The influence of RNA secondary structure on efficiency of siRNA silencing

IFMBE Proceedings

Volumn 39 IFMBE, Issue , 2013, Pages 398-401

  Sun, Ying ^a   Gui, Jianbin ^a   Chen, Zhaoxue ^a  

^a UNIVERSITY OF SHANGHAI FOR SCIENCE AND TECHNOLOGY   (China)

Author keywords

RNA interference; RNA secondary structure; siRNA silence efficiency

Indexed keywords

RNA INTERFERENCE; RNA SECONDARY STRUCTURES; SECONDARY STRUCTURES; SIRNA DESIGN; SIRNA SILENCING; TARGET GENES;

BIOMEDICAL ENGINEERING; EFFICIENCY; PHYSICS; RESEARCH;

RNA;

EID: 84876022532     PISSN: 16800737     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/978-3-642-29305-4_106     Document Type: Conference Paper

References (24)

1. Reynolds A, Leake D, Boese Q, Searinge S, Marshall W S, Khvorova A. Rational siRNA design for RNA interference[J].Nat Biotechnol,2004,22:326-330. (Pubitemid 38295766)
2. Amarzguioui M, Prydz H. An algorithm for selection of functional siRNA sequences[J]. Biochem Bioph Res Co, 2004,315:1050-1058. (Pubitemid 38369059)
3. Chalk A M, Wahlestedt C, Sonnhammer E L L. Improved and automated prediction of effective siRNA[J]. Biochem Bioph Res Co,2004,319:264-274. (Pubitemid 38670189)
4. Schubert S,Grunweller A,Erdmann V A and Kurreck J. Local RNA Target Structure Influences siRNA Efficacy:Systematic Analysis of Intentionally Designed Binding Regions[J]. J. Mol. Biol.2005,348:883-893. (Pubitemid 40544389)
5. Overhoff M, Alken M, Far R K, Lemaitre M, Lebleu B, Sczakiel G,Robbins L. Local RNA Target Structure Influences siRNA Efficacy: A Systematic Global Analysis[J]. J. Mol. Biol.2005,348:871-881. (Pubitemid 40544388)
6. Watts J M, Dang K K, Gorelick R J, Leonard C W,Bess J W, Swanstrom R, Burch C L & Weeks K M. Architecture and secondary structure of an entire HIV-1 RNA genome[J]. Nature.2009,460:711-719.
7. Fualig B, Richter C, Wolmert J, Schwalbe H.NMR spectroscopy of RNA[J]. Claembiochem. 2003,4(10):936-962. (Pubitemid 37267582)
8. Tinoco I, Uhlenbeck O C, Levine M D. Estimation of secondary structure in ribonucleic acids[J].Nature,1971,230(5293):362-367.
9. Jaeger J A, Turner D H, Zuker M.Improved perdiction of secondary structures for RNA[J].Proceedings of the National Academy of Sciences,1989,86(20):7706-7710. (Pubitemid 19265257)
10. Mathews DH,Sabina J, Zukel M,Turner DH. Expand sequence dependence of thermoaynamic parameters improves prediction of RNA secondary structure[J]. Journal of Molecular Biology, 1999,288(5):911-940.
11. Witwer C,Hofacker I L, Stadler P F.Prediction of Consensus RNA Secondary Sructures Including Pseudoknots[J].IEEE/ACM Transactions on Computational Biology and Bioinformatics,2004,1(2):66-77. (Pubitemid 40010918)
12. Jihong Ren,Baharak Rastegari,Anne Condom,Holger H. Hoos. Hot-Knots:Heuristic prediction of RNA secondary structures including pseudoknots[J].RNA,2005,11(10):1495-1504.
13. Ying Sun, Shenghua Ye, Hongwei Lu, Study of RNA Secondary Structure Prediction Algorithms, Advanced Materials Research, Vols. 393-395 (2012) pp 955-960
14. Heale B S E,Soifer H S, Bowers C and Rossi J J. siRNA target site secondary structure predictions using local stable substructures[J]. Nucleic Acids Research, 2005, Vol 33, No 3.
15. Patzel V, Rutz S, Dietrich I, Köberle C, Scheffold A & Kaufmann S H E. Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency[J]. Nature Biotechnology,2005,23(11): 1440-1444. (Pubitemid 41679398)
16. T. Holen, M. Amarzguioui, M.T. Wiiger, E. Babaie, H. Prydz. Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor[J]. Nucleic Acids Res. 2002:1757-1766. (Pubitemid 34679753)
17. Luo K Q,Chang D C. The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region[J]. Biochemical and Biophysical Research Communications 318,2004:303-310. (Pubitemid 38526280)
18. S. M. Yiu, Prudence W. H. Wong, T. W. Lam, Y. C. Mui,H. F. Kung, Marie Lin and Y. T. Cheung. Filtering of Ineffective siRNAs and Improved siRNA Design Tool[J]. Bioinformatics,2005,vol 21,issue 2:144-151.
19. WEI Ling,LIU Xuan,CAO Cheng. Research of siRNA Inhibition Effect in HIV-1 Gene Expression [J]Progress in Biochemistry and Biophysics,2006,33(10):1007- 1013.
20. Ding Y, Chan C Y, Lawrence C E. Sfold web server for statistical folding and rational design of nucleic acids[J]. Nucleic Acids Res, 2004, 32: W135-W141. (Pubitemid 38997315)
21. Li Jianlong,Wang Zhengzhi. Study on the relationship between SiRNA activity and mRNA secondary structure [J]. JOURNAL OF BIOMEDICAL ENGINEERING RESEARCH,2006,1(25):46-69.
22. Wang Yu-qian LI Qin-xi. Design of siRNA Showing High Gene Silence Effect [J]. Journal of Xiamen University(Natural Science),2005,44:150-153.
23. Matveeva O, Nechipurenko Y, Rossi L, et al. Comparison of approaches for rational siRNA design leading to a new efficient and transparent method[J]. Nucleic Acids Res, 2007, 35(8): 63-73.
24. hibin Qiu, Coen M. Adema and Terran Lane. A computational study of off-target effects of RNA interference[J]. Nucleic Acids Research, 2005, 33(6):1834-1847.