siRNA efficiency: Structure or sequence - That is the question

Journal of Biomedicine and Biotechnology

Volumn 2006, Issue , 2006, Pages

  Kurreck, Jens ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; MICRORNA; SMALL INTERFERING RNA;

ALGORITHM; BINDING SITE; GENE SEQUENCE; GENE SILENCING; GENE TARGETING; REVIEW; RISK FACTOR; RNA INTERFERENCE; RNA SEQUENCE; RNA STRUCTURE; SYSTEMATIC REVIEW; THERMODYNAMICS; WEB BROWSER;

EID: 33746907851     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/JBB/2006/83757     Document Type: Review

References (56)

1. Eckstein F. Small non-coding RNAs as magic bullets. Trends in Biochemical Sciences. 2005;30(8):445-452.
2. Ryther RCC, Flynt AS, Phillips JA III, Patton JG. siRNA therapeutics: big potential from small RNAs. Gene Therapy. 2005;12(1):5-11.
3. Grünweller A, Hartmann RK. RNA interference as a gene-specific approach for molecular medicine. Current Medicinal Chemistry. 2005;12(26):3143-3161.
4. Jayasena SD. Designer siRNAs to overcome the challenges in a stolen natural process. Journal of RNAi and Gene Silencing. 2006;2(1):109-117.
5. MacRae IJ, Zhou K, Li F, et al. Structural basis for double-stranded RNA processing by Dicer. Science. 2006;311(5758):195-198.
6. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature. 2001;411(6836):494-498.
7. Bertrand J-R, Pottier M, Vekris A, Opolon P, Maksimenko A, Malvya C. Comparison of antisense oligonucleotides and siRNAs in cell culture and in vivo. Biochemical and Biophysical Research Communications. 2002;296(4):1000-1004.
8. Grünweller A, Wyszko E, Bieber B, Jahnel R, Erdmann VA, Kurreck J. Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2'O-methyl RNA, phosphorothioates and small interfering RNA. Nucleic Acids Research. 2003;31(12):3185-3193.
9. Miyagishi M, Hayashi M, Taira K. Comparison of the suppressive effects of antisense oligonucleotides and siRNAs directed against the same targets in mammalian cells. Antisense and Nucleic Acid Drug Development. 2003;13(1):1-7.
10. Leung RKM, Whittaker PA. RNA interference: from gene silencing to gene-specific therapeutics. Pharmacology and Therapeutics. 2005;107(2):222-239.
11. Sioud M, Iversen PO. Ribozymes, DNAzymes and small interfering RNAs as therapeutics. Current Drug Targets. 2005;6(6):647-653.
12. Shankar P, Manjunath N, Lieberman J. The prospect of silencing disease using RNA interference. Journal of the American Medical Association. 2005;293(11):1367-1373.
13. Uprichard SL. The therapeutic potential of RNA interference. FEBS Letters. 2005;579(26):5996-6007.
14. Ambros V. The functions of animal microRNAs. Nature. 2004;431(7006):350- 355.
15. Stein CA. Antisense that comes naturally. Nature Biotechnology. 2001;19(8):737-738.
16. Holen T, Amarzguioui M, Wiiger MT, Babaie E, Prydz H. Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Research. 2002;30(8):1757-1766.
17. Elbashir SM, Harborth J, Weber K, Tuschl T. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods. 2002;26(2):199-213.
18. Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell. 2003;115(2):209-216.
19. Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD. Asymmetry in the assembly of the RNAi enzyme complex. Cell. 2003;115(2):199-208.
20. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A. Rational siRNA design for RNA interference. Nature Biotechnology. 2004;22(3):326-330.
21. Ui-Tei K, Naito Y, Takahashi F, et al. Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Research. 2004;32(3):936-948.
22. Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences. Biochemical and Biophysical Research Communications. 2004;316(4):1050-1058.
23. Chalk AM, Wahlestedt C, Sonnhammer ELL. Improved and automated prediction of effective siRNA. Biochemical and Biophysical Research Communications. 2004;319(1):264-274.
24. Sandy P, Ventura A, Jacks T. Mammalian RNAi: a practical guide. BioTechniques. 2005;39(2):215-224.
25. Huesken D, Lange J, Mickanin C, et al. Design of a genomewide siRNA library using an artificial neural network. Nature Biotechnology. 2005;23(8):995-1001.
26. Hutvagner G. Small RNA asymmetry in RNAi: function in RISC assembly and gene regulation. FEBS Letters. 2005;579(26):5850-5857.
27. Liu J, Carmell MA, Rivas FV, et al. Argonaute2 is the catalytic engine of mammalian RNAi. Science. 2004;305(5689):1437-1441.
28. Song J-J, Smith SK, Hannon GJ, Joshua-Tor L. Crystal structure of argonaute and its implications for RISC slicer activity. Science. 2004;305(5689):1434-1437.
