11/21/2005 11:36 AM TAIR: Arabidopsis Protocols Page 1 of 71 file:///Users/Leonore/Desktop/protocols_to_add/Protocols_Mundy2.html STANDARD PLANT MOLECULAR BIOLOGY PROTOCOLS Kindly provided by John Mundy , Institute of Molecular Biology, Copenhagen, Denmark. Agrobacterium competent cells Agrobacterium electroporation Agrobacterium miniprep Agrobacterium miniprep (phenol free) Arabidopsis transformation (infiltration) cDNA probes Colony hybridization Concanavalin A Blots DNA PAGE E coli competent cells (CaCl2) E coli competent cells (RuCl2) E coli transformation End labelled probe preparation Filter washing Fluorography of PAG Fluorometer/Luminometer Wallac Victor II Footprint with DNAse1 Gelshift Genomic DNA from cereal leaves GST fusion protein purification GUS histochemical assay GUS & LUC bombardment assay GUS luminometric assay
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STANDARD PLANT MOLECULAR BIOLOGY PROTOCOLS
Kindly provided by John Mundy, Institute of Molecular Biology, Copenhagen, Denmark.
Agrobacterium competent cells
Agrobacterium electroporation
Agrobacterium miniprep
Agrobacterium miniprep (phenol free)
Arabidopsis transformation (infiltration)
cDNA probes
Colony hybridization
Concanavalin A Blots
DNA PAGE
E coli competent cells (CaCl2)
E coli competent cells (RuCl2)
E coli transformation
End labelled probe preparation
Filter washing
Fluorography of PAG
Fluorometer/Luminometer Wallac Victor II
Footprint with DNAse1
Gelshift
Genomic DNA from cereal leaves
GST fusion protein purification
GUS histochemical assay
GUS & LUC bombardment assay
GUS luminometric assay
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HIS-tagged protein purification
Hormone treatments
Hormones & inhibitors
Hybridization selection of cloned DNA
Immunoprecipitation from in vitro translations
Isotachophoresis probe isolation
In vitro transcription
In vitro translation
Isolation of Lambda DNA by plate lysate
Lambda lysate
Leaf PCR
Maxam Gilbert sequencing
Microsomal preps for membrane proteins
Miniprep - alkaline lysis
NEpHGE Non-equilibrium pH gel electrophoresis
Northern blot in formaldehyde gel
Nuclear extract preparation
Nuclei prep
Nuclear prep from protoplasts
Oligo dT cellulose purification of mRNA
Oligo probe hybridization
Oligonucleotide probe preparation
Phage strains
Plasmid prep with CsCl
Primer extension with synthetic oligonucleotide
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Progeny analysis of plants
RNA extraction in GT w/ CsCl spin
RNA large scale from starchy tissue
RNA miniprep 1
RNA miniprep 2
RT-PCR
SDS-PAGE for proteins
Seed sterilization for cereals
Silver staining of proteins in PAG
Soluble protein extraction
Southwestern blotting
T4 polymerase fill in rxn
Western blotting
Whole cell extracts
AGROBACTERIUM COMPETENT CELLS
You should double up this protocol - it is almost the same amount of work and you can thus get some 80tubes.
1. Inoculate colony O/N in 2 ml YEP + antibiotics at 28C shaker. ABI - 50 KAN & 25
Chlor, gv3101 - 25GEN 2. Transfer O/N culture to 200ml YEP in a sterile 500ml flask and shake at 250rpmuntil the OD is 0.3 (4-5hrs)
3. Spin in sterile 50ml screw cap tubes 4C 5krpm 10‚. Check to make sure cells are pelleted, if not repeat athigher speed.
6. After aspirating, resuspend pellet in 2ml ice cold 10% glycerol (sterile filtered).
7, ASAP dipense in 40ul aliquots in pre-chilled, sterile eppis, freeze in lN2 and store -70C
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AGROBACTERIUM ELECTROPORATION
Safety precautions
1. Never change any other settings than stated while unit is charging (this may damage both theelectroporator and power supply)
2. Keep unit away from water in a dry area and away from flammable materials.
3. Never short circuit terminals.
4. Whilst delivering pulse, keep hands away from chamber and cuvette. The result may otherwise beshocking.
DNA preparations
DNA for electroporation must be free of salt, RNA or protein. DNA (in TE buffer) should be first treatedwith RNase, then twice extracted with phenol/chloroform.
