Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency

Nature Biotechnology

Volumn 23, Issue 11, 2005, Pages 1440-1444

  Patzel, Volker ^a   Rutz, Sascha ^b   Dietrich, Isabell ^a   Köberle, Christian ^a   Scheffold, Alexander ^b   Kaufmann, Stefan H E ^a  

^a MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY   (Germany)

^b DEUTSCHES RHEUMA FORSCHUNGSZENTRUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION METHODS; GENES; STRUCTURE (COMPOSITION);

MRNA TARGETS; RNA-INDUCED SILENCING;

RNA;

COMPLEMENTARY DNA; JAGGED1; SMALL INTERFERING RNA;

ARTICLE; BASE PAIRING; GENE SILENCING; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; RNA INTERFERENCE; RNA SEQUENCE; RNA STRUCTURE; TERMINAL SEQUENCE; THERMODYNAMICS;

ALGORITHMS; BIOTECHNOLOGY; CELL LINE; DNA PRIMERS; GENE SILENCING; GREEN FLUORESCENT PROTEINS; HUMANS; MICRORNAS; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES, ANTISENSE; PLASMIDS; RNA; RNA INTERFERENCE; RNA, GUIDE; RNA, SMALL INTERFERING; THERMODYNAMICS;

EID: 27944473306     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt1151     Document Type: Article

References (29)

1. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498 (2001).
2. Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. Identification of novel genes coding for small expressed RNAs. Science 294, 853-858 (2001).
3. Lau, N.C., Lim, L.P., Weinstein, E.G. & Bartel, D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862 (2001).
4. Lee, R.C. & Ambros, V. An extensive class of small RNAs in Caenorhabditis elegans. Science 294, 862-864 (2001).
5. Meister, G. et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185-197 (2004).
6. Fagard, M., Boutet, S., Morel, J.B., Bellini, C. & Vaucheret, H. AGO1, QDE-2, and RDE-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc. Natl. Acad. Sci. USA 97, 11650-11654 (2000).
7. Hammond, S.M., Boettcher, B., Caudy, A.A., Kobayashi, R. & Hannon, G.J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146-1150 (2001).
8. Tomari, Y., Matranga, C., Haley, B., Martinez, N. & Zamore, P.D. A protein sensor for siRNA asymmetry. Science 306, 1377-1380 (2004).
9. Khvorova, A., Reynolds, A. & Jayasena, S.D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209-216 (2003).
10. Schwarz, D.S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208 (2003).
11. Reynolds, A. et al. Rational siRNA design for RNA interference. Nat. Biotechnol. 22, 326-330 (2004).
12. Ui-Tei, K. et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res. 32, 936-948 (2004).
13. Kretschmer-Kazemi Far, R. & Sczakiel, G. The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides. Nucleic Acids Res. 31, 4417-4424 (2003).
14. Bohula, E.A. et al. The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript. J. Biol. Chem. 278, 15991-15997 (2003).
15. Vickers, T.A. Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem. 278, 7108-7118 (2003).
16. Heale, B.S.E., Soifer, H.S., Bowers, C. & Rossi, J.J. SiRNA target site secondary structure predictions using local stable substructures. Nucleic Acids Res. 33, e30 (2005).
17. Schubert, S., Grunweller, A., Erdmann., V.A. & Kurreck, J. Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. J. Mol. Biol. 348, 883-893 (2005).
18. Overhoff, M. et al. Local RNA target structure influences siRNA efficacy: a systematic global analysis. J. Mol. Biol. 348, 871-881 (2005).
19. Zuker, M. & Stiegler, P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133-148 (1981).
20. McCaskill, J.S. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119 (1990).
21. Griffiths-Jones, S. The microRNA registry. Nucleic Acids Res. 32 Database issue, D109-111 (2004).
22. Doench, J.G. & Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504-511 (2004).
23. Haley, B. & Zamore, P. Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol. 11, 599-606 (2004).
24. Schwarz, D.S., Hutvágner, G., Haley, B. & Zamore, P.D. Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol. Cell 10, 537-548 (2002).
25. Ma, J-B. et al. Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434, 666-670 (2005).
26. Rivas, F.V. et al. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat. Struct. Mol. Biol. 12, 340-349 (2005).
27. Patzel, V. & Sczakiel, G. Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells. Nat. Biotechnol. 16, 64-68 (1998).
28. Mathews, D.H., Burkard, M.E., Freier, S.M., Wyatt, J.R. & Turner, D.H. Predicting oligonucleotide affinity to nucleic acid targets. RNA 5, 1458-1469 (1999).
29. Hofacker, I.L. Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429-3431 (2003).