29. Rivas FV, Tolia NH, Song JJ, et al. Purified Argonaute2 and an siRNA form recombinant human RISC. Nature Structural & Molecular Biology. 2005;12(4):340-349.
30. Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD. A protein sensor for siRNA asymmetry. Science. 2004;306(5700):1377-1380.
31. Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell. 2005;123(4):631-640.
32. Matranga C, Tomari Y, Shin C, Bartel DP, Zamore PD. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell. 2005;123(4):607-620.
33. Rand TA, Petersen S, Du F, Wang X. Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell. 2005;123(4):621-629.
34. Chendrimada TP, Gregory RI, Kumaraswamy E, et al. TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature. 2005;436(7051):740-744.
35. 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 Research. 2003;31(15):4417-4424.
36. Bohula EA, Salisbury AJ, Sohail M, 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. Journal of Biological Chemistry. 2003;278(18):15991-15997.
37. Vickers TA, Koo S, Bennett CF, Crooke ST, Dean NM, Baker BF. Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. Journal of Biological Chemistry. 2003;278(9):7108-7118.
38. Luo KQ, Chang DC. The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region. Biochemical and Biophysical Research Communications. 2004;318(1):303-310.
39. Yoshinari K, MiyagishiM, Taira K. Effects on RNAi of the tight structure, sequence and position of the targeted region. Nucleic Acids Research. 2004;32(2):691-699.
40. Overhoff M, Alken M, Kretschmer-Kazemi Far R, et al. Local RNA target structure influences siRNA efficacy: a systematic global analysis. Journal of Molecular Biology. 2005;348(4):871-881.
41. Brown KM, Chu C-Y, Rana TM. Target accessibility dictates the potency of human RISC. Nature Structural and Molecular Biology. 2005;12(5):469-470.
42. Schubert S, Grünweller A, Erdmann VA, Kurreck J. Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. Journal of Molecular Biology. 2005;348(4):883-893.
43. Wilson JA, Jayasena S, Khvorova A, et al. RNA interference blocks gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(5):2783-2788.
44. Phipps KM, Martinez A, Lu J, Heinz BA, Zhao G. Small interfering RNA molecules as potential anti-human rhinovirus agents: in vitro potency, specificity, and mechanism. Antiviral Research. 2004;61(1):49-55.
45. Werk D, Schubert S, Lindig V, et al. Developing an effective RNA interference strategy against a plus-strand RNA virus: silencing of coxsackievirus B3 and its cognate coxsackievirus-adenovirus receptor. Biological Chemistry. 2005;386(9):857-863.
46. Schubert S, Grunert H-P, Zeichhardt H, Werk D, Erdmann VA, Kurreck J. Maintaining inhibition: siRNA double expression vectors against coxsackieviral RNAs. Journal ofMolecular Biology. 2005;346(2):457-465.
47. Yuan J, Cheung PKM, Zhang HM, Chau D, Yang D. Inhibition of Coxsackievirus B3 replication by small interfering RNAs requires perfect sequencematch in the central region of the viral positive strand. Journal of Virology. 2005;79(4):2151-2159.
48. Ding Y, Chan CY, Lawrence CE. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Research. 2004;32(web server issue):W135-W141.
49. Schramm G, Ramey R. siRNA design including secondary structure target site prediction. Nature Methods. 2005;2(8):1-2. application note.
50. Patzel V, Rutz S, Dietrich I, Köberle C, Scheffold A, Kaufmann SHE. Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nature Biotechnology. 2005;23(11):1440-1444.
51. Kittler R, Putz G, Pelletier L, et al. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature. 2004;432(7020):1036-1040.
52. Kim D-H, Behlke MA, Rose SD, Chang M-S, Choi S, Rossi JJ. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nature Biotechnology. 2005;23(2):222-226.
53. Siolas D, Lerner C, Burchard J, et al. Synthetic shRNAs as potent RNAi triggers. Nature Biotechnology. 2005;23(2):227-231.
54. Rose SD, Kim D-H, Amarzguioui M, et al. Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Research. 2005;33(13):4140-4156.
55. Stegmeier F, Hu G, Rickles RJ, Hannon GJ, Elledge SJ. A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference inmammalian cells. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(37):13212-13217.
56. Silva JM, Li MZ, Chang K, et al. Second-generation shRNA libraries covering the mouse and human genomes. Nature Genetics. 2005;37(11):1281-1288.