Design of small interfering rnas for antiviral applications

Methods in Molecular Biology

Volumn 721, Issue , 2011, Pages 267-292

  Rothe, Diana ^a   Wade, Erik J ^a   Kurreck, Jens ^a  

^a TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Cell viability assay; Plaque assay; RNA interference; Short hairpin RNA; shRNA; Small interfering RNA

Indexed keywords

ANIMALIA; MURINAE;

LUCIFERASE; NUCLEOTIDE; SMALL INTERFERING RNA;

ANIMAL; ARTICLE; BIOLOGY; CELL SURVIVAL; CHEMISTRY; DRUG EFFECT; GENETIC TRANSFECTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HELA CELL; HUMAN; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; REPORTER GENE; RNA INTERFERENCE; RNA STABILITY; VIRAL PHENOMENA AND FUNCTIONS; VIRUS; VIRUS CULTURE; WESTERN BLOTTING;

ANIMALS; BASE SEQUENCE; BLOTTING, WESTERN; CELL SURVIVAL; COMPUTATIONAL BIOLOGY; GENES, REPORTER; HELA CELLS; HUMANS; LUCIFERASES; NUCLEOTIDES; PLAQUE ASSAY; RNA INTERFERENCE; RNA STABILITY; RNA, SMALL INTERFERING; TRANSFECTION; VIRUS PHYSIOLOGICAL PHENOMENA; VIRUSES;

EID: 79960043811     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-037-9_17     Document Type: Article

References (22)

1. Fox, J. L. (2007) Antivirals become a broader enterprise. Nat Biotechnol 25, 1395-1402. (Pubitemid 350233129)
2. Grimm, D. (2009) Small silencing RNAs: state-of-the-art. Adv Drug Deliv Rev 61, 672-703.
3. Kurreck, J. (2009) RNA interference: from basic research to therapeutic applications. Angew Chem Int Ed Engl 48, 1378-1398.
4. Castanotto, D., and Rossi, J. J. (2009) The promises and pitfalls of RNA-interferencebased therapeutics. Nature 457, 426-433.
5. Haasnoot, J., Westerhout, E. M., and Berkhout, B. (2007) RNA interference against viruses: strike and counterstrike. Nat Biotechnol 25, 1435-1443. (Pubitemid 350233142)
6. Kurreck, J. (2006) siRNA efficiency: structure or sequence-that is the question. J Biomed Biotechnol 2006, 83757.
7. Wang, X., Wang, X., Varma, R. K., Beauchamp, L., Magdaleno, S., and Sendera, T. J. (2009) Selection of hyperfunctional siRNAs with improved potency and specificity. Nucleic Acids Res 37, e152.
8. Lee, H. S., Ahn, J., Jee, Y., Seo, I. S., Jeon, E. J., Jeon, E. S., Joo, C. H., Kim, Y. K., and Lee, H. (2007) Universal and mutation-resistant antienteroviral activity: potency of small interfering RNA complementary to the conserved cis-acting replication element within the enterovirus coding region. J Gen Virol 88, 2003-2012. (Pubitemid 47017984)
9. ter Brake, O., t Hooft, K., Liu, Y. P., Centlivre, M., von Eije, K. J., and Berkhout, B. (2008) Lentiviral vector design for multiple shRNA expression and durable HIV-1 inhibition. Mol Ther 16, 557-564. (Pubitemid 351314996)
10. Merl, S., and Wessely, R. (2007) Anticoxsackieviral efficacy of RNA interference is highly dependent on genomic target selection and emergence of escape mutants. Oligonucleotides 17, 44-53. (Pubitemid 46651427)
11. Behlke, M. A. (2008) Chemical modification of siRNAs for in vivo use. Oligonucleotides 18, 305-319. (Pubitemid 352791344)
12. Morrissey, D. V., Blanchard, K., Shaw, L., Jensen, K., Lockridge, J. A., Dickinson, B., McSwiggen, J. A., Vargeese, C., Bowman, K., Shaffer, C. S., Polisky, B. A., and Zinnen, S. (2005) Activity of stabilized short interfering RNA in a mouse model of hepatitis B virus replication. Hepatology 41, 1349-1356. (Pubitemid 40770288)
13. Jackson, A. L., Burchard, J., Leake, D., Reynolds, A., Schelter, J., Guo, J., Johnson, J. M., Lim, L., Karpilow, J., Nichols, K., Marshall, W., Khvorova, A., and Linsley, P. S. (2006) Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA 12, 1197-1205. (Pubitemid 43990545)
14. Dutkiewicz, M., Grunert, H. P., Zeichhardt, H., Lena, S. W., Wengel, J., and Kurreck, J. (2008) Design of LNA-modified siRNAs against the highly structured 5′ UTR of coxsackievirus B3. FEBS Lett 582, 3061-3066.
15. Reynolds, A., Leake, D., Boese, Q., Scaringe, S., Marshall, W. S., and Khvorova, A. (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22, 326-330. (Pubitemid 38295766)
16. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31, 3406-3415. (Pubitemid 37442169)
17. Patzel, V., Rutz, S., Dietrich, I., Koberle, C., Scheffold, A., and Kaufmann, S. H. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat Biotechnol 23, 1440-1444. (Pubitemid 41679398)
18. Schubert, S., Grunweller, A., Erdmann, V. A., and Kurreck, J. (2005) Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. J Mol Biol 348, 883-893. (Pubitemid 40544389)
19. Westerhout, E. M., Ooms, M., Vink, M., Das, A. T., and Berkhout, B. (2005) HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome. Nucleic Acids Res 33, 796-804. (Pubitemid 40361009)
20. Sun, G., and Rossi, J. J. (2009) Problems associated with reporter assays in RNAi studies. RNA Biol 6, 406-411.
21. Elmen, J., Thonberg, H., Ljungberg, K., Frieden, M., Westergaard, M., Xu, Y., Wahren, B., Liang, Z., Orum, H., Koch, T., and Wahlestedt, C. (2005) Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality. Nucleic Acids Res 33, 439-447. (Pubitemid 40276964)
22. Rothe, D., Werk, D., Niedrig, S., Horbelt, D., Grunert, H. P., Zeichhardt, H., Erdmann, V. A., and Kurreck, J. (2009) Antiviral activity of highly potent siRNAs against echovirus 30 and its receptor. J Virol Methods 157, 211-218.