SiRNA-like double-stranded RNAs are specifically protected against degradation in human cell extract

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Hoerter, John A H ^a,b   Krishnan, Vishalakshi ^a   Lionberger, Troy A ^a   Walter, Nils G ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL EXTRACT; DICER; DOUBLE STRANDED RNA; RIBONUCLEASE H; SMALL INTERFERING RNA; RIBONUCLEASE HI; RIBONUCLEASE III;

ARTICLE; CONTROLLED STUDY; DEGRADATION KINETICS; DNA RNA HYBRIDIZATION; FLUORESCENCE RESONANCE ENERGY TRANSFER; HUMAN; HUMAN CELL; RNA ANALYSIS; RNA DEGRADATION; RNA INTERFERENCE; RNA PROBE; RNA STABILITY; BLOOD; GENETICS; HELA CELL; INTRACELLULAR SPACE; METABOLISM; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE;

EUKARYOTA;

BASE SEQUENCE; CELL EXTRACTS; FLUORESCENCE RESONANCE ENERGY TRANSFER; HELA CELLS; HUMANS; INTRACELLULAR SPACE; NUCLEIC ACID HYBRIDIZATION; RIBONUCLEASE H; RIBONUCLEASE III; RNA INTERFERENCE; RNA, DOUBLE-STRANDED; RNA, SMALL INTERFERING;

EID: 79957755711     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020359     Document Type: Article

References (45)