This will remove protein and RNA. To remove salt, EtOH precipitate the DNA and wash twice with 70%ethanol. Resuspend the DNA at 0.4 -1 ug/ml.
Preparing the electroporator
There are two types of cuvettes 1 and 2mm. Most Agro protocols use 2mm (Invitrogen #650009 w/bluelids).
1. Make sure power supply is off.
2. With Charge/Pulse switch of the electroporator in the PULSE position, connect the leads from the powersupply to the corresponding coloured terminals on the back of the electroporator.
3. Set Arm/Disarm dial to disarmed
4. Set Capacitance selector to 50 mF
5. Set Load resistance to 200W
6. Turn on power supply
7. Set maximum power to 25 W
8. Set current to 25 mA
9. Set voltage to 1800 V
10. Allow power supply to stabilize (still in pulse position)
11. Select the CHARGE position using the Charge/Pulse switch. After 20-30 seconds, the charging light will
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glow.
12. Check that voltage meter still reads 1800 V
13. Set Arm/Disarm to the ARMED position and the armed light will glow.
14. Switch the Charge/Pulse to the PULSE position. The pulse light will glow briefly and both the chargingand armed lights will go out.
15. Set Arm/Disarm to the DISARMED position (the armed light should be off)
Electroporating
Electrocompetent bacterial cells, YEP media and DNA solutions must be kept on ice before mixing. Notethat the following steps should be carried out in under 1' and that you should be wearing glasses and gloves
16. mix 1-2ml DNA (600 ng) with 40ml cells
17. Transfer the DNA/cell mixture to a cuvette on ice avoiding air bubbles by gently shaking the cuvette
18. Dry outside of the cuvette with tissue paper and insert the cuvette into the cuvette chamber with notchfacing towards you
19. Close cuvette chamber lid
20. Set Arm/Disarm to ARM (arm light comes on)
21. Set Charge/Pulse to pulse and the pulse light will come on briefly
22. When pulse light is off, set Arm/Disarm to DISARM (arm light comes on) and remove cuvette
23. With DNA/agro mix still in cuvette, add 500ml cold YEP (no antibiotics) and mix solution by gentlypitppeting up and down
24. Transfer the cells to an eppi and incubate at 28C for 2-4 hour
25. Leave the electroporator with the switch in the PULSE position
26. Plate 200ml on YEP + antibiotics
27. Incubate at 28C and colonies will appear in 2-3 days
Re-using cuvettes
Fill a used cuvette w/ 0.1M H2SO4 and let stand 15'. Rinse 6x w/ dH20, then 2x w/ 96% EtOH. Store themwell-covered in 70% EtOH
AGROBACTERIUM MINIPREP
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Agros to be used for plant transformation should be checked for the presence of the Ti plasmid as planttransformation and the analysis of transgenic plants is time consuming. The easiest way to do this is to makean agro miniprep and to use PCR to determine that the cells contain your construct. PCR is necessary herebecause the Ti plasmid is single copy and you can barely see it on agarose gels.
1. Grow cells overnight in 5 ml LB or YEP with antibiotics.
For pMONs in ABI - 50ug/ml KAN, 50ug/ml Spec, 25ug/ml Chlor
For pBI types in gv3101 - 50ug/ml KAN, 25ug/ml GEN
2. Remove 1 ml cells to two microfuge tube
3. Centrifuge 45 sec and remove the supernatant with aspiration
4. Add 1 ml cells more to both tubes and repeat step 3
5. Vortex the pellet, add 100 l MPS1 solution, vortex again and incubate the tubes at room temperature for 5min
6. Add 20 l of a 20 mg/ml lysozyme solution, vortex-spin 1 sec and incubate 15 min at 37C.
7. Add 200 l MPS2 solution( freshly made), mix gently by turning the rack 3-4 times and incubate 5 min onice
8. Add150 l MPS3, vortex for at least 10 sec and incubate 5 min on ice
9. Centrifuge for 5 min and remove the supernatant to new tubes
10. Add 400 l phenol/chloroform/isoamyl alcohol (25:24:1), vortex, centrifuge for 5 min and remove thesupernatant to new tubes
