Sniffing for gene-silencing efficiency of siRNAs in HeLa cells in comparison with that in HEK293T cells: Correlation between knockdown efficiency and sustainability of siRNAs revealed by FRET-based probing

Nucleic Acid Therapeutics

Volumn 23, Issue 2, 2013, Pages 152-159

  Shin, Seonmi ^a   Kim, Yea Seul ^a   Kim, Jisu ^a   Kwon, Hyun Mi ^b   Kim, Dong Eun ^b   Hah, Sang Soo ^a  

^a Kyung Hee University   (South Korea)

^b Konkuk University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

ARTICLE; CONTROLLED STUDY; DISSOCIATION; FEMALE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE SILENCING; HUMAN; HUMAN CELL; IMAGE ANALYSIS; PRIORITY JOURNAL; RNA DEGRADATION; RNA PROBE; SNIFFING;

FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; GENE KNOCKDOWN TECHNIQUES; GENE SILENCING; HEK293 CELLS; HELA CELLS; HUMANS; NANOTECHNOLOGY; RNA, SMALL INTERFERING; TRANSFECTION;

EID: 84876264039     PISSN: 21593337     EISSN: None     Source Type: Journal    
DOI: 10.1089/nat.2012.0396     Document Type: Article

References (35)

1. AMARZGUIOUI, M., HOLEN, T., BABAIE, E., and PRYDZ, H. (2003). Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res. 31, 589-595.
2. BARTLETT, D.W., and DAVIS, M.E. (2007). Effect of siRNA nuclease stability on the in vitro and in vivo kinetics of siRNAmediated gene silencing. Biotechnol. Bioeng. 97, 909-921.
3. BEREZHNA, S.Y., SUPEKOVA, L., SUPEK, F., and SCHULTZ, P.G. (2006). siRNA in human cells selectively localizes to target RNA sites. Proc. Natl. Acad. Sci. U. S. A. 103, 7682-7687.
4. BRAASCH, D.A., JENSEN, S., LIU, Y., KAUR, K., ARAR, K., WHITE, M.A., and COREY, D.R. (2003). RNA interference in mammalian cells by chemically modified RNA. Biochemistry 42, 7967-7975.
5. CASTANOTTO, D., and ROSSI, J.J. (2009). The promises and pitfalls of RNA-interference-based therapeutics. Nature 457, 426-433.
6. CHIU, Y.L., and RANA, T.M. (2003). siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034-1048.
7. CZAUDERNA, F., FECHTNER, M., DAMES, S., AYGUN, H., KLIPPEL, A., PRONK, G.J., GIESE, K., and KAUFMANN, J. (2003). Structural variations and stabilizing modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res. 31, 2705-2716.
8. ELBASHIR, S.M., LENDECKEL, W., and TUSCHL, T. (2001A). RNA interference is mediated by 21-and 22-nucleotide RNAs. Genes Dev. 15, 188-200.
9. ELBASHIR, S.M., HARBORTH, J., LENDECKEL, W., YALCIN, A., WEBER, K., and TUSCHL, T. (2001B). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498.
10. FILIPOWICZ, W. (2005). RNAi: the nuts and bolts of the RISC machine. Cell 122, 17-20.
11. FIRE, A., XU, S., MONTGOMERY, M.K., KOSTAS, S.A., DRIVER, S.E., and MELLO, C.C. (1998). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806-811.
12. HOLEN, T., AMARZGUIOUI, M., WIIGER, M.T., BABAIE, E., and PRYDZ, H. (2002). Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res. 30, 1757-1766.
13. JAGANNATH, A., and WOOD, M.J. (2009). Localization of double-stranded small interfering RNA to cytoplasmic processing bodies is Ago2 dependent and results in up-regulation of GW182 and Argonaute-2. Mol. Biol. Cell 20, 521-529.
14. JÄRVE, A., MULLER, J., KIM, I.H., ROHR, K., MACLEAN, C., FRICKER, G., MASSING, U., EBERLE, F., DALPKE, A., ET AL. (2007). Surveillance of siRNA integrity by FRET imaging. Nucleic Acids Res. 35, e124.
