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Bioinformatics of siRNA Design

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1097)

Abstract

RNA interference mediated by small interfering RNAs is a powerful tool for investigation of gene functions and is increasingly used as a therapeutic agent. However, not all siRNAs are equally potent, and although simple rules for the selection of good siRNAs were proposed early on, siRNAs are still plagued with widely fluctuating efficiency. Recently, new design tools incorporating both the structural features of the targeted RNAs and the sequence features of the siRNAs substantially improved the efficacy of siRNAs. In this chapter we will present a review of sequence and structure-based algorithms behind them.

Key words

Accessibility Binding sites Computer simulation Drug design Gene targeting RNA interference RNA, small interfering/genetics Sequence analysis RNA structure 
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References

  1. 1.
    Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391(6669):806–811. http://www.hubmed.org/display.cgi?uids=9486653 Google Scholar
  2. 2.
    Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411(6836):494–498. http://www.hubmed.org/display.cgi?uids=11373684 Google Scholar
  3. 3.
    Stein CA (2001) Antisense that comes naturally. Nat Biotechnol 19(8):737–738. doi:10.1038/90783. http://dx.doi.org/10.1038/90783 Google Scholar
  4. 4.
    Holen T, Amarzguioui M, Wiiger MT, Babaie E, Prydz H (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res 30(8):1757–1766. http://www.hubmed.org/display.cgi?uids=11937629 Google Scholar
  5. 5.
    Patzel V (2007) In silico selection of active siRNA. Drug Discov Today 12(3–4):139–148. doi:10.1016/j.drudis.2006.11.015. http://dx.doi.org/10.1016/j.drudis.2006.11.015
  6. 6.
    Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J 20(23): 6877–6888. http://www.hubmed.org/display.cgi?uids=11726523 Google Scholar
  7. 7.
    Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115(2):209–216. http://www.hubmed.org/display.cgi?uids=14567918 Google Scholar
  8. 8.
    Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115(2):199–208PubMedCrossRefGoogle Scholar
  9. 9.
    Amarzguioui M, Prydz H (2004) An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 316(4):1050–1058. http://www.hubmed.org/display.cgi?uids=15044091 Google Scholar
  10. 10.
    Hohjoh H (2004) Enhancement of RNAi activity by improved siRNA duplexes. FEBS Lett 557(1–3):193–198. http://www.hubmed.org/display.cgi?uids=14741366 Google Scholar
  11. 11.
    Hsieh AC, Bo R, Manola J, Vazquez F, Bare O, Khvorova A, Scaringe S, Sellers WR (2004) A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens. Nucleic Acids Res 32(3):893–901. http://www.hubmed.org/display.cgi?uids=14769947 Google Scholar
  12. 12.
    Takasaki S, Kotani S, Konagaya A (2004) An effective method for selecting siRNA target sequences in mammalian cells. Cell Cycle 3(6):790–795PubMedCrossRefGoogle Scholar
  13. 13.
    Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res 32(3):936–948. http://www.hubmed.org/display.cgi?uids=14769950 Google Scholar
  14. 14.
    Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22(3):326–330. http://www.hubmed.org/display.cgi?uids=14758366 Google Scholar
  15. 15.
    Patzel V, Rutz S, Dietrich I, Köberle C, Scheffold A, Kaufmann SH (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat Biotechnol 23(11):1440–1444. doi:10.1038/nbt1151. http://dx.doi.org/10.1038/nbt1151 Google Scholar
  16. 16.
    Saetrom P (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics 20(17):3055–3063. http://www.hubmed.org/display.cgi?uids=15201190 Google Scholar
  17. 17.
    Ren Y, Gong W, Xu Q, Zheng X, Lin D, Wang Y, Li T (2006) siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics 22(8):1027–1028. doi:10.1093/bioinformatics/btl026. http://dx.doi.org/10.1093/bioinformatics/btl026 Google Scholar
  18. 18.
    Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D, Labow M, Reinhardt M, Natt F, Hall J (2005) Design of a genome-wide siRNA library using an artificial neural network. Nat Biotechnol 23(8):995–1001. http://www.hubmed.org/display.cgi?uids=16025102 Google Scholar
  19. 19.