11. Repeat step 10
12. Repeat this step with chloroform alone
13. Add 300 l isopropanol and incubate on ice for 10 min
14. Centrifuge for 5 min and wash pellet with 70 % EtOH
15. Dry pellet and resuspend the two tubes in a total of 50 l TE-buffer+RNase, use 2ml for a PCR, freezethe rest.
MPS1 for 50 ml Stock
50 mM glucose 1M 2,5 ml
10 mM EDTA 0,5mM 1 ml
25 mM Tris pH=8.0 1M 1,25 ml
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MPS2 for 10 ml
0,2 N NaOH 10N 200 ml
1% SDS 10% 1 ml
H2O 8,8 ml
MPS3 for 100 ml
5 M potassium acetate 60 ml
glacial acetic acid 11,5 ml
H2O 28,5ml
AGROBACTERIUM PROTEASE K MINIPREP (PHENOL FREE)
1) Resuspend pellet from 3ml cultures in 200uls STET
2) Add 10ul Lysozyme/RNase solution and incubate for15min at 37 C.
3) Add 1ul 10mg/ml Protease K solution and incubate at 50 C for 15min.
4) Incubate at 94 C 1min then vortex vigourously 30 sec.
5) Remove gooey supernatant to new tube and add 5uls 5% CTAB. Wait 5min then spin 5min.
6) Remove supernatant and rususpend in 300uls 1.25M NaCl by vigourous vortexing. Spin tubes for 1minand transfer supernatant to new tube with 750uls 96% EtOH + 1mM PMSF. 5min RT, 30min spin.
7) Wash pellet in 70% EtOH+ 1mM PMSF, dry and resuspend in 40uls TE 8.0
Can visualize 10uls in a restriction digest.
ARABIDOPSIS TRANSFORMATION BY VACUUM INFILTRATION
This protocol is modified from Bechtold, Ellis and Pelletier (1993). "In planta Agrobacterium mediated genetransfer by infiltration of adult Arabidopsis thaliana plants". [C.R. Acad. Sci. Paris, Life Sciences 316: 1194-1199].
PLANT GROWTH:
1. Take seeds with a brush and place them into 8cm square pots filled with soil. Don't compress the soil toomuch and water the pots thoroughly with 2-3 pot-vol to remove excess nutrients. Place 12-16 seeds in eachpot.
Place the pots in the cold room for two days before transfering them to the growth chamber. Grow the plants
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for three weeks in short days (10 hr or less) to get large plants and a greater seed yield. Transfer the pots tolong days to induce bolting. Grow plants to a stage at which bolts are around 10 cm tall.
2. Clip off emerging bolts close to rosette leaves to encourage growth of multiple secondary bolts.Infiltration will be done 7 to 9 days after clipping (plants will be 10-15 cm high and the biggest of theinflorescens will have made the first tiny silique. Do not water the plants the day before vacuum infiltration.
VACUUM INFILTRATION:
3. Start a 4ml agrobacterium culture (YEP+antibiotics) inoculated from a -800C stock or from a plate. Growcells O/N to 48h depending on the strain. Add this culture to 250 ml of YEP+antibiotics (A 250ml culturewill give enough cells for infiltration of 6 pots). Grow the culture between O/N and 2 days (depending onthe strain) to OD600 = 1.2-1.8. The culture will have a mother of pearl appearance (not lumpy or black).
4. Spin down agros at 5000rpm for 10 min in 250ml centrifuge bottles, resuspend in infiltration media to anOD600 = 0.8 in a minimum volume of 300ml.
5. Poor the agro suspension into a beaker of an appropiate size (400ml is ok). Place the beaker into thevacuum jar. Degass the solution by drawing vacuum until bubles form. Place a paper towel under the beakerto avoid that the beaker gets stuck in the bottom of the vacuum jar.
6. Sprinkle the plants with water 5 min prior to infiltration (optional) and then invert plants into the culturesolution. Make sure that all the flowers are submerged and leave 2cm between the rosettes leaves and theagro suspension. Don't let the culture contact the rosette or soil as this could kill the plants. Avoid that thesolution boils over when you pull the vacuum. Make sure that the soil is only moist, so that the water fromthe pots does not enter into the culture suspension (therefore we recommend not to water the plants the daybefore infiltation). Draw vacuum for 15-20 min for WS and 30 min for Col-0 at a pressure close to 0.05 Bar(we are using an oil pump).
