KCF系列快开式静密封磁力搅拌反应釜结构及使用简介 jz.docin.com...
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KoshlandLab,CarnegieInstitutehttp://www.ciwemb.edu/labs/koshland/Protocols/MICROTUBULE/mmb.html- DeterminetheOD600andcorrelatethecelldensityfromthechart.Setupfour100mLYPDculturesatthefollowingdensities:0.7x105,1x105,and3.0x105cells/mL
- GROWTHOFCELLS
- Grow100mLofcellstoOD600=0.7-0.8at23oC.
- Add5-10ulofBME,15minutesbeforespin.
- Harvestcellsintwo50mLconicaltubes,spin1.5-2.0Kfor8-10min.
- SPHEROPLASTING.ResUSPendcellsin4mLYWB.*NOTE:Ifcellshavebeenarrestedwithnocodazoleoralphafactor,includetheinhibitorintheYWB.Letsitatroomtemperaturefor2-3min.Addoxalyticase[12uL1mg/mlstock].Incubateat23oCwithgentleshakingtoformspheroplasts.Spheroplastingshouldbecompletewithinonehour;avoidincubationslongerthan1h,15min
- TransferspheroplastedcellstoaTOMYtube.Spinat3.5Kfor7min.Resuspendcellsin4mLYWB(containing5%glyceroland1mMPMSF[0.2Mstockin100%EtOH])bygentlypipettingupanddown,usinga1mLpipet.Spinat3.5Kfor7min.
- Gentlyresuspendcellsin2.5mL1xEBB(containing5%glyceroland0.4mMPMSF).
- Allowcellsto"swell"for10min.atroomtemperature,thentransfertohomogenizer.[RinsedouncewithH2O,EtOHtoclean.RinsedouncewithEBBbeforeusing.]Homogenizecellswith5pestlestrokes(upanddownisonestroke).Avoidintroducingair.TransfertocleanTOMYtube.
- Add150uL5MNaCl(finalconcentration~0.3M).Incubateatroomtemperaturefor5min.
- Add5mL1xEBB-plus(containing5%glycerol,0.1mMDTTand150ug/mLBSA).Thus,finalconcentrationsin7.5mLlysateare0.1MNaCl.Incubateatroomtemperaturefor45min.
- Meanwhile,thawmicrotubule"seeds"andputat37oCfor30min.Addtaxolto10uM(e.g.1ul0.13mMtaxolto15ulMTseeds)andincubateanadditional15min.
- Remove250ulsampleforTOTALMATERIAL("1T").Keepthistubeatroomtemperature,soastobecomparabletotheothersamples.DivideremaininglysatebetweenEppendorfstubes.
- CLARIFYLYSATES
- Spineppendorftubesat15Kfor20min.Poolsupernatantsina15mLconicaltubeandmixgently.Aliquotlysatetomicrofugetubes(between800uland1ml).Spinmicrofugetubesat15Kfor20min.
- Remove250ulTOTALSUPERNATANT("1TS")toafreshtube.
- Remove500ulclarifiedlysatefromeachmicrofugetubetoafreshtube.Add5ul1mMtaxol(inDMSO)toeachtube-finalconcentrationis10uMtaxol.Mixgently.
- Forastandardtitrationofbindingactivity,addmicrotubulestoeachtubeindecreasingamount.Normally,8,4,2,1,0.5and0uls(MTsmadefrom~3-6mg/mlPCbovinetubulin).For0.5ul,makea10-folddilutionofMTsinBRB80/30%glycerolbuffer(containing10uMtaxol).Allowbindingtoproceedatroomtemperaturefor15min.
- Pelletmicrotubule/minichromosomemixat15Kfor8min.ItshouldbepossIBLetoseethelargerMTpellets.
- Remove250ulofeachsupernatanttofreshtube.ThesearetheSUPERNATANTFRACTIONS.AspirateallresidualliquidwithdrawnoutPasteurpipets.
- ResuspendMTpelletsin250ulof1xEBB(containing0.1mMDTT,100mMNaCl,5%glyceroland1mg/mlBSA,butNOPMSF!).ThesearethePELLETFRACTIONS.NOTE:Ultimately,PELLETswillbe2xconcentratedrelativetoSUPs.
- Add250ulof2xASSAULTbuffer(containingtRNAandøX174)toallsamples.Removeproteinbyadding20ulsofProteinaseKsolution(15mg/mlfromBoehringerMannheim)toeachtube.Incubatetubesat50oCfor~1-1.5h(longerisbetter).
- AfterProteinaseKtreament,precipitateDNAbyadding250ul6MNH4OAcand700mlisopropanol.Storeat-20oCovernight.
