siRNA target site secondary structure predictions using local stable substructures

被引:107
作者
Heale, BSE [1 ]
Soifer, HS [1 ]
Bowers, C [1 ]
Rossi, JJ [1 ]
机构
[1] Beckman Res Inst City Hope, Grad Sch Biol Sci, Duarte, CA 91010 USA
关键词
D O I
10.1093/nar/gni026
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The crystal structure based model of the catalytic center of Ago2 revealed that the siRNA and the mRNA must be able to form an A-helix for correct positing of the scissile phosphate bond for cleavage in RNAi. This suggests that base pairing of the target mRNA with itself, i.e. secondary structure, must be removed before cleavage. Early on in the siRNA design, GC-rich target sites were avoided because of their potential to be involved in strong secondary structure. It is still unclear how important a factor mRNA secondary structure is in RNAi. However, it has been established that a difference in the thermostability of the ends of an siRNA duplex dictate which strand is loaded into the RNA-induced silencing complex. Here, we use a novel secondary structure prediction method and duplex-end differential calculations to investigate the importance of a secondary structure in the siRNA design. We found that the differential duplex-end stabilities alone account for functional prediction of 60% of the 80 siRNA sites examined, and that secondary structure predictions improve the prediction of site efficacy. A total of 80% of the non-functional sites can be eliminated using secondary structure predictions and duplex-end differential.
引用
收藏
页码:1 / 10
页数:10
相关论文
共 43 条
[21]   Structure and nucleic-acid binding of the Drosophila Argonaute 2 PAZ domain [J].
Lingel, A ;
Simon, B ;
Izaurralde, E ;
Sattler, M .
NATURE, 2003, 426 (6965) :465-469
[22]   Argonaute2 is the catalytic engine of mammalian RNAi [J].
Liu, JD ;
Carmell, MA ;
Rivas, FV ;
Marsden, CG ;
Thomson, JM ;
Song, JJ ;
Hammond, SM ;
Joshua-Tor, L ;
Hannon, GJ .
SCIENCE, 2004, 305 (5689) :1437-1441
[23]   The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region [J].
Luo, KQ ;
Chang, DC .
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2004, 318 (01) :303-310
[24]   Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain [J].
Ma, JB ;
Ye, KQ ;
Patel, DJ .
NATURE, 2004, 429 (6989) :318-322
[25]   RISC is a 5′ phosphomonoester-producing RNA endonuclease [J].
Martinez, J ;
Tuschl, T .
GENES & DEVELOPMENT, 2004, 18 (09) :975-980
[26]   Predicting oligonucleotide affinity to nucleic acid targets [J].
Mathews, DH ;
Burkard, ME ;
Freier, SM ;
Wyatt, JR ;
Turner, DH .
RNA, 1999, 5 (11) :1458-1469
[27]   Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure [J].
Mathews, DH ;
Sabina, J ;
Zuker, M ;
Turner, DH .
JOURNAL OF MOLECULAR BIOLOGY, 1999, 288 (05) :911-940
[28]   THE EQUILIBRIUM PARTITION-FUNCTION AND BASE PAIR BINDING PROBABILITIES FOR RNA SECONDARY STRUCTURE [J].
MCCASKILL, JS .
BIOPOLYMERS, 1990, 29 (6-7) :1105-1119
[29]   A KINETIC APPROACH TO THE PREDICTION OF RNA SECONDARY STRUCTURES [J].
MIRONOV, AA ;
DYAKONOVA, LP ;
KISTER, AE .
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1985, 2 (05) :953-962
[30]   REGULATION OF MESSENGER-RNA ACCUMULATION BY A HUMAN-IMMUNODEFICIENCY-VIRUS TRANSACTIVATOR PROTEIN [J].
MUESING, MA ;
SMITH, DH ;
CAPON, DJ .
CELL, 1987, 48 (04) :691-701