7. Before removing the plants from the vacuum jar place a plastic bag over the pot and beaker. Pull out andremove plants from the beaker, lay pots on their side (to avoid that excess infiltration media runs down intothe soil). Fold over the top of the plastic bag and staple them twice. The other possibility is to place the potslaying on their side into a tray and cover the whole box with saranwrap. Put them in a growth chamber forone night. Next day move them to the green house. Put the plants in vertical position and open the bags.Next day get rid off the bags. In case you have the plants in trays: put also the plants in vertical position anduse sticks and saranwrap to make a kind of a tend around the plants. Next day remove the plastic. In hotsummers, we recommend to give plants a shower after we have placed them in vertical position (the purposeof this is to remove the sugars from the infiltration media which decrease fungal infection).
8. Grow plants for approx. four weeks, keeping bolts from each pot together but separated fromneighbouring pots
9. When the siliques begin to turn yellow, place the pot on its side with the plants inside a big envelope.Leave them for one week to dry out and cut off the plants. Let the seeds dry in the envelope and clean them10 days later (keep all the seeds from one pot together). Store the seeds in the cold room for one weekbefore plating them.
KANAMYCIN SELECTION PROTOCOL
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1. Sterilisation of seeds:
aliquot seeds in 15ml falcon tubes (approx 700 seeds/tube, you can estimate the ammount of seeds by firstdrawing a square plate of 9cmx9cm on a paper and spreading the seeds on it). Add 10 ml of hypocloritesolution. Shake tubes for 10 min. Remove the solution and add 10ml of 70% ethanol. Wait 2 minutes.Discard EtOH and wash seeds 2-3 times with 10ml of sterile water.
Resuspend seeds with 8ml 0.7% top agar (no warmer than 55oC ). 2. Spread seeds onto selection plates(MS+Kan). Dry plates in laminar flow hood until the top agar has solidified.
3. Vernalize plates for two nights in the cold room at 4oC. Transfer the plates to the growth chamber (21oCwith continous light).
4. After aprox 7 days transformants should be clearly identifiable as dark green plants with healthy greensecondary leaves and roots that extend into the selective medium. Root growth is the most clear maker toidentify transformants at an early stages.
To make sure that the transformants are positive transfer them to a new MS+Kan plate and leave them therefor a few days (if they turn yellow is because they are faulse positives). Transfer the seedlings to soil.
If you have contamination on your plates at this step, transfer the transformants as early as possible to soil.
5. Grow the plants and collect the seeds.
Infiltration Media
1/2 x Murashige&Skoog salts (SIGMA #5524)
1X B5 vitamines (1ml of 1000x stock) (SIGMA; #G-2519) Gamborg's vitamine powder, to prepare the1000x stock disolve 11.2g in 100ml water.
5% sucrose
adjust to pH 5.7 before autoclaving
after autoclaving add:
- Benzylamino Purine (BAP), 10 µl per liter of a 1 mg/ml stock in DMSO. By adding the hormone justbefore use, you can keep infiltration media as a stock for at least one week prior to infiltration.
- we recommend to add 0.01% silwet to the infiltration media to increase transformation efficiencyespecially for Landsberg and colombia ecotypes. (silwet is from LEHLE SEEDS, cat no VIS-01 VAC-IN-STUFF (silwet L-77)
Selection plates:
1x Murashige&Skoog salts
1% sucrose
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adjust pH 5.7 with 1M KOH.
0.7% Difco agar.
autoclave, cool, and add:
1x MS vitamines (SIGMA #M-7150). Take 1ml of 1000x stock prepared by disolving 10.3gr in 100ml ofwater.
antibiotic (kanamycin 50mg/l).
Top agar:
1x Murashige&Skoog salts.
1% sucrose.
adjust pH 5.7 with 1M KOH.
0.7% Difco agar.
autoclave.
before use: boil in the microwave and keep in water bath at 50-550C.
YEP media (liquid):
10 g /l Bacto peptone (Difco)
10 g/l Yeast extract (Difco)
5 g /l NaCl
For YEP plates add 15gr/l Difco bacto agar.
Hypoclorite solution:
for 50 ml:
4ml Na Hypoclorite 15%
255l Tween-20
water to 50ml
cDNA PROBES
mRNA 1-5ug
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H2O 50ul
oligoDt (10mg/ml) 2ul
heat 90C 2', ice
5xRT buffer 20
10mM dA,G,T 2 ea.
