title: Validating siRNA using a reporter made from synthetic DNA oligonucleotides.
abstract: Only a small fraction of all siRNAs are effective in silencing their target genes, and siRNA efficacy can only be determined experimentally. Previously described reporter-based siRNA validation methods all rely on the availability of physical cDNA clones, and this limits the high throughput applicability of the method. In the current report, we used short synthetic DNA fragment containing a siRNA targeting site, instead of cDNA, to fuse with a reporter gene. When targeting such transcripts with different siRNAs, we found that such constructs can faithfully report the efficacy of the corresponding siRNAs in a sequence specific manner, even when the inserted DNA fragment is essentially only long enough to cover the targeting site. The efficacy of both vector-based siRNA and synthetic siRNA can be evaluated using this system. Since only readily available short synthetic DNA fragments are needed for forming the evaluation vector, this method provides an appealing way of validating siRNAs in high throughput.
authors.affiliation: Center for Genomics and Bioinformatics, Karolinska Institutet, 171 77 Stockholm, Sweden.
authors.forename: Quan
authors.initials: Q
authors.lastname: Du
authors.forename: Håkan
authors.initials: H
authors.lastname: Thonberg
authors.forename: Hong-Yan
authors.initials: HY
authors.lastname: Zhang
authors.forename: Claes
authors.initials: C
authors.lastname: Wahlestedt
authors.forename: Zicai
authors.initials: Z
authors.lastname: Liang
mesh_terms: D000818:Animals; D020137:Base Pair Mismatch; D001483:Base Sequence; D001681:Biological Assay / Q000191:economics / Q000379:methods; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D005786:Gene Expression Regulation; D017930:Genes, Reporter; D006801:Humans; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000378:metabolism*; D016366:Open Reading Frames; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism*
chemical_list: D009841:Oligonucleotides; D034741:RNA, Small Interfering; D004247:DNA