- SpindownDNAat15K,30min.4oC.Carefullyaspirateordecantsupernatants,removingasmuchsupernatantaspossible.NOTE:The"PELLETSAMPLE"precipitatedpelletsareoftensmall.WashallDNApelletswith100-200ul70%ethanol.Spinbriefly(~5min)andaspiratetheethanolsupernatant.AllowDNApelletstoairdry.Donotinverttubes.
- ResuspendallDNApelletsin30ulTE,incubatingatroomtemperatureor4oCforseveralhours.
- PREPARATIONOFSAMPLESFORSOUTHERNANALYSIS.
- Remove15ulofeachsampletoafreshtube.Add1ulDNase-freeRNase(BoehringerMannheim,1:1000dilutionof2U/ulstock)to1T,1Ts,andallSUPERNATANTfraction.ThePELLETfractionsdonothavetobe"RNased".Incubateatroomtemperatureforatleast30min.Addsamplebuffertoalltubes.
- Loadsamplesontoa0.6%agarosegelcontainingEtBrat0.2ug/ml.Includeasmallamountofsupercoiledtestplasmid(e.g.pDK370)intheDNAsizestandardstoserveasapositivecontrolforhybridization.Thefinalconcentrationofsupercoiledplasmidshouldbesuchthat~0.1ngisloaded.Rungelat20or30Vovernight.
- Photographgel.NotewhethertheintensitiesoftheøX174bandsareeveninalllanesandwhether2ucircleDNAisvisibleintheSUPERNATANTfractions.
- ProcessgelfortransfertoGeneScreenPlusaccordingtothePosiblotprotocol.Transferforatleast90min.UVcrosslinkDNAtomembrane.Airdry.
- HYBRIDIZATION.
- Prehybridizeblotat65oCfor~3hinChurchbuffercontaining0.5mg/mldenaturesalmonspermDNA(usually14mlChurchbufferplus0.7ml10mg/mlSSDNAperblot).Addprobe105cpmsperlane)andhybridizeat65oCovernight(atleast18h).Washblot2xwithBuffer1,15mineachat65oCand2xwithBuffer2,15mineachat65oC.Monitortheblot--thelastwashmaynotbenecessary.NOTE:Usethe0.9kbSmaI/PstIURA3fragmentfrompDK377tovisualizepDK370orotherURA3-containingplasmids.Usethe1.8kbSalI/ClaILEU2fragmentfrompDK255tovisualizeYCp41orotherLEU2-containingplasmids.Usethe~2kbXhoI/SalIfragmentfromCV13tovisualizeendogenous2ucircleDNA.Note:makeuptheYWB,EBB2Xassaultbufferfresheachexperiment.
YWBper10ml5mL2MSorbitol(ifNZarrested,add40uL1.5mg/mL0.336mL1MK2HPO4N2to4mLYWB)0.064mL1MKH2PO44.6mLdH2O | YWB,glycerol,PMSF5mL2MSorbitol0.336mL1MK2HPO40.064mL1MKH2PO40.5mL100%ultrapureglycerol0.05mL0.2MPMSF4.05mLdH2O | 1XEBB,glycerol,PMSF(5mL)1mL5XEBB0.25mL100%glycerol12.5uL0.2MPMSF3.75uLdH2O | 1XEBB,glycerol,DTT,BSA(10mL)2mL5XEBB0.5mLglycerol10uL100mg/mLBSA10uL0.1MDTT7.48mLdH2O | 1XEBB,DTT,NaCl,BSA5mL1mL5XEbb5uL0.1MDTT0.1mL5MNaCl50uL100mg/mLBSA0.25mLglycerol3.6mLdH2O2mLEBB0.2mLNaCl0.1BSA | |
REAGENTS | | YWB:50mL2Msorbitol16.8mL0.2MK2HPO43.2mL0.2MKH2PO430mLH2O | 0.1MDTT | 0.2MPMSFinethanolorispropanol | Glusulase | 5XEBB:5mL1MMgCl25mLTRIS-HCl,pH7.40.1mL0.5MEDTA90mLH2O | 5MNaCl | 1mMtaxolinDMSO | 2XASSAULTBUFFER:5mL10%SDS,UltraPure5mL0.5MEDTA5mLHEPES-KOH,pH7.6[7.5w/NaOH]85mLH2O**2XA.B.canbefrozenin10mLaliquots.[3.5mLAssaultbuffer,0.5mLtRNA/øX174] | tRNA/øX174DNA:1mL1mg/mLtRNAinH2O0.1mL10ug/mLuncutøX174DNA | 5XBRB80100mLs5Xstock80mMPipespH6.8(KOH)10mL800mMPipespH6.8(KOH)1mMEGTA1ml100mMEGTA1mMMgCl20.1mL1MMgCl2 | MINICHROMOSOME-MICROTUBULEBINDINGASSAY- GROWTHOFCELLS.Grow100mLofcellstoOD600=0.7-0.8at23oC.Forgoodbindingactivityithasprovedimportanttomaintaincellsinlogphase.Normally,2dayspriortodayofexperiment,asinglemedium-sizedcologyispickedfromselectivemediumandinoculatedinto5mLYPS(or-URA,asIdo).Twoadditionaldilutionsaremadefromthis"neat"inoculum(e.g.1:10and1:25).Thegoalistohavelatelogphaseculturesthenextday(~4x107cells/mL).