1mM dC 2
1M DTT 1
dCTP* 10
RT 6
inc 42C, 1h
+
4M NaOH 15
10% SDS 7.5
0.25M EDTA 19
H2O 8.5
inc 37C 1h
+ 3ul Hac
PCHCl3 ext
separate from free nucs over G-50 column
use106cpm/mlhyb
COLONY HYBRIDIZATION
filter prep: S&S BA 85 Nc
1) lay filters on plates to moisten
2) replicaplate colonies to them
3) grow o/n
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4) transfer filters to 3mm paper on saran wrap soaked w/ 10% SDS. This will lyze colonies; they subsideslightly, inc 5'
5) trans filter to dry 3mm briefly
6) trans 2x to 3mm soaked in 0.5M NaOH to denature DNA, inc 5'
7) trans to dry 3mm briefly
8) trans to 3mm soaked w/ 1M Tris 7.5 to neutralize, inc 5'
9) trans to dry 3mm
10)trans to 3mm w/ o.5M Tris/1.5M NaCl to bind DNA, inc 5'
1)Plates: Long plates for sequencing and oligo preparations, medium for S1s and strand separations, shortfor gel shifts and restriction digests. Clean plates w/ soap & H2O, rinse w/ deion H2O, then EtOH, wipedry. Siliconize notched plate, wash excess w/ EtOH. Taping is unnecessary, use 3 sided spacers and plug w/2ml gel mix + 2ul TEMED in pasteur pipette.
2) Gels: Acryl stocks are filter sterilized. First warm urea in H2O to dissolve.
Cast gels last 5-7d RT, are made 0.5 x TBE. prerun for sequencing, unecessary for prep gels.
9) Insert film (AXR5 Kodak) and store at -70 C till development.
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LSWB 2X SSC, 0.1% SDS
HSWB 0.2X SSC, 0.1% SDS
The easiest way to heat these solution is to submerge large, double zipper plastic bags in water bath.
The temperature used varies for different probes and samples. Make sure you know what tempt to use. 60 Cis standard for homologous DNA/DNA/RNA hybs.
FLUOROGRAPHY OF PAG
1) fix as usual
2) rinse 2-3x1h or overnight in 50% EtOH
3) incubate 1hr in DMSO in fume hood in metal/glass tray. If the gel starts turning white, put in back in50% EtOH and wash longer. You can keep reusing the
DMSO, but the gel should see some fresh DMSO each time before it goes into the DMSO/PPO.
4) rinse 2 x 1hr in 20% PPO/DMSO (poisonous), then 1hr in 20% PPO/DMSO with 3% glycerol. Thesesolutions can be kept separately and used in the same order several times.
5) soak in H2O w/ washing 10' to ppt PPO in gel. With gloved hand gently wipe gel surface free of excessPPO. Plenty of water and gentle agitation required here.
6) dry gel on cellulose sheets (Biorad) above thick paper 60C, 2-3h w/ good vacuum. Everygeldryer/vaccuum system is different. You need a good setup for this. Handle the dried gel carefully andtape it to the cassette screens. The gels curl like crazy when frozen
7) expose at 70C to prevent swelling
FLUOROMETER/LUMINOMETER WALLAC VICTOR II
Samples for both Glucuronidase (MUG) and Luciferase assays should be prepared according to the "GUS &LUC bombardment assay" protocol.
1. Switch the Victor II and the computer on. Windows 95 launches automatically the "Wallac 1420manager" program.
2. In the "Tools" menu, check that the "User level" is set on "Advanced". Otherwise, the "Routine" menuwould disable any system operation which means that you could not change any setting, even in your ownprotocols.
3. Select a protocol available in the list in the "Instrument control" menu (then go to step 5) or create yourown protocol (see step 4).
4. Creation of a new protocol menu
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4.1 Click with the left button (LB) on "Explorer" in the "Tools" menu in order to launch the "Wallac 1420Explorer" program. By clicking with the right button (RB) on the "Users" folder, you will be able to create anew protol and then name it.
4.2 Open your new protocol (double-LB). This operation starts the "Protocol Editor" window which shouldbe left open all the time you will work with the Victor II. This program enables you to define all theoperations to perform (see step 4.4), to select which wells will be measured (step 4.3) and other things suchas the format of the saved files, etc.