    Lima WF, Monia BP, Ecker DJ, Freier SM (1992) Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31(48):12055–12061PubMedCrossRefGoogle Scholar
  20. 20.
    Vickers TA, Wyatt JR, Freier SM (2000) Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res 28(6):1340–1347. http://www.hubmed.org/display.cgi?uids=10684928 Google Scholar
  21. 21.
    Mir KU, Southern EM (1999) Determining the influence of structure on hybridization using oligonucleotide arrays. Nat Biotechnol 17(8):788–792. doi:10.1038/11732. http://dx.doi.org/10.1038/11732 Google Scholar
  22. 22.
    Milner N, Mir KU, Southern EM (1997) Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol 15(6):537–541. doi:10.1038/nbt0697-537. http://dx.doi.org/10.1038/nbt0697-537 Google Scholar
  23. 23.
    Zhao JJ, Lemke G (1998) Rules for ribozymes. Mol Cell Neurosci 11(1–2):92–97. doi:10.1006/mcne.1998.0669. http://www.hubmed.org/display.cgi?uids=9608536 Google Scholar
  24. 24.
    Ding Y, Lawrence CE (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res 29(5):1034–1046PubMedCentralPubMedCrossRefGoogle Scholar
  25. 25.
    Bohula EA, Salisbury AJ, Sohail M, Playford MP, Riedemann J, Southern EM, Macaulay VM (2003) 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. J Biol Chem 278(18):15991–15997. http://www.hubmed.org/display.cgi?uids=12604614 Google Scholar
  26. 26.
    Kretschmer-Kazemi Far R, Sczakiel G (2003) The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides. Nucleic Acids Res 31(15):4417–4424PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Xu Y, Zhang H-Y, Thormeyer D, Larsson O, Du Q, Elmén J, Wahlestedt C, Liang Z (2003) Effective small interfering RNAs and phosphorothioate antisense DNAs have different preferences for target sites in the luciferase mRNAs. Biochem Biophys Res Commun 306(3):712–717PubMedCrossRefGoogle Scholar
  28. 28.
    Vickers TA, Koo S, Bennett CF, Crooke ST, Dean NM, Baker BF (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J Biol Chem 278(9):7108–7118. http://www.hubmed.org/display.cgi?uids=12500975 Google Scholar
  29. 29.
    Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32(Web Server issue):W135–W141. doi: 10.1093/nar/gkh449. http://dx.doi.org/10.1093/nar/gkh449
  30. 30.
    Shao Y, Chan CY, Maliyekkel A, Lawrence CE, Roninson IB, Ding Y (2007) Effect of target secondary structure on RNAi efficiency. RNA 13(10):1631–1640. doi:10.1261/rna.546207. http://dx.doi.org/10.1261/rna.546207 Google Scholar
  31. 31.
    Luo KQ, Chang DC (2004) The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region. Biochem Biophys Res Commun 318(1):303–310. http://www.hubmed.org/display.cgi?uids=15110788 Google Scholar
  32. 32.
    Yoshinari K, Miyagishi M, Taira K (2004) Effects on RNAi of the tight structure, sequence and position of the targeted region. Nucleic Acids Res 32(2):691–699. http://www.hubmed.org/display.cgi?uids=14762201 Google Scholar
  33. 33.
    Overhoff M, Alken M, Far RK, Lemaitre M, Lebleu B, Sczakiel G, Robbins I (2005) Local RNA target structure influences siRNA efficacy: a systematic global analysis. J Mol Biol 348(4):871–881. http://www.hubmed.org/display.cgi?uids=15843019 Google Scholar
  34. 34.
    Schubert S, Grünweller A, Erdmann VA, Kurreck J (2005) Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions. J Mol Biol 348(4):883–893. http://www.hubmed.org/display.cgi?uids=15843020 Google Scholar
  35. 35.
    Brown JR Sanseau P (2005) A computational view of microRNAs and their targets. Drug Discov Today 10(8):595–601. http://www.hubmed.org/display.cgi?uids=15837603 Google Scholar
  36. 36.
    Ameres SL, Martinez J, Schroeder R (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130(1):101–112. doi:10.1016/j.cell.2007.04.037. http://dx.doi.org/10.1016/j.cell.2007.04.037 Google Scholar
  37. 37.
    Lu ZJ, Mathews DH (2008) Oligowalk: an online siRNA design tool utilizing hybridization thermodynamics. Nucleic Acids Res 36(Web Server issue):W104–W108. doi:10.1093/nar/gkn250. http://dx.doi.org/10.1093/nar/gkn250
  38. 38.
    Lu ZJ, Mathews DH (2008) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res 36(2):640–647. doi:10.1093/nar/gkm920. http://dx.doi.org/10.1093/nar/gkm920 Google Scholar
  39. 39.
    Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL (2008) The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26(5):578–583. doi:10.1038/nbt1404. http://dx.doi.org/10.1038/nbt1404 Google Scholar
  40. 40.
    Boese Q, Leake D, Reynolds A, Read S, Scaringe SA, Marshall WS, Khvorova A (2005) Mechanistic insights aid computational short interfering RNA design. Methods Enzymol 392:73–96. doi:10.1016/S0076-6879(04)92005-8. http://dx.doi.org/10.1016/S0076-6879(04)92005-8 Google Scholar
  41. 41.
    Mückstein U, Tafer H, Hackermüller J, Bernhart SH, Stadler PF, Hofacker IL (2006) Thermodynamics of RNA-RNA binding. Bioinformatics 22(10):1177–1182. doi:10.1093/bioinformatics/btl024. http://www.hubmed.org/display.cgi?uids=16446276 Google Scholar
  42. 42.
    Mückstein U, Tafer H, Bernhard SH, Hernandez-Rosales M, Vogel J, Stadler PF, Hofacker IL (2008) Translational control by RNA-RNA interaction: improved computation of RNA-RNA binding thermodynamics. In: Elloumi M, Küng J, Linial M, Murphy R, Schneider K, Toma C (eds) Bioinformatics research and development. Communications in computer and information science, vol 13. Springer, Berlin, pp 114–127. doi:10.1007/978-3-540-70600-7_9CrossRefGoogle Scholar
  43. 43.
    Hornung V, Guenthner-Biller M, Bourquin C, Ablasser A, Schlee M, Uematsu S, Noronha A, Manoharan M, Akira S, de Fougerolles A, Endres S, Hartmann G (2005) Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med 11(3):263–270. doi:10.1038/nm1191. http://dx.doi.org/10.1038/nm1191 Google Scholar
  44. 44.
    de Haro C, Méndez R, Santoyo J (1996) The eIF-2alpha kinases and the control of protein synthesis. FASEB J 10(12): 1378–1387PubMedGoogle Scholar
  45. 45.
    Marques JT, Williams BRG (2005) Activation of the mammalian immune system by siRNAs. Nat Biotechnol 23(11):1399–1405. doi:10.1038/nbt1161. http://dx.doi.org/10.1038/nbt1161 Google Scholar
  46. 46.
    Shao XD, Wu KC, Guo XZ, Xie M-J, Zhang J, Fan D-M (2008) Expression and significance of HERG protein in gastric cancer. Cancer Biol Ther 7(1):45–50PubMedCrossRefGoogle Scholar
  47. 47.
    Saetrom P, Snove O (2004) A comparison of siRNA efficacy predictors. Biochem Biophys Res Commun 321(1):247–253. http://www.hubmed.org/display.cgi?uids=15358242 Google Scholar
  48. 48.
    Vert JP, Foveau N, Lajaunie C, Vandenbrouck Y (2006) An accurate and interpretable model for siRNA efficacy prediction. BMC BioinformaticsGoogle Scholar
  49. 49.
    Matveeva O, Nechipurenko Y, Rossi L, Moore B, Saetrom P, Ogurtsov AY, Atkins JF, Shabalina SA (2007) Comparison of approaches for rational sirna design leading to a new efficient and transparent method. Nucleic Acids ResGoogle Scholar
  50. 50.
    Ding Y, Lawrence CE (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31(24):7280–7301PubMedCentralPubMedCrossRefGoogle Scholar
  51. 51.
    Harborth J, Elbashir SM, Vandenburgh K, Manninga H, Scaringe SA, Weber K, Tuschl T (2003) Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing. Antisense Nucleic Acid Drug Dev 13(2):83–105. doi:10.1089/108729003321629638. http://dx.doi.org/10.1089/108729003321629638
  52. 52.
    Shabalina SA, Spiridonov AN, Ogurtsov AY (2006) Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics 7:65. doi:10.1186/1471-2105-7-65. http://dx.doi.org/10.1186/1471-2105-7-65 Google Scholar
  53. 53.
    Bernhart SH, Tafer H, Mückstein U, Flamm C, Stadler PF, Hofacker IL (2006) Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol 1(1):3. doi:10.1186/1748-7188-1-3. http://www.hubmed.org/display.cgi?uids=16722605 Google Scholar
  54. 54.
    Bompfünewerer AF, Backofen R, Bernhart SH, Hertel J, Hofacker IL, Stadler PF, Will S (2008) Variations on RNA folding and alignment: lessons from benasque. J Math Biol 56:119–144. doi:10.1007/s00285-007-0107-5Google Scholar
  55. 55.
    Haley B, Zamore PD (2004) Kinetic analysis of the RNAi enzyme complex. Nat Struct Mol Biol 11(7):599–606. http://www.hubmed.org/display.cgi?uids=15170178 Google Scholar
  56. 56.
    Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS ( 2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21(6):635–637. http://www.hubmed.org/display.cgi?uids=12754523 Google Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Institut fur InformatikUniversitat LeipzigLeipzigGermany

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