Production of highly potent recombinant siRNAs in Escherichia coli

Nature Protocols

Volumn 8, Issue 12, 2013, Pages 2325-2336

  Huang, Linfeng ^a,b   Lieberman, Judy ^a,b  

^a BOSTON CHILDREN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; PROTEIN P19; RECOMBINANT RNA; RNA BINDING PROTEIN; SHORT HAIRPIN RNA; SMALL INTERFERING RNA;

3' UNTRANSLATED REGION; ARTICLE; ESCHERICHIA COLI; GENE SEQUENCE; GENE SILENCING; GENE TARGETING; MOLECULAR WEIGHT; PRIORITY JOURNAL; PROTEIN EXPRESSION; RNA PURIFICATION; RNA SEQUENCE; RNA SYNTHESIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA;

BASE SEQUENCE; CELL LINE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; ESCHERICHIA COLI; GENE EXPRESSION; GENE KNOCKDOWN TECHNIQUES; HELA CELLS; HUMANS; PLASMIDS; RNA INTERFERENCE; RNA, BACTERIAL; RNA, SMALL INTERFERING;

EID: 84888384910     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.149     Document Type: Article

References (35)

1. Fire, A. et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811 (1998).
2. Hamilton, A.J. & Baulcombe, D.C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286, 950-952 (1999).
3. Knight, S.W. & Bass, B.L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269-2271 (2001).
4. Bohmert, K. et al. AGO1 defines a novel locus of Arabidopsis controlling leaf development. EMBO J. 17, 170-180 (1998).
5. Carmell, M.A., Xuan, Z., Zhang, M.Q. & Hannon, G.J. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev. 16, 2733-2742 (2002).
6. Baulcombe, D. RNA silencing in plants. Nature 431, 356-363 (2004).
7. Ding, S.W. & Voinnet, O. Antiviral immunity directed by small RNAs. Cell 130, 413-426 (2007).
8. Elbashir, S.M. et al. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498 (2001).
9. Caplen, N.J., Parrish, S., Imani, F., Fire, A. & Morgan, R.A. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc. Natl. Acad. Sci. USA 98, 9742-9747 (2001).
10. Yang, D. et al. Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc. Natl. Acad. Sci. USA 99, 9942-9947 (2002).
11. Myers, J.W., Jones, J.T., Meyer, T. & Ferrell, J.E. Jr. Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat. Biotechnol. 21, 324-328 (2003).
12. Kittler, R. et al. Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies. Nat. Methods 4, 337-344 (2007).
13. Myers, J.W. et al. Minimizing off-target effects by using diced siRNAs for RNA interference. J. RNAi Gene Silencing 2, 181-194 (2006).
14. Stewart, S.A. et al. Lentivirus-delivered stable gene silencing by RNAi in primary cells. RNA 9, 493-501 (2003).
15. Zhao, H.F. et al. High-throughput screening of effective siRNAs from RNAi libraries delivered via bacterial invasion. Nat. Methods 2, 967-973 (2005).
16. Li, Z., Fortin, Y. & Shen, S.H. Forward and robust selection of the most potent and noncellular toxic siRNAs from RNAi libraries. Nucleic Acids Res. 37, e8 (2009).
17. Xiang, S., Fruehauf, J. & Li, C.J. Short hairpin RNA-expressing bacteria elicit RNA interference in mammals. Nat. Biotechnol. 24, 697-702 (2006).
18. Tenllado, F., Martinez-Garcia, B., Vargas, M. & Diaz-Ruiz, J.R. Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus infections. BMC Biotechnol. 3, 3 (2003).
19. Aalto, A.P. et al. Large-scale production of dsRNA and siRNA pools for RNA interference utilizing bacteriophage phi6 RNA-dependent RNA polymerase. RNA 13, 422-429 (2007).
20. Huang, L. et al. Efficient and specific gene knockdown by small interfering RNAs produced in bacteria. Nat. Biotechnol. 31, 350-356 (2013).
21. Blau, J.A. & McManus, M.T. Renewable RNAi. Nat. Biotechnol. 31, 319-320 (2013).
22. Voinnet, O., Pinto, Y.M. & Baulcombe, D.C. Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc. Natl. Acad. Sci. USA 96, 14147-14152 (1999).
23. Silhavy, D. et al. A viral protein suppresses RNA silencing and binds silencing-generated, 21-to 25-nucleotide double-stranded RNAs. EMBO J. 21, 3070-3080 (2002).
24. Ye, K., Malinina, L. & Patel, D.J. Recognition of small interfering RNA by a viral suppressor of RNA silencing. Nature 426, 874-878 (2003).
25. Jin, J., Cid, M., Poole, C.B. & McReynolds, L.A. Protein mediated miRNA detection and siRNA enrichment using p19. Biotechniques 48, xvii-xxiii (2010).
26. Xiao, J., Feehery, C.E., Tzertzinis, G. & Maina, C.V. E. coli RNase III(E38A) generates discrete-sized products from long dsRNA. RNA 15, 984-991 (2009).
27. Smith, D.B. & Corcoran, L.M. Expression and purification of glutathione-S-transferase fusion proteins. Curr. Protoc. Mol. Biol. 28, 16.7.1-16.7.7 (2001).
28. Henschel, A., Buchholz, F. & Habermann, B. DEQOR: a web-based tool for the design and quality control of siRNAs. Nucleic Acids Res. 32, W113-W120 (2004).
29. Surendranath, V., Theis, M., Habermann, B.H. & Buchholz, F. Designing efficient and specific endoribonuclease-prepared siRNAs. Methods Mol. Biol. 942, 193-204 (2013).
30. Lee, S.K. et al. Lentiviral delivery of short hairpin RNAs protects CD4 T cells from multiple clades and primary isolates of HIV. Blood 106, 818-826 (2005).
31. Boese, Q. et al. Mechanistic insights aid computational short interfering RNA design. Methods Enzymol. 392, 73-96 (2005).
32. Chen, P.Y. et al. Strand-specific 5′-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA 14, 263-274 (2008).
33. Jackson, A.L. et al. Position-specific chemical modification of siRNAs reduces 'off-target' transcript silencing. RNA 12, 1197-1205 (2006).
34. Jackson, A.L. et al. Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21, 635-637 (2003).
35. Robbins, M. et al. 2′-O-methyl-modified RNAs act as TLR7 antagonists. Mol. Ther. 15, 1663-1669 (2007).