentrotus pulcherrimus.
  Zoolog Sci, 27, 477-486.  
20403450 Z.Xie, K.Khanna, and S.Ruan (2010).
Expression of microRNAs and its regulation in plants.
  Semin Cell Dev Biol, 21, 790-797.  
19298824 A.Alian, A.DeGiovanni, S.L.Griner, J.S.Finer-Moore, and R.M.Stroud (2009).
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
  J Mol Biol, 388, 785-800.
PDB code: 3dh3
19850910 C.Addo-Quaye, J.A.Snyder, Y.B.Park, Y.F.Li, R.Sunkar, and M.J.Axtell (2009).
Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome.
  RNA, 15, 2112-2121.  
19822745 C.Mui Chan, C.Zhou, J.S.Brunzelle, and R.H.Huang (2009).
Structural and biochemical insights into 2'-O-methylation at the 3'-terminal nucleotide of RNA by Hen1.
  Proc Natl Acad Sci U S A, 106, 17699-17704.
PDB codes: 3jwg 3jwh 3jwi 3jwj
19389436 D.D.Rao, J.S.Vorhies, N.Senzer, and J.Nemunaitis (2009).
siRNA vs. shRNA: similarities and differences.
  Adv Drug Deliv Rev, 61, 746-759.  
19900888 D.Moazed (2009).
Molecular biology. Rejoice--RNAi for yeast.
  Science, 326, 533-534.  
19276153 D.de Jong, M.Eitel, W.Jakob, H.J.Osigus, H.Hadrys, R.Desalle, and B.Schierwater (2009).
Multiple dicer genes in the early-diverging metazoa.
  Mol Biol Evol, 26, 1333-1340.  
19820710 H.W.Wang, C.Noland, B.Siridechadilok, D.W.Taylor, E.Ma, K.Felderer, J.A.Doudna, and E.Nogales (2009).
Structural insights into RNA processing by the human RISC-loading complex.
  Nat Struct Mol Biol, 16, 1148-1153.  
19859542 H.Wu, C.Ye, D.Ramirez, and N.Manjunath (2009).
Alternative processing of primary microRNA transcripts by Drosha generates 5' end variation of mature microRNA.
  PLoS One, 4, e7566.  
19942857 I.Djupedal, I.C.Kos-Braun, R.A.Mosher, N.Söderholm, F.Simmer, T.J.Hardcastle, A.Fender, N.Heidrich, A.Kagansky, E.Bayne, E.G.Wagner, D.C.Baulcombe, R.C.Allshire, and K.Ekwall (2009).
Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA.
  EMBO J, 28, 3832-3844.  
19666782 J.P.de Haro, S.Calo, M.Cervantes, F.E.Nicolás, S.Torres-Martínez, and R.M.Ruiz-Vázquez (2009).
A single dicer gene is required for efficient gene silencing associated with two classes of small antisense RNAs in Mucor circinelloides.
  Eukaryot Cell, 8, 1486-1497.  
19815526 K.L.Patrick, H.Shi, N.G.Kolev, K.Ersfeld, C.Tschudi, and E.Ullu (2009).
Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei.
  Proc Natl Acad Sci U S A, 106, 17933-17938.  
19646895 L.J.Luense, M.Z.Carletti, and L.K.Christenson (2009).
Role of Dicer in female fertility.
  Trends Endocrinol Metab, 20, 265-272.  
19158786 M.Jinek, and J.A.Doudna (2009).
A three-dimensional view of the molecular machinery of RNA interference.
  Nature, 457, 405-412.  
19229243 M.M.Ghodgaonkar, R.G.Shah, F.Kandan-Kulangara, E.B.Affar, H.H.Qi, E.Wiemer, and G.M.Shah (2009).
Abrogation of DNA vector-based RNAi during apoptosis in mammalian cells due to caspase-mediated cleavage and inactivation of Dicer-1.
  Cell Death Differ, 16, 858-868.  
19341774 N.Manjunath, H.Wu, S.Subramanya, and P.Shankar (2009).
Lentiviral delivery of short hairpin RNAs.