- Thedaypriortoexperiment,makea1:10dilutionofthesuitable5mLovernight.DeterminetheOD600andcorrelatingcelldensityfromthechart.Setupthree100mLYPDculturesatthefollowingdensities:~0.7x105,1x105and1.5x105cells/mL.
- Harvestcellsintwo50mLconicaltubes,1.5-2.0Kfor8-10min.WashwithH2Oandconsolidatecellsinonetube.Re-spin.NOTE:Ifcellshavebeenarrestedwithnocodazoleorafactor,includetheinhibitorintheH2Owash.
- SPHEROPLASTING.
- Re-suspendcellsin4mLYWB(containing10mMbeta-mercaptoethanoland1mMPMSF).Lesitatroomtemperaturefor2-3min.Add100uLglusulase.Incubateat23oCwithgentleshakingtoformspheroplasts.Spheroplstingshouldbecompletewithinonehour;avoidincubationslongerthan1h,15min.NOTE:Ifcellshavebeenarrestedwithnocodaoleoralphafactor,includetheinhibitorintheYWB.
- TransferspheroplastedcellstoaTOMYtube.Spinat3.5Kfor7min.Re-suspendcellsin4mLYWB(containing1mMPMSFonly)bygentlypipettingupanddown,usinga1mLplasticpipet.Re-spin.Repeatwashprocess,foratotaloftwowashes.NOTE:Ifcellshavebeenarrestedwithnocodazoleoralphafactor,includetheinhibitorintheFIRSTWASHONLY.
- Gentlyreuspendcellsin2.5mL1XEBB(containing0.1mMDTTand0.5mMPMSF).Transfertohomogenizer.
- Allowcellsto"swell"for10minatroomtemperature,thenhomogenizecellswith5pestlestrokes(upanddownisonestroke).Avoidintroducingair.TransfertocleanTOMYtube.
- Add150uL5MNaCl(finalconcentration~0.3M).Incubateatroomtemperaturefor5min.
- Add5mL1XEBB-plus(containing0.1mMDTT,150ug/mLBSA,and0.5mMPMSF).Thus,finalconcentrationsin7.5mLlysateare0.1MNaCland100ug/mLBSA.Incubateatroomtemperaturefor45min.
- Thawmicrotubule"seeds"andputat37oCfor30min.Addtaxolto10uM(e.g.1uL0.13mMtaxolto12uLMTs)andincubateanadditional15min.
- Remove250uLsampleforTOTALMATERIAL(so-called"1T").Keepthistube(and1Ts,seebelow)atroomtemperature,soastobecomparabletotheothersamples.DivideremaininglysatebetweentwoTOMYtubes.
- CLARIFYLYSATES.
- SpinTOMYtubesat15Kfor20min.Poolsupernatantsina10mLconicaltubeandmixgently.Aliquotlysatetomicrofugetubes.Theminimumnumberoftubesis[1thenumberofbindingreactionsplanned](usually0.7-1mLextractpertube).Spinmicrofugetubesat15Kfor20min.
- Remove250uLSTARTINGMATERIAL("1TS")toafreshtube.
- Remove500uLclarifiedlysatefromeachmicrofugetubetoafreshtube.Add5uL1mMtaxol(inDMSO)toeachtube-finalconcentrationis10uMtaxol.Mixgently.
- Forastandardtitrationofbindingactivity,addmicrotubulestoeachtubeinincreasingamount.Normally,0,0.2,0.5,1,2,and4uLFor0.2uLand0.5uL,makea10-folddilutionofMTsinBRB80/30%glycerolbuffer(containing10uMtaxol).Allowbindingtoproceedatroomtemperaturefor15min.
- PelletMTs(andassociatedminichromosomes)at15Kfor8min.ItshouldbepossibletoseethelargerMTpellets(usuallybluish-white).