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
2. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, et al. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411: 494-498.
3. Rana TM, (2007) Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 8: 23-36.
4. Siomi H, Siomi MC, (2009) On the road to reading the RNA-interference code. Nature 457: 396-404.
5. Castanotto D, Rossi JJ, (2009) The promises and pitfalls of RNA-interference-based therapeutics. Nature 457: 426-433.
6. Lee SK, Kumar P, (2009) Conditional RNAi: towards a silent gene therapy. Adv Drug Deliv Rev 61: 650-664.
7. Amarzguioui M, Holen T, Babaie E, Prydz H, (2003) Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res 31: 589-595.
8. Bartlett DW, Davis ME, (2007) Effect of siRNA nuclease stability on the in vitro and in vivo kinetics of siRNA-mediated gene silencing. Biotechnol Bioeng 97: 909-921.
9. Braasch DA, Jensen S, Liu Y, Kaur K, Arar K, et al. (2003) RNA interference in mammalian cells by chemically-modified RNA. Biochemistry 42: 7967-7975.
10. Chiu YL, Rana TM, (2003) siRNA function in RNAi: a chemical modification analysis. RNA 9: 1034-1048.
11. Czauderna F, Fechtner M, Dames S, Aygun H, Klippel A, et al. (2003) Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucleic Acids Res 31: 2705-2716.
12. Hoerter JA, Walter NG, (2007) Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum. RNA 13: 1887-1893.
13. Layzer JM, McCaffrey AP, Tanner AK, Huang Z, Kay MA, et al. (2004) In vivo activity of nuclease-resistant siRNAs. RNA 10: 766-771.
14. Soutschek J, Akinc A, Bramlage B, Charisse K, Constien R, et al. (2004) Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs. Nature 432: 173-178.
15. Zimmermann TS, Lee AC, Akinc A, Bramlage B, Bumcrot D, et al. (2006) RNAi-mediated gene silencing in non-human primates. Nature 441: 111-114.
16. Potenza N, Moggio L, Milano G, Salvatore V, Di Blasio B, et al. (2008) RNA Interference in Mammalia Cells by RNA-3′-PNA Chimeras. Int J Mol Sci 9: 299-315.
17. Behlke MA, (2008) Chemical modification of siRNAs for in vivo use. Oligonucleotides 18: 305-319.
18. Watts JK, Deleavey GF, Damha MJ, (2008) Chemically modified siRNA: tools and applications. Drug Discov Today 13: 842-855.
19. de Fougerolles A, Vornlocher HP, Maraganore J, Lieberman J, (2007) Interfering with disease: a progress report on siRNA-based therapeutics. Nat Rev Drug Discov 6: 443-453.
20. Ohrt T, Schwille P, (2008) siRNA modifications and sub-cellular localization: a question of intracellular transport? Curr Pharm Des 14: 3674-3685.
21. Ohrt T, Merkle D, Birkenfeld K, Echeverri CJ, Schwille P, (2006) In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5. Nucleic Acids Res 34: 1369-1380.
22. Berezhna SY, Supekova L, Supek F, Schultz PG, Deniz AA, (2006) siRNA in human cells selectively localizes to target RNA sites. Proc Natl Acad Sci USA 103: 7682-7687.
23. Raemdonck K, Remaut K, Lucas B, Sanders NN, Demeester J, et al. (2006) In situ analysis of single-stranded and duplex siRNA integrity in living cells. Biochemistry 45: 10614-10623.
24. Jagannath A, Wood MJ, (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.
25. Jarve A, Muller J, Kim IH, Rohr K, MacLean C, et al. (2007) Surveillance of siRNA integrity by FRET imaging. Nucleic Acids Res 35: e124.
26. Uhler SA, Cai D, Man Y, Figge C, Walter NG, (2003) RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer. J Am Chem Soc 125: 14230-14231.
27. Kim DH, Behlke MA, Rose SD, Chang MS, Choi S, et al. (2005) Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 23: 222-226.
28. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R, Tuschl T, (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110: 563-574.
29. Schein CH, (1997) From housekeeper to microsurgeon: the diagnostic and therapeutic potential of ribonucleases. Nat Biotechnol 15: 529-536.
30. Pileur F, Andreola ML, Dausse E, Michel J, Moreau S, et al. (2003) Selective inhibitory DNA aptamers of the human RNase H1. Nucleic Acids Res 31: 5776-5788.
31. Pham JW, Pellino JL, Lee YS, Carthew RW, Sontheimer EJ, (2004) A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell 117: 83-94.
32. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD, (2004) A protein sensor for siRNA asymmetry. Science 306: 1377-1380.
33. MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA, (2008) In vitro reconstitution of the human RISC-loading complex. Proc Natl Acad Sci USA 105: 512-517.
34. Wang HW, Noland C, Siridechadilok B, Taylor DW, Ma E, et al. (2009) Structural insights into RNA processing by the human RISC-loading complex. Nat Struct Mol Biol 16: 1148-1153.
35. Rawlings RA, Krishnan V, Walter NG, (2011) Viral RNAi Suppressor Reversibly Binds siRNA to Outcompete Dicer and RISC via Multiple Turnover. J Mol Biol in press.
36. Pellino JL, Jaskiewicz L, Filipowicz W, Sontheimer EJ, (2005) ATP modulates siRNA interactions with an endogenous human Dicer complex. Rna 11: 1719-1724.
37. Raines RT, (1998) Ribonuclease A. Chem Rev 98: 1045-1066.
38. Cerritelli SM, Crouch RJ, (2009) Ribonuclease H: the enzymes in eukaryotes. FEBS J 276: 1494-1505.
39. Walter NG, Burke JM, (2000) Fluorescence assays to study structure, dynamics, and function of RNA and RNA-ligand complexes. Methods Enzymol 317: 409-440.
40. Walter NG, (2002) Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET). Curr Protoc Nucleic Acid Chem 11.10: 11.10.11-11.10.23.
41. Hoerter JA, Lambert MN, Pereira MJ, Walter NG, (2004) Dynamics inherent in helix 27 from Escherichia coli 16S ribosomal RNA. Biochemistry 43: 14624-14636.
42. Dignam JD, Lebovitz RM, Roeder RG, (1983) Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res 11: 1475-1489.
43. Ramirez-Carrozzi V, Kerppola T, (2001) Gel-based fluorescence resonance energy transfer (gelFRET) analysis of nucleoprotein complex architecture. Methods 25: 31-43.
44. Pereira MJ, Harris DA, Rueda D, Walter NG, (2002) Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis. Biochemistry 41: 730-740.
45. Harris DA, Tinsley RA, Walter NG, (2004) Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme. J Mol Biol 341: 389-403.