  Adv Drug Deliv Rev, 61, 732-745.  
19145005 P.Muhonen, and H.Holthofer (2009).
Epigenetic and microRNA-mediated regulation in diabetes.
  Nephrol Dial Transplant, 24, 1088-1096.  
19836333 P.W.Lau, C.S.Potter, B.Carragher, and I.J.MacRae (2009).
Structure of the human Dicer-TRBP complex by electron microscopy.
  Structure, 17, 1326-1332.  
19175700 P.W.Lau, and I.J.Macrae (2009).
The molecular machines that mediate microRNA maturation.
  J Cell Mol Med, 13, 54-60.  
19221817 Q.Liu, Y.Feng, and Z.Zhu (2009).
Dicer-like (DCL) proteins in plants.
  Funct Integr Genomics, 9, 277-286.  
19120484 R.Aliyari, and S.W.Ding (2009).
RNA-based viral immunity initiated by the Dicer family of host immune receptors.
  Immunol Rev, 227, 176-188.  
19239886 R.W.Carthew, and E.J.Sontheimer (2009).
Origins and Mechanisms of miRNAs and siRNAs.
  Cell, 136, 642-655.  
19476539 S.M.Schlauder, A.Ahmad, and T.D.Horn (2009).
Dicer and micro-RNAs in cutaneous disease.
  J Cutan Pathol, 36, 607-610.  
19487243 V.De Riso, R.Raniello, F.Maumus, A.Rogato, C.Bowler, and A.Falciatore (2009).
Gene silencing in the marine diatom Phaeodactylum tricornutum.
  Nucleic Acids Res, 37, e96.  
19022417 V.Dincbas-Renqvist, G.Pépin, M.Rakonjac, I.Plante, D.L.Ouellet, A.Hermansson, I.Goulet, J.Doucet, B.Samuelsson, O.Rådmark, and P.Provost (2009).
Human Dicer C-terminus functions as a 5-lipoxygenase binding domain.
  Biochim Biophys Acta, 1789, 99.  
19165215 V.N.Kim, J.Han, and M.C.Siomi (2009).
Biogenesis of small RNAs in animals.
  Nat Rev Mol Cell Biol, 10, 126-139.  
  20333187 X.S.Chen, L.J.Collins, P.J.Biggs, and D.Penny (2009).
High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis.
  Genome Biol Evol, 1, 165-175.  
19812675 Y.Huang, L.Ji, Q.Huang, D.G.Vassylyev, X.Chen, and J.B.Ma (2009).
Structural insights into mechanisms of the small RNA methyltransferase HEN1.
  Nature, 461, 823-827.
PDB code: 3htx
19155326 Y.Tagami, H.Motose, and Y.Watanabe (2009).
A dominant mutation in DCL1 suppresses the hyl1 mutant phenotype by promoting the processing of miRNA.
  RNA, 15, 450-458.  
19043559 A.A.Saraiya, and C.C.Wang (2008).
snoRNA, a novel precursor of microRNA in Giardia lamblia.
  PLoS Pathog, 4, e1000224.  
18924215 A.Henn, A.Joachimi, D.P.Gonçalves, D.Monchaud, M.P.Teulade-Fichou, J.K.Sanders, and J.S.Hartig (2008).
Inhibition of dicing of guanosine-rich shRNAs by quadruplex-binding compounds.
  Chembiochem, 9, 2722-2729.  
19079052 C.G.Prucca, I.Slavin, R.Quiroga, E.V.Elías, F.D.Rivero, A.Saura, P.G.Carranza, and H.D.Luján (2008).
Antigenic variation in Giardia lamblia is regulated by RNA interference.
  Nature, 456, 750-754.  
18956013 C.L.Beisel, T.S.Bayer, K.G.Hoff, and C.D.Smolke (2008).
Model-guided design of ligand-regulated RNAi for programmable control of gene expression.
  Mol Syst Biol, 4, 224.  
