Designing dual-targeting siRNA duplexes having two active strands that combine siRNA and microRNA-like targeting

Methods in Molecular Biology

Volumn 942, Issue , 2013, Pages 169-177

  Sætrom, Pal ^a  

^a NONE

Author keywords

Bioinformatics; Design; RNA interference; SiRNA

Indexed keywords

DUAL TARGETING SMALL INTERFERING RNA; MICRORNA; SMALL INTERFERING RNA; UNCLASSIFIED DRUG;

ARTICLE; CALCULATION; COMPUTER PROGRAM; DOWN REGULATION; GENE SEQUENCE; GENE TARGETING; PRIORITY JOURNAL;

EID: 84934438901     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-119-6_9     Document Type: Article

References (16)

1. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A (2006) 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3:199-204
2. Jackson AL, Burchard J, Schelter J, Chau BN, Cleary M, Lim L, Linsley PS (2006) Widespread siRNA "off-target" transcript silencing mediated by seed region sequence complementarity. RNA 12:1179-1187
3. Lin X, Ruan X, Anderson MG, McDowell JA, Kroeger PE, Fesik SW, Shen Y (2005) siRNAmediated off-target gene silencing triggered by a 7 nt complementation. Nucleic Acids Res 33:4527-4535
4. Tiemann K, Hohn B, Ehsani A, Forman SJ, Rossi JJ, Saetrom P (2010) Dual-targeting siRNAs. RNA 16:1275-1284
5. Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216
6. Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199-208
7. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22:326-330
8. Saetrom P (2004) Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming. Bioinformatics 20:3055-3063
9. Saetrom P, Snove O Jr (2004) A comparison of siRNA efficacy predictors. Biochem Biophys Res Commun 321:247-253
10. Hossbach M, Gruber J, Osborn M, Weber K, Tuschl T (2006) Gene silencing with siRNA duplexes composed of target-mRNA-complementary and partially palindromic or partially complementary single-stranded siRNAs. RNA Biol 3:82-89
11. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ (2004) The UCSC table browser data retrieval tool. Nucleic Acids Res 32:D493-496
12. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429-3431
13. Kim DH, Behlke MA, Rose SD, Chang MS, Choi S, Rossi JJ (2005) Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol 23:222-226
14. Rose SD, Kim DH, Amarzguioui M, Heidel JD, Collingwood MA, Davis ME, Rossi JJ, Behlke MA (2005) Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res 33: 4140-4156
15. Halaas A, Svingen B, Nedland M, Saetrom P, Snove O, Birkeland OR (2004) A recursive MISD architecture for pattern matching. Ieee T Vlsi Syst 12:727-734
16. Navarro G (2001) NR-grep: a fast and flexible pattern-matching tool. Software Pract Exper 31:1265-1312