- Remove250uLofeachsupernatanttofreshtube.ThesearetheSUPERNATANTFRACTIONS.AspirateallresidualliquidwithdrawnoutPasteurpipets.
- ResuspendMTpelletsin250uLof1XEBB(containing0.1mMDTT,100mMNaCl,and1mg/mlBSA,butNOPMSF!).ThesearethePELLETFRACTIONS.NOTE:Ultimately,PELLETswillbe2XconcentratedrelativetoSUPs.
- Add250uLof2XASSAULTbuffer(containingtRNAandøX174DNA)toallsamples(i.e.allsupsandpellets,aswellas1Tand1Ts).Removeproteinbyadding5mLofProteinaseKsolution(20mg/mLfromBoehringerMannheim)toeachtube.Incubatetubesat50oCfor~1-1.5h.(longerisbetter).
- AfterProteinaseKtreatment,precipitateDNAbyadding250uL6MNH4OAcand500uLisopropanol.Storeat-20oCovernight.
- SpindownDNAinTOMYat15K,30min.4oC.Carefullyaspirateordecantsupernatants,removingasmuchsupernatantaspossible.NOTE:The"PELLET"pelletsareoftensmall.WashallDNApelletswith100-200uL70%ethanol.Spinbriefly(~5min.)andaspiratetheethanolsupernatant.AllowDNApelletstoairdry.Donotinverttubes.
- ResuspendallDNApelletsin30uLTE,incubatingatroomtemperatureor4oCforseveralhours.
- PREPARATIONOFSAMPLESFORSOUTHERNANALYSIS.
- Remove15uLofeachsampletoafreshtube.Add1uLDNase-freeRnase(BoehringerMannheim,1:1000dilutionof2U/uLstock)to1T,1Ts,andallSUPERNATANTfractions.ThePELLETfractionsdonothavetobe"RNased".Incubateatroomtemperatureforatleast30min.Addsamplebuffertoalltubes.
- Loadsamplesontoa0.6%agarosegelcontainingEtBrat0.2ug/mL.Includeasmallamountofsupercoiledtestplasmid(e.g.pDK370)intheDNAsizestandardstoserveasapositivecontrolforhybridization.Thefinalconcentrationofsupercoiledplasmidshouldbesuchthat~0.1ngisloaded.Rungelat20or30Vovernight.
- Photographgel.NotewhethertheintensititesoftheøX174bandsareeveninalllanesandwhether2ucircleDNAisvisibleintheSUPERNATANT(hopefully)fractions.
- ProcessgelfortransfertoGeneScreenPlusaccordingtothePosiblotprotocol.Transferforatleast90min.UVcrosslinkDNAtomembrane.Airdry.
- HYBRIDIZATION.
- Prehybridizeblotat65oCfor~3h.inChurchbuffercontaining0.5mg/mLdenaturedsalmonspermDNA(usually14mLChurchbufferplus0.7mL10mg/mLSSDNAperblot).Addprobe(105cpmsperlane)andhybridizaeat65oCovernight(atleast18h.).Washblot2XwithBuffer1,15min.eachat65oCand2XwithBuffer2,15min.eachat65oC.Monitortheblot-thelastwashmaynotbenecessary.NOTE:Usethe0.9kbSma1/Pst1URA3fragmentfrompDK377tovisualizepDK370orotherURA3-containingplasmids.Usethe1.8kbSal1/Cla1LEU2fragmentfrompDK255tovisualizeYCp41orotherLEU2-containingplasminds.Usethe~2kbXho1/Sal1fragmentfromCV13tovisualizeendogenous2ucircleDNA.
YWBforspheroplasting:5mLYWB25uL0.2MPMSF3.5uLbeta-ME | YWBforwash:8mLYWB40uL0.2MPMSF | 1XEBB(tobreak):2mL5XEBB25uL0.2MPMSF10uL0.1MDTT8mLH2O | 1XEBB-plus(todilute):1mL5XEBB12.5uL0.2MPMSF5uL0.1MDTT75uL100mg/mlBSA4mLH2O | 1XEBB-doubleplus(forMTpellets):1mL5XEBB12.5uL0.2MPMSF5uL0.1MDTT50uL100mg/mlBSA100uL5MNaCl3.9mLH2O | 2XAssaultBuffer:XmL2XASSAULTBUFFER(X=0.25mLx#samples)0.1xXmLtRNA/øX174DNA | 3.75dH2O | 0.25EDTA | 0.25SDS | 0.25HEPES | 0.5tRNAøX174 | |
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