18508075 E.Ma, I.J.MacRae, J.F.Kirsch, and J.A.Doudna (2008).
Autoinhibition of human dicer by its internal helicase domain.
  J Mol Biol, 380, 237-243.  
18566193 E.V.Dolgosheina, R.D.Morin, G.Aksay, S.C.Sahinalp, V.Magrini, E.R.Mardis, J.Mattsson, and P.J.Unrau (2008).
Conifers have a unique small RNA silencing signature.
  RNA, 14, 1508-1515.  
18211225 G.Ku, and M.T.McManus (2008).
Behind the scenes of a small RNA gene-silencing pathway.
  Hum Gene Ther, 19, 17-26.  
18927112 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).
A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs.
  Nucleic Acids Res, 36, 6511-6522.  
17981733 M.P.Perron, and P.Provost (2008).
Protein interactions and complexes in human microRNA biogenesis and function.
  Front Biosci, 13, 2537-2547.  
18322526 M.Parisien, and F.Major (2008).
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data.
  Nature, 452, 51-55.  
18094473 P.H.Zwart, R.W.Grosse-Kunstleve, A.A.Lebedev, G.N.Murshudov, and P.D.Adams (2008).
Surprises and pitfalls arising from (pseudo)symmetry.
  Acta Crystallogr D Biol Crystallogr, 64, 99.  
18160966 R.A.Laskowski, and J.M.Thornton (2008).
Understanding the molecular machinery of genetics through 3D structures.
  Nat Rev Genet, 9, 141-151.  
19000009 R.M.Patel, J.A.van Kan, A.M.Bailey, and G.D.Foster (2008).
RNA-mediated gene silencing of superoxide dismutase (bcsod1) in Botrytis cinerea.
  Phytopathology, 98, 1334-1339.  
18715673 S.A.Shabalina, and E.V.Koonin (2008).
Origins and evolution of eukaryotic RNA interference.
  Trends Ecol Evol, 23, 578-587.  
18486981 S.H.Kim, J.H.Jeong, S.H.Lee, S.W.Kim, and T.G.Park (2008).
Local and systemic delivery of VEGF siRNA using polyelectrolyte complex micelles for effective treatment of cancer.
  J Control Release, 129, 107-116.  
18344671 S.Kang, and Y.S.Hong (2008).
RNA interference in infectious tropical diseases.
  Korean J Parasitol, 46, 1.  
18596982 S.Saayman, S.Barichievy, A.Capovilla, K.V.Morris, P.Arbuthnot, and M.S.Weinberg (2008).
The efficacy of generating three independent anti-HIV-1 siRNAs from a single U6 RNA Pol III-expressed long hairpin RNA.
  PLoS ONE, 3, e2602.  
18369775 X.Ye, and Q.Liu (2008).
Expression, purification, and analysis of recombinant Drosophila Dicer-1 and Dicer-2 enzymes.
  Methods Mol Biol, 442, 11-27.  
18632569 Z.Dong, M.H.Han, and N.Fedoroff (2008).
The RNA-binding proteins HYL1 and SE promote accurate in vitro processing of pri-miRNA by DCL1.
  Proc Natl Acad Sci U S A, 105, 9970-9975.  
18268334 Z.Du, J.K.Lee, R.Tjhen, R.M.Stroud, and T.L.James (2008).
Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage.
  Proc Natl Acad Sci U S A, 105, 2391-2396.
PDB codes: 3c4b 3c4t
18454937 d.o. .H.Lim, J.Kim, S.Kim, R.W.Carthew, and Y.S.Lee (2008).
Functional analysis of dicer-2 missense mutations in the siRNA pathway of Drosophila.
  Biochem Biophys Res Commun, 371, 525-530.  
17638526 A.V.Vlassov, B.Korba, K.Farrar, S.Mukerjee, A.A.Seyhan, H.Ilves, R.L.Kaspar, D.Leake, S.A.Kazakov, and B.H.Johnston (2007).
shRNAs targeting hepatitis C: effects of sequence and structural features, and comparision with siRNA.
