Dual-targeting siRNAs.
We have developed an algorithm for the prediction of dual-targeting short interfering RNAs (siRNAs) in which both strands are deliberately designed to separately target different mRNA transcripts with complete complementarity. An advantage of this approach versus the use of two separate duplexes is that only two strands, as opposed to four, are competing for entry into the RNA-induced silencing complex. We chose to design our dual-targeting siRNAs as Dicer substrate 25/27mer siRNAs, since design features resembling pre-microRNAs (miRNAs) can be introduced for Dicer processing. Seven different dual-targeting siRNAs targeting genes that are potential targets in cancer therapy have been developed including Bcl2, Stat3, CCND1, BIRC5, and MYC. The dual-targeting siRNAs have been characterized for dual target knockdown in three different cell lines (HEK293, HCT116, and PC3), where they were as effective as their corresponding single-targeting siRNAs in target knockdown. The algorithm developed in this study should prove to be useful for predicting dual-targeting siRNAs in a variety of different targets and is available from http://demo1.interagon.com/DualTargeting/.
Tiemann
Katrin
K
Department of Molecular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.
Höhn
Britta
B
Ehsani
Ali
A
Forman
Stephen J
SJ
Rossi
John J
JJ
Saetrom
Pål
P
D000465:Algorithms; D001483:Base Sequence; D002460:Cell Line; D016259:Genes, myc; D006801:Humans; D007668:Kidney; D016133:Polymerase Chain Reaction / Q000379:methods; D014176:Protein Biosynthesis; D051560:Proto-Oncogene Proteins c-bcl-6 / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics*; D050796:STAT3 Transcription Factor / Q000235:genetics; D013489:Suppression, Genetic; D014158:Transcription, Genetic
D051560:Proto-Oncogene Proteins c-bcl-6; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D050796:STAT3 Transcription Factor
J Virol. 2003 Nov;77(21):11531-5
14557638
Cell. 2005 Nov 18;123(4):621-9
16271385
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
14681465
Nucleic Acids Res. 2008 May;36(9):e53
18420656
RNA Biol. 2006 Apr;3(2):82-9
17114944
Mol Ther. 2008 Jan;16(1):170-7
17726454
Cell. 2003 Oct 17;115(2):209-16
14567918
Nucleic Acids Res. 2008 Jan;36(Database issue):D707-14
18000006
Cell. 2003 Oct 17;115(2):199-208
14567917
Br J Haematol. 2004 Dec;127(5):519-30
15566355
Nucleic Acids Res. 2005 Feb 18;33(3):e30
15722476
RNA. 2004 Oct;10(10):1507-17
15383676
Nucleic Acids Res. 2007;35(7):2333-42
17389647
Nat Med. 2004 Dec;10(12):1329-35
15531890
Oligonucleotides. 2008 Dec;18(4):305-19
19025401
Nat Biotechnol. 2004 Mar;22(3):326-30
14758366
Biochem Biophys Res Commun. 2004 Aug 13;321(1):247-53
15358242
Nat Methods. 2006 Mar;3(3):199-204
16489337
Nat Biotechnol. 2009 Jun;27(6):549-55
19465925
RNA. 2007 Oct;13(10):1631-40
17684233
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4
15608248
Biochem Biophys Res Commun. 2004 Dec 17;325(3):769-73
15541356
Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
12824340
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
16199517
Bioinformatics. 2004 Nov 22;20(17):3055-63
15201190
RNA. 2006 Jul;12(7):1179-87
16682560
Cell. 2005 Nov 18;123(4):607-20
16271386
Genome Res. 2007 Dec;17(12):1865-79
17989255
RNA. 2006 Jul;12(7):1197-205
16682562