Analysis of siRNA specificity on targets with double-nucleotide mismatches.

@article{citeulike:2793891, abstract = {Although RNA interference as a tool for gene knockdown is a great promise for future applications, the specificity of small interfering RNA (siRNA)-mediated gene silencing needs to be thoroughly investigated. Most research regarding siRNA specificity has involved analysis of affected off-target genes instead of exploring the specificity of the siRNA itself. In this study we have developed an efficient method for generating a siRNA target library by combining a siRNA target validation vector with a nucleotide oligomix. We have used this library to perform an analysis of the silencing effects of a functional siRNA towards its target site with double-nucleotide mismatches. The results indicated that not only the positions of the mismatched base pair have an impact on silencing efficiency but also the identity of the mismatched nucleotide. Our data strengthen earlier observations of widespread siRNA off-target effects and shows that approximately 35\% of the double-mutated target sites still causes knockdown efficiency of >50\%. We also provide evidence that there may be substantial differences in knockdown efficiency depending on whether the mutations are positioned within the siRNA itself or in the corresponding target site.}, address = {Department of Molecular Medicine and Surgery, Karolinska Institutet, CMM L8:01, 171 76 Stockholm, Sweden Institute of Molecular Medicine, Peking University, Beijing 100871, China and Neuroscience Discovery, Scripps Florida, 5353 Parkside Drive RF2, Jupiter, FL 33458, USA.}, author = {Dahlgren, Cecilia and Zhang, Hong-Yan Y. and Du, Quan and Grahn, Maria and Norstedt, Gunnar and Wahlestedt, Claes and Liang, Zicai }, citeulike-article-id = {2793891}, doi = {10.1093/nar/gkn190}, issn = {1362-4962}, journal = {Nucleic acids research}, keywords = {rnai}, month = {April}, posted-at = {2008-05-13 09:18:29}, priority = {2}, title = {Analysis of siRNA specificity on targets with double-nucleotide mismatches.}, url = {http://dx.doi.org/10.1093/nar/gkn190}, year = {2008} }

TY - JOUR ID - citeulike:2793891 L3 - citeulike-article-id:2793891 TI - Analysis of siRNA specificity on targets with double-nucleotide mismatches. JF - Nucleic acids research AD - Department of Molecular Medicine and Surgery, Karolinska Institutet, CMM L8:01, 171 76 Stockholm, Sweden Institute of Molecular Medicine, Peking University, Beijing 100871, China and Neuroscience Discovery, Scripps Florida, 5353 Parkside Drive RF2, Jupiter, FL 33458, USA. SN - 1362-4962 N2 - Although RNA interference as a tool for gene knockdown is a great promise for future applications, the specificity of small interfering RNA (siRNA)-mediated gene silencing needs to be thoroughly investigated. Most research regarding siRNA specificity has involved analysis of affected off-target genes instead of exploring the specificity of the siRNA itself. In this study we have developed an efficient method for generating a siRNA target library by combining a siRNA target validation vector with a nucleotide oligomix. We have used this library to perform an analysis of the silencing effects of a functional siRNA towards its target site with double-nucleotide mismatches. The results indicated that not only the positions of the mismatched base pair have an impact on silencing efficiency but also the identity of the mismatched nucleotide. Our data strengthen earlier observations of widespread siRNA off-target effects and shows that approximately 35% of the double-mutated target sites still causes knockdown efficiency of >50%. We also provide evidence that there may be substantial differences in knockdown efficiency depending on whether the mutations are positioned within the siRNA itself or in the corresponding target site. KW - rnai AU - Dahlgren, Cecilia AU - Zhang, Hong-Yan AU - Du, Quan AU - Grahn, Maria AU - Norstedt, Gunnar AU - Wahlestedt, Claes AU - Liang, Zicai PY - 2008/04/17/ UR - http://dx.doi.org/10.1093/nar/gkn190 ER -