Application of Equilibrium Models of Solution Hybridization to Microarray Design and Analysis 英文参考文献.docVIP

Application of Equilibrium Models of Solution Hybridization to Microarray Design and Analysis 英文参考文献.doc

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Application of Equilibrium Models of Solution Hybridization to Microarray Design and Analysis 英文参考文献

ApplicationofEquilibriumModelsofSolution HybridizationtoMicroarrayDesignandAnalysis RaadZ.Gharaibeh1,JoshuaM.Newton2,JenniferW.Weller1,CynthiaJ.Gibas1* 1Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America, 2Department of PhysicianAssistantStudies,WakeForestUniversitySchoolofMedicine,Winston-Salem,NorthCarolina,UnitedStatesofAmerica Abstract Background:Theprobepercentboundvalue,calculatedusingmulti-stateequilibriummodelsofsolutionhybridization,is shown to be useful in understanding the hybridization behavior of microarray probes having 50 nucleotides, with and without mismatches. These longer oligonucleotides are in widespread use on microarrays, but there are few controlled studiesoftheirinteractionswithmismatchedtargetscomparedto25-merbasedplatforms. PrincipalFindings:50-meroligonucleotideswithcentrallyplacedsingle,doubleandtriplemismatcheswerespottedonan array.Overarangeoftargetconcentrationsitwaspossibletodiscriminatebindingtoperfectmatchesandmismatches,and the type of mismatch could be predicted accurately in the concentration midrange (100pM to 200pM) using solution hybridizationmodelingmethods.Theseresultshaveimplicationsformicroarraydesign,optimizationandanalysismethods. Conclusions:Ourresultshighlighttheimportanceofincorporatingbiophysicalfactorsinboththedesignandtheanalysis ofmicroarrays.Useoftheprobe‘‘percentbound’’valuepredictedbyequilibriummodelsofhybridizationisconfirmedtobe important for predicting and interpreting the behavior of long oligonucleotide arrays, as has been shown for short oligonucleotidearrays. Citation: Gharaibeh RZ, Newton JM, Weller JW, Gibas CJ (2010) Application of Equilibrium Models of Solution Hybridization to Microarray Design and Analysis.PLoSONE5(6):e11048.doi:10.1371/journal.pone.0011048 Editor:ArkadyB.Khodursky,UniversityofMinnesota,UnitedStatesofAmerica ReceivedMarch5,2010;AcceptedMay17,2010;PublishedJune10,2010 Copyright: ?2010 Ghara

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