Improved asymmetry prediction for short interfering RNA s
dc.contributor.author | Malefyt, Amanda P. | en_US |
dc.contributor.author | Wu, Ming | en_US |
dc.contributor.author | Vocelle, Daniel B. | en_US |
dc.contributor.author | Kappes, Sean J. | en_US |
dc.contributor.author | Lindeman, Stephen D. | en_US |
dc.contributor.author | Chan, Christina | en_US |
dc.contributor.author | Walton, S. Patrick | en_US |
dc.date.accessioned | 2014-01-08T20:34:34Z | |
dc.date.available | 2015-03-02T14:35:34Z | en_US |
dc.date.issued | 2014-01 | en_US |
dc.identifier.citation | Malefyt, Amanda P.; Wu, Ming; Vocelle, Daniel B.; Kappes, Sean J.; Lindeman, Stephen D.; Chan, Christina; Walton, S. Patrick (2014). "Improved asymmetry prediction for short interfering RNA s." FEBS Journal (1): 320-330. | en_US |
dc.identifier.issn | 1742-464X | en_US |
dc.identifier.issn | 1742-4658 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/102096 | |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | Asymmetry | en_US |
dc.subject.other | Enhanced Green Fluorescent Protein | en_US |
dc.subject.other | Short Interfering RNA | en_US |
dc.subject.other | Ds RNA ‐Dependent Protein Kinase R | en_US |
dc.title | Improved asymmetry prediction for short interfering RNA s | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Biological Chemistry | en_US |
dc.subject.hlbtoplevel | Science | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/102096/1/febs12599.pdf | |
dc.identifier.doi | 10.1111/febs.12599 | en_US |
dc.identifier.source | FEBS Journal | en_US |
dc.identifier.citedreference | Yang X & Chan C ( 2009 ) Repression of PKR mediates palmitate‐induced apoptosis in HepG2 cells through regulation of Bcl‐2. Cell Res 19, 469 – 486. | en_US |
dc.identifier.citedreference | Noland CL, Ma E & Doudna JA ( 2011 ) siRNA repositioning for guide strand selection by human dicer complexes. Mol Cell 43, 110 – 121. | en_US |
dc.identifier.citedreference | Betancur JG & Tomari Y ( 2012 ) Dicer is dispensable for asymmetric RISC loading in mammals. RNA 18, 24 – 30. | en_US |
dc.identifier.citedreference | Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS & Khvorova A ( 2004 ) Rational siRNA design for RNA interference. Nat Biotechnol 22, 326 – 330. | en_US |
dc.identifier.citedreference | Amarzguioui M & Prydz H ( 2004 ) An algorithm for selection of functional siRNA sequences. Biochem Biophys Res Commun 316, 1050 – 1058. | en_US |
dc.identifier.citedreference | Ui‐Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki‐Hamazaki H, Juni A, Ueda R & Saigo K ( 2004 ) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res 32, 936 – 948. | en_US |
dc.identifier.citedreference | Lu ZJ & Mathews DH ( 2008 ) Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res 36, 640 – 647. | en_US |
dc.identifier.citedreference | Ichihara M, Murakumo Y, Masuda A, Matsuura T, Asai N, Jijiwa M, Shinmi J, Yatsuya H, Qiao S, Takahashi M et al. ( 2007 ) Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activites. Nucleic Acids Res 35, e123. | en_US |
dc.identifier.citedreference | Walton SP, Wu M, Gredell JA & Chan C ( 2010 ) Designing highly active siRNAs for therapeutic applications. FEBS J 277, 4806 – 4813. | en_US |
dc.identifier.citedreference | Laraki G, Clerzius G, Daher A, Melendez‐Pena C, Daniels S & Gatignol A ( 2008 ) Interactions between the double‐stranded RNA‐binding proteins TRBP and PACT define the Medipal domain that mediates protein–protein interactions. RNA Biol 5, 92 – 103. | en_US |
dc.identifier.citedreference | Birmingham A, Anderson E, Sullivan K, Reynolds A, Boese Q, Leake D, Karpilow J & Khvorova A ( 2007 ) A protocol for designing siRNAs with high functionality and specificity. Nat Protoc 2, 2068 – 2078. | en_US |
dc.identifier.citedreference | Mysara M, Garibaldi JM & El Hefnawi M ( 2011 ) MysiRNA‐Designer: a workflow for efficient siRNA design. PLoS ONE 6, e25642. | en_US |
