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