Prediction for Target Sites of Small Interfering RNA Duplexes in SARS Coronavirus.docx

PredictionforTargetSitesofSmallInterferingRNADuplexesinSARSCoronavirusThisinformationhasnotbeenpeer-reviewed.Responsibilityforthefindingsrestssolelywiththeauthor(三).DepositedresearcharticlePredictionforTargetSitesofSmallInterferingRNDuplexesinSRSCoronavirusFengminJi1and1.iaofu1.uo23Addresses:1InstituteforBiologicalScienceandTechnology,FacultyofSciences,NorthJiaotongUniversity,Beijing,100044China.21.aboratoryofTheoreticalBiophysics,FacultyofSciencesandTechnology,InnerMongoliaUniversity,Hohhot,010021China.3CenterforTheoreticalBiology,PekingUniversity,Beijing,100871China.Correspondence:1.iaofu1.uo.E-mail:lfluomail.imu.eduPosted:16January2004Received:14January2001GenomeBiology2001,5:P6Theelectronicversionofthisarticleisthecompleteoneandcanbefoundonlineat200452P6Thisisthefirstversionofthisarticletobemadeavailableublicly.2004BioMedCentral1.td.depositedresearchASASERVICETOTHERESEARCHCOMMUNlTY,GEN0MEBlO1.OGYPROVIDESA'PREPRINT'DEPOSITORYT0WHICHANYORIGINA1.RESEARCHCANBESUBMITTEDANDWHlCHA1.1.INDIVIDUA1.SCANACCESSFREEOFCHARGE.ANYARTIC1.ECANBESUBMITTEDBYAUT1IORS,WH0HAVESO1.ERESPONSTBI1.ITYFORTHEARTIC1.E,SCONTENT.THEON1.YSCREENINGISTOENSURERE1.EVNCEOFTHEPREPRINTTOGENOMEBIO1.OGY,SSCOPEANDTOAVOIDABUSIVE,1.IBE1.1.OUSORINDECENTARTIC1.ES.ARTIC1.ESINTHISSECTIONOFTHEJOURNA1.HAVENOTBEENPEER-REVIEWED.EACHPREPRINTHASPERMNENTUR1.,BYWHICHITCANBECITED.RESEARCHSUBMITTEDTOTHEPREPRINTDEPOSITORYMAYBESIMU1.TNEOUS1.YORSUBSEQUENT1.YSUBMITTEDTOGENOMEBIO1.OGYORANYOTHERPUB1.ICATIONFORPEERREVIEW;THEON1.YREQUIREMENTISANEXP1.ICITCITTIONOF,AND1.INKTO,THEPREPRINTINANYVERSIONOFTHEARTIC1.ETHATISEVENTUA1.1.YPUB1.ISHED.IFPOSSIB1.E,GENOMEBIO1.OGYWI1.1.PROVIDEARECIPROCA1.1.INKFROMTHEPREPRINTTOTHEPUB1.ISHEDARTIC1.E.GenomeBiology2004,5:P6PredictionforTargetSitesofSmallInterferingRNADuplexesinSARSCoronavirusFengminJi11.iaofu1.uo2,3*1InstituteforBiologicalScienceandTechnology,FacultyofSciences,NorthJiaotongUniversity,Beijing,100044China;21.aboratoryofTheoreticalBiophysics,FacultyofSciencesandTechnology,InnerMongoliaUniversity,Hohhot,010021China;3CenterforTheoreticalBiology,PekingCoronavirus,SmallInterferingRNADuplex,TargetSite,Anti-virusdrugdesignRunningheadTargetSitesofsiRNAinSARS-CoV*correspondingauthor,towhomcorrespondenceshouldbeaddressed.Mailingaddress:1.iaofu1.uo1.aboratoryofTheoreticalBiophysics,FacultyofSciencesandTechnology,InnerMongoliaUniversity,Hohhot,010021ChinaEmai1address:IfIUoWmail.imu.eduFax:0086-471-49517611AbstractRNinterferenceisusedforSARS-rcIatedpharmaceuticalresearchanddevelopment.Followingbioinformaticmethodtwentyseven21'25base-longsequencesegmentsinSARS-CoVgenomearepredictedastheoptimaltargetsitesofsmallinterferingRNAduplexes.SARS(severeacuterespiratorysyndrome)wasfirstidentifiedinGuangdongProvince,ChinaandrapidlyspreadtomanyregionsinChinaandaroundtheworld.Itcauseddeathanddisastertothousandsofhumanbeings.However,theactivedrugintreatingSARShasnotbeenfoundyet.Thegenomesequencesdeterminedbyseveralgroupsl-3showthatitisavariantofcoronaviruses,belongingtosingle-strandedplussenseRNviruses.Thegenomeisabout30kbinlength,anditsseveralencodedproteinshavebeenseparatedandpurified.ThisUniversity,Beijing,100871ChinaKeywordsSRSprovidesasoundbasisforSARSrelatedpharmaceuticalresearchanddevelopment.Theuseofdouble-strandedRNA(dsRN)tomanipulategeneexpression(RNAinterferenceorRNAi)hasbeenpi'ovedhighlyeffective,atleast10timesmoreeffectivethaneitherusingsenseorantisenseRNAsalone4.TheRNAitriggeredbydsRNAisaphenomenonofhomo1ogy-dependentgenesilencing567.Itwasfoundthatthesmal1interferingRNA(SiRNA,21-25nt1ong)playsanimportantroleinRNAi-relatedgenesilencingpathways8.Progresshasalsobeenmadeinanti-HIVandanti-HCVdrugdesignbyapplyingthemethodofRNinterference9-10.TodesignanIi-SARS-CoVdrug,onestrategyistosearchforsiRNAswhichspecificallyinterferethegeneexpressionandblockthegenomereplicationofSARS-associatedcoronavirus.Inthisnoteweshal1maketheoreticalpredictiononthepossibletargetsitesofsiRNAsinthevirusgenome.2Uponinfectionofanappropriatehostcell,theviralenvelopeisfusedwithcel1membraneandtheviralplussenseRNAentersthehostcell.Thenthe5mostORFoftheviralgenomeistranslatedintoseveralnonstructuralproteinsincludinganRNA-dependentRNApolymeraseandanATPasehelicase.Theseproteinsinturnareresponsibleforreplicatingtheviralgenomeaswellasgeneratingnestedtranscriptsthatareusedinthesynthesisoftheviralproteins.Thetranscriptionallyactive,SUbgenomiC-SiZeminusstrandsarealsodiscovered2.ThesiRNA-mediatedRNAinterferencehasstrongspecificity,andmayplaycertainrolesinaffectingtheprocessofvirusexpressionandproliferation.RNAsecondarystructureiscomposedofdouble-strandedregionofstackedbasepairs(stem)andsingle-strandedregion(loop).RNAstructurepredictionscomprisebase-pairedandnon-base-pairedregionsinvarioustypesofloopandjunctionarrangements(includinghairpinloop,bulgeloop,interior1oopandjunctionsormulti-loopsl1).Only21'25ntlong(ormore)non-base-pairedregionscanbeservedasthetargetsitesofsiRNA.Theyarecalledfreesegments.Thelongnon-