  Oligonucleotides, 17, 223-236.  
17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.
  Nat Rev Mol Cell Biol, 8, 479-490.  
18023283 H.K.Kini, and S.P.Walton (2007).
In vitro binding of single-stranded RNA by human Dicer.
  FEBS Lett, 581, 5611-5616.  
17704568 I.J.MacRae, and J.A.Doudna (2007).
An unusual case of pseudo-merohedral twinning in orthorhombic crystals of Dicer.
  Acta Crystallogr D Biol Crystallogr, 63, 993-999.
PDB code: 2qvw
17194582 I.J.MacRae, and J.A.Doudna (2007).
Ribonuclease revisited: structural insights into ribonuclease III family enzymes.
  Curr Opin Struct Biol, 17, 138-145.  
17873886 I.J.MacRae, K.Zhou, and J.A.Doudna (2007).
Structural determinants of RNA recognition and cleavage by Dicer.
  Nat Struct Mol Biol, 14, 934-940.  
17189683 J.A.Worrall, and B.F.Luisi (2007).
Information available at cut rates: structure and mechanism of ribonucleases.
  Curr Opin Struct Biol, 17, 128-137.  
17169989 J.Jiang, J.Sheng, N.Carrasco, and Z.Huang (2007).
Selenium derivatization of nucleic acids for crystallography.
  Nucleic Acids Res, 35, 477-485.
PDB codes: 1z7i 2dlj 2gpx 2h05
17288571 M.D.Woodhams, P.F.Stadler, D.Penny, and L.J.Collins (2007).
RNase MRP and the RNA processing cascade in the eukaryotic ancestor.
  BMC Evol Biol, 7, S13.  
17401559 M.Meissner, C.Agop-Nersesian, and W.J.Sullivan (2007).
Molecular tools for analysis of gene function in parasitic microorganisms.
  Appl Microbiol Biotechnol, 75, 963-975.  
17459519 M.Thomas, J.J.Lu, J.Chen, and A.M.Klibanov (2007).
Non-viral siRNA delivery to the lung.
  Adv Drug Deliv Rev, 59, 124-133.  
17955462 R.Cottam, W.Ranson, and R.Vounckx (2007).
Re-mapping Robert Rosen's (M,R)-systems.
  Chem Biodivers, 4, 2352-2368.  
17466622 S.Hur, and R.M.Stroud (2007).
How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.
  Mol Cell, 26, 189-203.
PDB codes: 2nqp 2nr0 2nre
17658285 S.U.Colmenares, S.M.Buker, M.Buhler, M.Dlakić, and D.Moazed (2007).
Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi.
  Mol Cell, 27, 449-461.  
17704815 S.Y.Sohn, W.J.Bae, J.J.Kim, K.H.Yeom, V.N.Kim, and Y.Cho (2007).
Crystal structure of human DGCR8 core.
  Nat Struct Mol Biol, 14, 847-853.
PDB code: 2yt4
17228249 T.Federici, and N.M.Boulis (2007).
Ribonucleic acid interference for neurological disorders: candidate diseases, potential targets, and current approaches.
  Neurosurgery, 60, 3.  
17259216 T.Katoh, and T.Suzuki (2007).
Specific residues at every third position of siRNA shape its efficient RNAi activity.
  Nucleic Acids Res, 35, e27.  
17299129 W.Ritchie, M.Legendre, and D.Gautheret (2007).
RNA stem-loops: to be or not to be cleaved by RNAse III.
  RNA, 13, 457-462.  
17586815 X.S.Chen, T.S.Rozhdestvensky, L.J.Collins, J.Schmitz, and D.Penny (2007).
Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis.
  Nucleic Acids Res, 35, 4619-4628.  
17155910 A.A.Seyhan, A.V.Vlassov, and B.H.Johnston (2006).
RNA interference from multimeric shRNAs generated by rolling circle transcription.
  Oligonucleotides, 16, 353-363.  
16518387 A.Cook, and E.Conti (2006).
Dicer measures up.