4.3 Select the wells which should be measured in the "Sample" menu (LB), the default setting is 96 wells.NB: we use the standard 96 wells white microtiter plates.
4.4 Define the operations to perform in the "Measurement" menu. Select measurement "by plate". To add anoperation, you can either click (LB) on the small icons displayed on the left or click in the white operationwindow (RB). The following operations can be chosen : dispense (if injectors installed), delay (to waitinbetween the measurement of two wells), shake, or label (to select the kind of detection : fluorometry,luminescence, ...). To perform a MUG assay, select "label" (LB) then, in the "fluorometry" menu, select theicon represented with a locker "Umbelliferone (1.0s)" (LB). You have now the possibility to select thisprotocol (double-LB) and use the default Umbelliferone measurement or make a "copy" of this protocolwith an other name. Important : you can not change the settings of any default protocol represented as anicon with a locker. If you want to change some parameters (such as the counting time), you have to create anew protocol (by copying a default one). The default "Umbelliferone (1.0s)" protocol is well adapted to ourMUG assays.
4.5 Save your protocol which should now appear in the listing of the "Wallac 1420 Manager" window in the"Instrument control" menu. Select it (LB)
5. Run your protocol by pressing "Start". You can have a "Live display" of the measurement. I wouldrecommend to try your protocol once with an empty microtiter plate to check if everything works fine (goodconnexion with the Victor II, no mistake when you selected which wells should be measured,...).
6. How to run a MUG assay : mix both the extract and the substrate (MUG buffer + methanol) according tothe related protocol (GUS & LUC bombardment assay) but do not stop the reaction with CaCO3. Indeed,you can measure the activity at various time (t0, t1h, t2h,...) from the same wells. To do so, incubate themicrotiter plate at 37C in an incubator (remember to cover the plate to avoid evaporation). It isrecommended, especially when the GUS activity of the sample is totaly unknown, to make a series ofdilution (dilute the extract in the extraction buffer) to check wether activities will be proportional.
7. The data will be automatically saved in the same folder than your protocol (classified upon the date). Youcan open them (double-LB) then export them as an Excel file or other formats.
8. Leave both Fluorometer and computer on during the week. Switch them off during the weekend.
FOOTPRINTING WITH DNASE1
1)probe: same as used for gelshift), isolated by isotacelectrophoresis w/out EtOH ppt which can enaturedsDNA
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H2O80ml H2O 0.7g agarose boil to dissolve 10ml 10x buffer 100mM Tris 7.5, 10mM EDTA, 30mM NaOAc 10ml 30/0.8% acryl stock cool to 60C 60ul TEMED 100ul 10% APS let set for 2hr, prerun with circulation 30' at 100v and run w/ circulation
7)Gels are dried unfixed on Whatman DE 81 sheets at 80C on dryer.Expose o/n -70C w/screen.
GENOMIC DNA FROM CEREAL LEAVES
1)extract nuclei in nuclear homogenization buffer NHB from 1kg leaves (see nuclei prep steps 1-8)
2)resuspend in 35ml TE
3)add 35ml 2x nuclear lysis buffer NLB (see nucext.rcp)
4)add proteainase K to 0.2mg/ml
5)incubate 37C 1hr
6)spin 3k rpm 5' RT
7)add 1g/ml ground CsCl to supernatant
8)spin o/n vti50 45k rpm
9)puncture w/ 21 gauge needle 1cm from bottom, collect & pool viscous fractions
10)dyalize o/n vs. 2l TE in cold room
GST FUSION PROTEIN PURIFICATION
1) grow 20ml cells O/N 37 C, dilute 50X into prewarmed LB, grow to 0.6 OD or about
1hr. Induce w/ 2mM IPTG (238mg/0.5l), grow 3hr, spin 6k GS3 10', freeze at -70 C.
2) extract cells (from 500ml) in 25 mls. Heintz Buffer plus triton (HBT) by gentle pipette resuspending onice circa 10'after thawing.
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3) transfer to 50ml conical ss34 flip top tubes.
4) add 10mg lysozyme powder to the 50ml (cells from 1 liter now in 1 50ml tube), digest 15' on ice.
5) sonicate with large probe 1' 80% power, freeze in lN, thaw at 37 C, sonicate
again on ice, solution should become viscous.
6) add 1mg DNAse and RNAse, incubate on ice 15'.
