Modified siRNA Structure With a Single Nucleotide Bulge Overcomes Conventional siRNA-mediated Off-target Silencing

被引：26
作者：
Dua, Pooja [1 ,2 ]
Yoo, Jae Wook [1 ]
Kim, Soyoun [2 ]
Lee, Dong-ki [1 ]
机构：
[1] Sungkyunkwan Univ, Dept Chem, Global Res Lab RNAi Med, Suwon 440746, South Korea
[2] Dongguk Univ, Dept Biomed Engn, Seoul, South Korea
来源：
MOLECULAR THERAPY | 2011年 / 19卷 / 09期
关键词：
RNA INTERFERENCE; COMPETITION POTENCY; GUIDE STRAND; SEQUENCE; DUPLEXES; DETERMINANTS; STABILITY; IDENTIFICATION; ENHANCEMENT; MISMATCHES;
D O I：
10.1038/mt.2011.109
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
Off-target gene silencing is a major concern when using RNA interference. Imperfect pairing of the antisense strand with unintended mRNA targets is one of the main causes of small interfering RNA (siRNA) off-target silencing. To overcome this, we have developed "bulge-siRNA," a modified siRNA backbone structure with a single nucleotide (nt) bulge placed in the antisense strand. We found that siRNAs with a bulge at position 2 of the antisense strand were able to discriminate better between perfectly matched and mismatched targets, with no loss in silencing of the intended target. Genome-wide analysis also revealed that the bulge-siRNAs significantly reduced off-target silencing of transcripts with complementarity to the seed region of the siRNA antisense strand. When compared to 2'-methoxy ribosyl (2'-OMe) modified siRNAs previously developed to alleviate antisense off-target silencing; the bulge modification could better discriminate between on-versus off-targets. Our results suggest that the bulge-siRNA structure is a simple, yet superior alternative to chemical modifications for minimizing off-target silencing triggered by conventional siRNA structures.
引用
收藏
页码：1676 / 1687
页数：12
相关论文
共 48 条
[1]   3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets [J].
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 .
NATURE METHODS, 2006, 3 (03) :199-204
[2]   Non-nearest-neighbor dependence of the stability for RNA bulge loops based on the complete set of group I single-nucleotide bulge loops [J].
Blose, Joshua M. ;
Manni, Michelle L. ;
Klapec, Kelly A. ;
Stranger-Jones, Yukiko ;
Zyra, Allison C. ;
Sim, Vasiliy ;
Griffith, Chad A. ;
Long, Jason D. ;
Serra, Martin J. .
BIOCHEMISTRY, 2007, 46 (51) :15123-15135
[3]   A comparison of normalization methods for high density oligonucleotide array data based on variance and bias [J].
Bolstad, BM ;
Irizarry, RA ;
Åstrand, M ;
Speed, TP .
BIOINFORMATICS, 2003, 19 (02) :185-193
[4]   A screen of chemical modifications identifies position-specific modification by UNA to most potently reduce siRNA off-target effects [J].
Bramsen, Jesper B. ;
Pakula, Malgorzata M. ;
Hansen, Thomas B. ;
Bus, Claus ;
Langkjaer, Niels ;
Odadzic, Dalibor ;
Smicius, Romualdas ;
Wengel, Suzy L. ;
Chattopadhyaya, Jyoti ;
Engels, Joachim W. ;
Herdewijn, Piet ;
Wengel, Jesper ;
Kjems, Jorgen .
NUCLEIC ACIDS RESEARCH, 2010, 38 (17) :5761-5773
[5]   Principles of MicroRNA-target recognition [J].
Brennecke, J ;
Stark, A ;
Russell, RB ;
Cohen, SM .
PLOS BIOLOGY, 2005, 3 (03) :404-418
[6]   Asymmetric Shorter-duplex siRNA Structures Trigger Efficient Gene Silencing With Reduced Nonspecific Effects [J].
Chang, Chan Il ;
Yoo, Jae Wook ;
Hong, Sun Woo ;
Lee, Shi Eun ;
Kang, Hye Suk ;
Sun, Xiangao ;
Rogoff, Harry A. ;
Ban, Changill ;
Kim, Soyoun ;
Li, Chiang J. ;
Lee, Dong-ki .
MOLECULAR THERAPY, 2009, 17 (04) :725-732
[7]   Strand-specific 5′-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity [J].
Chen, Po Yu ;
Weinmann, Lasse ;
Gaidatzis, Dimos ;
Pei, Yi ;
Zavolan, Mihaela ;
Tuschl, Thomas ;
Meister, Gunter .
RNA, 2008, 14 (02) :263-274
[8]   Knockdown of TNFR1 by the sense strand of an ICAM-1 siRNA: dissection of an off-target effect [J].
Clark, Paul R. ;
Pober, Jordan S. ;
Kluger, Martin S. .
NUCLEIC ACIDS RESEARCH, 2008, 36 (04) :1081-1097
[9]   Analysis of siRNA specificity on targets with double-nucleotide mismatches [J].
Dahlgren, Cecilia ;
Zhang, Hong-Yan ;
Du, Quan ;
Grahn, Maria ;
Norstedt, Gunnar ;
Wahlestedt, Claes ;
Liang, Zicai .
NUCLEIC ACIDS RESEARCH, 2008, 36 (09)
[10]   siRNAs: Applications in functional genomics and potential as therapeutics [J].
Dorsett, Y ;
Tuschl, T .
NATURE REVIEWS DRUG DISCOVERY, 2004, 3 (04) :318-329
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