15. KIM, Y.S., KIM, M.Y., SONG, J.K., KIM, T.J., KIM, Y.D., and HAH, S.S. (2012A). Stepwise fluorescence changes of quantum dots: single-molecule spectroscopic studies on the properties of turn-on quantum dots. Chem. Commun. 48, 723-725.
16. KIM, M.Y., KIM, J., and HAH, S.S. (2012B). Poly(A)-targeting molecular beacons: FRET-based in vitro quantitation and time-dependent imaging in live cells. Anal. Biochem. 429, 92-98.
17. LAYZER, J.M., MCCAFFREY, A.P., TANNER, A.K., HUANG, Z., KAY, M.A., and SULLENGER, B.A. (2004). In vivo activity of nuclease-resistant siRNAs. RNA 10, 766-771.
18. LEE, S.K., and KUMAR, P. (2009). Conditional RNAi: Towards a silent gene therapy. Adv. Drug Deliv. Rev. 61, 650-664.
19. LEUSCHNER, P.J., AMERES, S.L., KUENG, S., and MARTINEZ, J. (2006). Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep. 7, 314-320.
20. LIU, Q., and PAROO, Z. (2010). Biochemical principles of small RNA pathways. Annu. Rev. Biochem. 79, 295-319.
21. MATRANGA, C., TOMARI, Y., SHIN, C., BARTEL, D.P., and ZAMORE, P.D. (2005). Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607-620.
22. MEISTER, G., LANDTHALER, M., PATKANIOWSKA, A., DORSETT, Y., TENG, G., and TUSCHL, T. (2004). Human argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15, 185-197.
23. MIYOSHI, K., TSUKUMO, H., NAGAMI, T., SIOMI, H., and SIOMI, M.C. (2005). Slicer function of Drosophila Argonautes and its involvement in RISC. Genes Dev. 19, 2837-2848.
24. NAKANISHI, K., WEINBERG, D.E., BARTEL, D.P., and PATEL, D.J. (2012). Structure of yeast Argonaute with guide RNA. Nature 486, 368-374.
25. NOVINA, C.D., MURRAY, M.F., DYKXHOOM, D.M., BERESFORD, P.J., RIESS, J., LEE, S.K., COLLMAN, R.G., LIEBERMAN, J., SHANKAR, P., and SHARP, P.A. (2002). siRNAdirected inhibition of HIV-1 infection. Nat. Med. 8, 681-686.
26. OHRT, T., MERKLE, D., BIRKENFELD, K., ECHEVERRI, C.J., and SCHWILLE, P. (2006). Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells. Nucleic Acids Res. 34, 1369-1380.
27. OHRT, T., and SCHWILLE, P. (2008). siRNA modifications and sub-cellular localization: a question of intracellular transport? Curr. Pharm. Des. 14, 3674-3685.
28. RAEMDONCK, K., REMAUT, K., LUCAS, B., SANDERS, N.N., DEMEESTER, J., and DE SMEDT, S.C. (2006). In situ analysis of single-stranded and duplex siRNA integrity in living cells. Biochemistry 45, 10614-10623.
29. RANA, T.M. (2007). Illuminating the silence: understanding the structure and function of small RNAs. Nat. Rev. Mol. Cell. Biol. 8, 23-36.
30. ROY, R., HOHNG, S., and HA, T. (2008). A practical guide to single-molecule FRET. Nat. Methods 5, 507-516.
31. SHIN, S., KWON, H.M., YOON, K.S., KIM, D.E., and HAH, S.S. (2011). FRET-based probing to gain direct information on siRNA sustainability in live cells: asymmetric degradation of siRNA strands. Mol. BioSyst. 7, 2110-2113.
32. SIOMI, H., and SIOMI, M.C. (2009). On the road to reading the RNA-interference code. Nature 457, 396-404.
33. SONTHEIMER, E.J. (2005). Assembly and function of RNA silencing complexes. Nat. Rev. Mol. Cell. Biol. 6, 127-138.
34. UHLER, S.A., CAI, D., MAN, Y., FIGGE, C., and WALTER, N.G. (2003). RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer. J. Am. Chem. Soc. 125, 14230-14231.
35. ZAMORE, P.D., TUSCHL, T., SHARP, P.A., and BARTEL, D.P. (2000). RNAi: double-stranded RNA directs the ATPdependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25-33.