7) spin 7.5k rpm 4 C ss34 10'.
8) transfer supernatants to conical screw caps, freeze in lN2, may store.
1) determine number of slides needed, multiply by 0.75ml
2) make up required vol of stain:
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for 10ml(4C) 5mg X-Gus
50ul nn dimethyl formamide, dissolve
+ 10ml 50mM NaPO4 pH 7
3) sections best cut with vibrating knife
for sections w/ chlorophyll, put in cell-wells w/ 500ul stain
for sections w/out chlorophyll, put directly on slides w/ stain
4) inc o/n 37C in humidity chamber
5) asp, inc 10'in FAA:
for 200ml (4C) 10ml formaldehyde
10ml HAc
75ml EtOH
H2O > vol
6) inc 2' 50% EtOH
7) inc 2' 100% EtOH
8) inc 1' H2O
GUS & LUC BOMBARDMENT ASSAY
1. Bombarded tissue is incubated according to the experiment
2. grind to a fine powdcr with a mortar and pestle in lN2
3. add 500u1 Extract Buffer l00nmM K2HPO4/kH2P04, pH 7.8 1mMDTT. Keep on ice until spin 10' 4C inmicrofuge. Aliquot about 450ul to a fresh tube. Freeze in lN2 and store -80C.
Fluorometric GUS
Mix pr assay 125u1 2 x MUG amd 50u1 100% Methanol
prewarm at 37C and at t0 add 75ul extract, mix.
When all have been done (up to 50) take out 50u1 aliquots to 250u1 0.3M Na2CO3 prealiquoted intofluoroscan microtiter plates (Microstrips black Ps, cat no. 9502177, Lab systems). These are measured inscanner (Flurorscan II, Labsystems, Finland) and the numbers are t0 values. Remember to include proper -
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control without bombardment for background (Tback0). Depending upon the levels of activity, generallyincubate the rest for 24hr although you can see a slight color change in 2-4 hr if levels are high. Calculatet24-T0 minus Tback24-Tback0. If the values are above 5000, make dilutions as measurements are not linearat this level.
Extract buffer: good for both GUS and LUC measurements
275ml O.2M K2HP04 plus ca. 20ml 0.2M KH2PO4, adjust to pH 7.8, then add 1 vol H20.
Autoclave. Just befrore use add DTT to lmM and leupeptin to 20ug/ml.
2 x MUG: 2mM MUG in 5OmM Na3PO4/Na2HPO4 pH 7, 10mM EDTA, 0.1% Triton X-100, 0.1%Sodium Lauryl Sarkosyl, lOmM DTT. Store in aliquots at -2OC.
MUG:4-methyl-umbelliferyl B-D-g1ucuronide.
Luminometric LUC assay:
1. Mix
20ul lO x (12.5x) LUC buffer
10ul 100mM ATP
1ul 100mg/ml BSA
169ul H20
total is 200ul/special tube for luminometer
2. add 50ul extract, mix
3. Inject 100ul diluted luciferin solution and take measurement after 5-15". This time interval must beconstant for all samples!
10 x LUC buffer
250mM Tricine, pH 7.8
150mM MgC12.
lOOmM ATP
in H20 adjust to pH 7.0, sterile filter, store aliquots at -20C
lOmM Luciferin stock:
D(-) Luciferin lOmg (cat 411400 (Boehringer). For 10mM stock, weigh out 1mg (light sensitive!), add 27ulDMSO to solubilize, then add 12ul 3M NaOAc, pH5, mix, then 275ul H2O, Don't make up large amountrs
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as this is not very stable, even at -80C.
Diluted luciferin solution: 0.5mM in H2O
GUS LUMINOMETRIC ASSAY
GUS-Light is a chemiluminescent reporter gene assay system designed for rapid, sensitive, and non-isotopicdetectjon of B-glucuronidase in cell extracts. The GUS-Light reporter gene assay incorporates GlucuronTMchemiluminescent substrate and a proprietary Light Emission Accelerator. The chemiluminescent assay hasa wide dynamic range, enabling detecfion of 0.6pg to 2 ng of B-glucuronidase.