dc.identifier.citedreference | Huesken D, Lange J, Mickanin C, Weiler J, Asselbergs F, Warner J, Meloon B, Engel S, Rosenberg A, Cohen D et al. ( 2005 ) Design of a genome‐wide siRNA library using an artificial neural network. Nat Biotechnol 23, 995 – 1001. | en_US |
dc.identifier.citedreference | Shabalina SA, Spiridonov AN & Ogurtsov AY ( 2006 ) Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics 7, 65. | en_US |
dc.identifier.citedreference | Yuan B, Latek R, Hossbach M, Tuschl T & Lewitter F ( 2004 ) siRNA selection server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res 32, W130 – W134. | en_US |
dc.identifier.citedreference | Takasaki S ( 2009 ) Selecting effective siRNA target sequences by using Bayes’ theorem. Comput Biol Chem 33, 368 – 372. | en_US |
dc.identifier.citedreference | Ladunga I ( 2006 ) More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature. Nucleic Acids Res 35, 433 – 440. | en_US |
dc.identifier.citedreference | Matveeva OV, Nechipurenko YD, Rossi L, Moore B, Saetrom P, Ogurtsov AY, Atkins JF & Shabalina SA ( 2007 ) Comparison of approaches for rational siRNA design leading to a new efficient and transparent method. Nucleic Acids Res 35, e63. | en_US |
dc.identifier.citedreference | Khvorova A, Reynolds A & Jayasena SD ( 2003 ) Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209 – 216. | en_US |
dc.identifier.citedreference | Overhoff M, Alken M, Far RK‐K, Lemaitre M, Lebleu B, Sczakiel G & Robbins I ( 2005 ) Local RNA target structure influences siRNA efficacy: a systematic global analysis. J Mol Biol 348, 871 – 881. | en_US |
dc.identifier.citedreference | Shao Y, Chan CY, Maliyekkel A, Lawrence CE, Roninson IB & Ding Y ( 2007 ) Effect of target secondary structure on RNAi efficiency. RNA 13, 1631 – 1640. | en_US |
dc.identifier.citedreference | Seitz H, Tushir J & Zamore P ( 2011 ) A 5′‐uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RNA‐induced silencing complex formation. Silence 2011, 2:4. | en_US |
dc.identifier.citedreference | Xia T, SantaLucia J Jr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C & Turner DH ( 1998 ) Thermodynamic parameters for an expanded nearest‐neighbor model for formation of RNA duplexes with Watson–Crick base pairs. Biochemistry 37, 14719 – 14735. | en_US |
dc.identifier.citedreference | Fire A, Xu S, Montgomery M, Kostas S, Driver S & Mello C ( 1998 ) Potent and specific genetic interference by double‐stranded RNA in Caenorhabditis elegans. Nature 391, 806 – 811. | en_US |
dc.identifier.citedreference | Matranga C, Tomari Y, Shin C, Bartel DP & Zamore PD ( 2005 ) Passenger‐strand cleavage facilitates assembly of siRNA into Ago2‐containing RNAi enzyme complexes. Cell 123, 607 – 620. | en_US |
dc.identifier.citedreference | Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K & Tuschl T ( 2001 ) Duplexes of 21‐nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494 – 498. | en_US |
dc.identifier.citedreference | Pollack A ( 2011 ) Drugmakers’ fever for the power of RNA interference has cooled. New York Times. | en_US |
dc.identifier.citedreference | Krieg AM ( 2011 ) Is RNAi dead? Mol Ther 19, 1001 – 1002. | en_US |
dc.identifier.citedreference | Gitig D ( 2012 ) Use of siRNA in therapeutic arena on the upswing. Genet Eng Biotech News, 12, 24 – 26. | en_US |
dc.identifier.citedreference | Davidson BL & McCray PB ( 2011 ) Current prospects for RNA interference‐based therapies. Nat Rev Genet 12, 329 – 340. | en_US |
dc.identifier.citedreference | Angart P, Vocelle D, Chan C & Walton SP ( 2013 ) Design of siRNA therapeutics from the molecular scale. Pharmaceuticals 6, 440 – 468. | en_US |
dc.identifier.citedreference | Portis AM, Carballo G, Baker GL, Chan C & Walton SP ( 2010 ) Confocal microscopy for the analysis of siRNA delivery by polymeric nanoparticles. Microsc Res Tech 73, 878 – 885. | en_US |
dc.identifier.citedreference | Lu JJ, Langer R & Chen JZ ( 2009 ) A novel mechanism is involved in cationic lipid‐mediated functional siRNA delivery. Mol Pharmaceut 6, 763 – 771. | en_US |
