Capture of a Transition State Using Molecular Dynamics Creation of an Intercalation Site in dsDNA with Ethidium Cation英文文献资料.docVIP

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Capture of a Transition State Using Molecular Dynamics Creation of an Intercalation Site in dsDNA with Ethidium Cation英文文献资料.doc

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Capture of a Transition State Using Molecular Dynamics Creation of an Intercalation Site in dsDNA with Ethidium Cation英文文献资料

SAGE-HindawiAccesstoResearch JournalofNucleicAcids Volume2010,ArticleID702317,4pages doi:10.4061/2010/702317 ResearchArticle CaptureofaTransitionStateUsingMolecularDynamics: CreationofanIntercalationSiteindsDNAwithEthidiumCation ReginaR.Monaco DepartmentofEnvironmentalChemistry,MailmanSchoolofPublicHealth,ColumbiaUniversity,NewYorkNY,10032,USA CorrespondenceshouldbeaddressedtoReginaR.Monaco,rm2441@ Received3June2009;Revised17November2009;Accepted28January2010 AcademicEditor:JohnA.Hartley Copyright?2010ReginaR.Monaco.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttributionLicense, whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited. ThemechanismofintercalationandtheabilityofdoublestrandedDNA(dsDNA)toaccommodateavarietyofligandsinthis mannerhasbeenwellstudied.Proposedmechanisticstepsalongthispathwayfortheclassicalintercalatorethidiumhavebeen discussedintheliterature.Somepreviousstudiesindicatethatthecreationofanintercalationsitemayoccurspontaneously,with theenergyforthisinteractionarisingeitherfromsolventcollisionsorsolitonpropagationalongthehelicalaxis.Asubsequent 1Ddi?usionalsearchbytheligandalongthehelicalaxisoftheDNAwillallowtheligandentrytothisintercalationsitefromits external,electrostaticallystabilizedposition.Othermechanisticstudiesshowthatethidiumcationparticipatesinthecreationofthe site,asaligandinteractingcloselywiththeexternalsurfaceoftheDNAcancauseunfavorablestericinteractionsdependingonthe ligands’orientation,whicharerelaxedduringthecreationofanintercalationsite.Brie?y,suchasiteiscreatedbythelengthening oftheDNAmoleculeviabondrotationbetweenthesugarsandphosphatesalongtheDNAbackbone,causinganunwindingofthe dsDNAitselfandseparationbetweentheadjacentbasepairslocaltothepositionoftheligand,whichbecomestheintercalation site.Previousexperimentalmeasurementsofthisinteractionmeasuretheenthalpiccostofthispartofthemechanismtobeabout ?8kcal/mol.Thispaperreportstheobservation,duringacomputationals