  Nat Struct Mol Biol, 13, 190-192.  
16896014 A.V.Pertzev, and A.W.Nicholson (2006).
Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III.
  Nucleic Acids Res, 34, 3708-3721.  
16858712 B.P.Davies, and C.Arenz (2006).
A homogenous assay for micro RNA maturation.
  Angew Chem Int Ed Engl, 45, 5550-5552.  
16715068 B.R.Cullen (2006).
Is RNA interference involved in intrinsic antiviral immunity in mammals?
  Nat Immunol, 7, 563-567.  
16606868 C.I.An, V.B.Trinh, and Y.Yokobayashi (2006).
Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction.
  RNA, 12, 710-716.  
17381284 D.J.Patel, J.B.Ma, Y.R.Yuan, K.Ye, Y.Pei, V.Kuryavyi, L.Malinina, G.Meister, and T.Tuschl (2006).
Structural biology of RNA silencing and its functional implications.
  Cold Spring Harb Symp Quant Biol, 71, 81-93.  
17381281 E.Lund, and J.E.Dahlberg (2006).
Substrate selectivity of exportin 5 and Dicer in the biogenesis of microRNAs.
  Cold Spring Harb Symp Quant Biol, 71, 59-66.  
17381339 G.J.Hannon, F.V.Rivas, E.P.Murchison, and J.A.Steitz (2006).
The expanding universe of noncoding RNAs.
  Cold Spring Harb Symp Quant Biol, 71, 551-564.  
16691418 H.Cerutti, and J.A.Casas-Mollano (2006).
On the origin and functions of RNA-mediated silencing: from protists to man.
  Curr Genet, 50, 81-99.  
17053086 H.Shi, C.Tschudi, and E.Ullu (2006).
An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei.
  RNA, 12, 2063-2072.  
17381283 I.J.Macrae, F.Li, K.Zhou, W.Z.Cande, and J.A.Doudna (2006).
Structure of Dicer and mechanistic implications for RNAi.
  Cold Spring Harb Symp Quant Biol, 71, 73-80.  
16527750 J.B.Preall, Z.He, J.M.Gorra, and E.J.Sontheimer (2006).
Short interfering RNA strand selection is independent of dsRNA processing polarity during RNAi in Drosophila.
  Curr Biol, 16, 530-535.  
16751099 J.Han, Y.Lee, K.H.Yeom, J.W.Nam, I.Heo, J.K.Rhee, S.Y.Sohn, Y.Cho, B.T.Zhang, and V.N.Kim (2006).
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex.
  Cell, 125, 887-901.  
17057371 J.Kurreck (2006).
siRNA Efficiency: Structure or Sequence-That Is the Question.
  J Biomed Biotechnol, 2006, 83757.  
16954143 M.Dlakić (2006).
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold.
  Bioinformatics, 22, 2711-2714.  
16927374 R.E.Collins, and X.Cheng (2006).
Structural and biochemical advances in mammalian RNAi.
  J Cell Biochem, 99, 1251-1266.  
16766680 S.T.Grivna, E.Beyret, Z.Wang, and H.Lin (2006).
A novel class of small RNAs in mouse spermatogenic cells.
  Genes Dev, 20, 1709-1714.  
16855311 X.Ji (2006).
Structural basis for non-catalytic and catalytic activities of ribonuclease III.
  Acta Crystallogr D Biol Crystallogr, 62, 933-940.  
17381280 Y.Lee, J.Han, K.H.Yeom, H.Jin, and V.N.Kim (2006).
Drosha in primary microRNA processing.
  Cold Spring Harb Symp Quant Biol, 71, 51-57.  
17027504 Y.R.Yuan, Y.Pei, H.Y.Chen, T.Tuschl, and D.J.Patel (2006).
A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA.
  Structure, 14, 1557-1565.
PDB codes: 2f8s 2f8t
17028594 Y.Zeng (2006).
Principles of micro-RNA production and maturation.
  Oncogene, 25, 6156-6162.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.