dc.identifier.citedreference | Siegwart DJ, Whitehead KA, Nuhn L, Sahay G, Cheng H, Jiang S, Ma M, Lytton‐Jean A, Vegas A, Fenton P et al. ( 2011 ) Combinatorial synthesis of chemically diverse core‐shell nanoparticles for intracellular delivery. Proc Natl Acad Sci USA 108, 12996 – 13001. | en_US |
dc.identifier.citedreference | Ameres SL, Martinez J & Schroeder R ( 2007 ) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130, 101 – 112. | en_US |
dc.identifier.citedreference | Brown KM, Chu C‐Y & Rana TM ( 2005 ) Target accessibility dictates the potency of human RISC. Nat Struct Mol Biol 12, 469 – 470. | en_US |
dc.identifier.citedreference | Gredell JA, Berger AK & Walton SP ( 2008 ) Impact of target mRNA structure on siRNA silencing efficiency: A large‐scale study. Biotechnol Bioeng 100, 744 – 755. | en_US |
dc.identifier.citedreference | Kiryu H, Terai G, Imamura O, Yoneyama H, Suzuki K & Asai K ( 2011 ) A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. Bioinformatics 27, 1788 – 1797. | en_US |
dc.identifier.citedreference | MacRae IJ, Ma E, Zhou M, Robinson CV & Doudna JA ( 2007 ) In vitro reconstitution of the human RISC‐loading complex. Proc Natl Acad Sci USA 105, 512 – 517. | en_US |
dc.identifier.citedreference | Maniataki E & Mourelatos Z ( 2005 ) A human, ATP‐independent, RISC assembly machine fueled by pre‐miRNA. Genes Dev 19, 2979 – 2990. | en_US |
dc.identifier.citedreference | Gredell JA, Dittmer MJ, Wu M, Chan C & Walton SP ( 2010 ) Recognition of siRNA asymmetry by TAR RNA binding protein. Biochemistry 49, 3148 – 3155. | en_US |
dc.identifier.citedreference | Kini HK & Walton SP ( 2009 ) Effect of siRNA terminal mismatches on TRBP and Dicer binding and silencing efficacy. FEBS J 276, 6576 – 6585. | en_US |
dc.identifier.citedreference | Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu JD, Hannon GJ & Joshua‐Tor L ( 2005 ) Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol 12, 340 – 349. | en_US |
dc.identifier.citedreference | Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K & Shiekhattar R ( 2005 ) TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature 436, 740 – 744. | en_US |
dc.identifier.citedreference | Haase AD, Jaskiewicz L, Zhang H, Laine S, Sack R, Gatignol A & Filipowicz W ( 2005 ) TRBP, a regulator of cellular PKR and HIV‐1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep 6, 961 – 967. | en_US |
dc.identifier.citedreference | Lima WF, Murray H, Nichols JG, Wu H, Sun H, Prakash TP, Berdeja AR, Gaus HJ & Crooke ST ( 2009 ) Human Dicer binds short single‐strand and double‐strand RNA with high affinity and interacts with different regions of the nucleic acids. J Biol Chem 284, 2535 – 2548. | en_US |
dc.identifier.citedreference | Kok KH, Ng MHJ, Ching YP & Jin DY ( 2007 ) Human TRBP and PACT directly interact with each other and associate with dicer to facilitate the production of small interfering RNA. J Biol Chem 282, 17649 – 17657. | en_US |
dc.identifier.citedreference | Lee Y, Hur I, Park SY, Kim YK, Suh MR & Kim VN ( 2006 ) The role of PACT in the RNA silencing pathway. EMBO J 25, 522 – 532. | en_US |
dc.identifier.citedreference | Ye X, Huang N, Liu Y, Paroo Z, Huerta C, Li P, Chen S, Liu Q & Zhang H ( 2011 ) Structure of C3PO and mechanism of human RISC activation. Nat Struct Mol Biol 18, 650 – 657. | en_US |
dc.identifier.citedreference | Tomari Y, Matranga C, Haley B, Martinez N & Zamore PD ( 2004 ) A protein sensor for siRNA asymmetry. Science 306, 1377 – 1380. | en_US |
dc.identifier.citedreference | Leuschner PJF, Ameres SL, Kueng S & Martinez J ( 2006 ) Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep 7, 314 – 320. | en_US |
dc.identifier.citedreference | Schwarz D, Hutvagner G, Du T, Xu Z, Aronin N & Zamore P ( 2003 ) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199 – 208. | en_US |
dc.identifier.citedreference | Frank F, Sonenberg N & Nagar B ( 2010 ) Structural basis for 5′‐nucleotide base‐specific recognition of guide RNA by human AGO2. Nature 465, 818 – 822. | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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