The B-glucuronidase detection assay is simple and fast. Cell lysate or purified glucuronidase is firstincubated with Reaction Buffer for 1 hour. Glucuron chemiluminescent substrate which is present inReaction Buffer is catalytically decomposed by the enzyme. The sample is then placed in a luminometerchamber and GUS Accelerator is added which terminates the B-glucuronidase activity and accelerates theemission of light. Chemiluminescence signal intensity is measured as a 5 second integral. The amount ofcell extract used in the assay should be adjusted to keep the assay within the linear range. High intensitysignals may saturate the detector of a luminometer resulting in artificially low values.
The GUS-Light system has been formulated for luminometers equipped with automatic injectors. Manualinjections may be performed, however signal intensities should be measured within approximately the sameinterval following the addition of GU5 Accelerator to each sample. Reaction components should be scaleddown if a luminometer with a smaller volume injector is used, however sensitivity may be affected slightly.Alternate lysis buffGrs mav be used, however we recommend that their performance is compared with theCUS Lysis Buffer to ensure optimum results of the assay. A Lysis buffer compatible with the luciferaseassay containing 0.1M potassium phosphate, 1mM DTT, and 1mg/ ml BSA has been tested with equivalentperformance to the GUS Lysis Buffer.
Bacterial contamination of plant material will cause high background. Best results
will be obtained with sterile preparations. Chlorophyll in concentrated samples may interfere with thechemiluminescent signal intensity. Therefore, if high levels of chlorophyll are present, several dilutions ofextract should be assayed.
II. SYSTEM COMPONENTS Each GUS-light (Cat. No. Bg100) contains rtagents sufficient for 200 tests.GUS- Light (Cat. No. BG30O) contains reagents sufficient for 600 tests. Glucuron ChemiluminescentSubstrate A l00X concentrate is diluted in GUS Reaction Buffer Diluent prior to use.
GUS Lysis Solution contains 50 mM sodium phosphate pH 7, 10 mM EDTA, 0.1% sodium lauryl sarcosine,0.1% Triton X-100 (Store at 4'C). Fresh B-mercaptoethanol should be added prior to use to a finalconcentration of 10mM (i).
GUS Reaction Buffer Diluent contains 0.1MNaPO4 pH7.0, 10 mM EDTA (store at 4 C) GUS Acceleratorcontains a ready to use luminescent accelerator (store at 4C)
III.PROCEDURE FOR B-GLUCURONIDASE DETECTION
Positive Control: Add 1ul B-glucuronidase (20 pg of B-glucuronidase, Sigma G-7896) to mock extract
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equivalent to the volume of experimental extract used.
Negative Control: Assay a volume of mock extract equivalent to the volume of experimental extract used.
It is recommended that all assays are performed in triplicate (step 6).
1. Grind tissue to a powder in lN2. These can be stored at -80C.
2 Aliquot the required amount of GUS Lysis Buffer. Add fresh B-mercaptoethanol to a final concentrationof 10mM. Note that the lysis buffer for GUS/LUC can also be used.
3 Add sufficient volume of GUS Lysis Solution to cover the tissue (250 uL of Lysis Buffer per 25 mg ofplant material).
4. centrifuge sample in a microfuge for 2 minutes to pellet debris.
5. Transfer supernatant to a fresh microfuge tube.
6. Dilute Glucuron substrate l00 fold with GUS Reaction Buffer Diluent to make GUS Reaction Buffer. Thismixture will remain stable for several weeks if stored uncontaminated at 4'C. It is recommended to onlydilute the amount of Glucuron substrate that will be used within a one month period.
7. Warm the volume of GUS Reaction Buffer required for the entire experiment to room temperature.
8. Aliquot 2 to 20uL of individual cell extracts into luminometer sample tubes. If less than 20 uL of sampleis used, Lysis Solution should be added to 20 uL final volume. Note: The amount of extract required mayvary depending upon the degree of expression and the specific luminometer utilized. Use 5ul of extract forpositive controls and 10 to 20ul of extract for experiments with potentially low levels of enzyme. It isimportant to vary the concentrations of extract in order to record the signal within the linear range of theassay.
9. Add 180 ul of GUS Reaction Buffer to a luminometer tube and mix gently.
Incubate for 60 minutes at room temperature. Incubations may be as short as 15 minutes (especially if highlevels of expression are expected), but the dynamic range of the assay may decrease. Note: Light intensitiesare time dependent.
Reaction Buffer should be added to sample extracts within the same time frame as they are measured in theluminometer. For example, if it takes 10 seconds to complete a measurement. then Reachon Buffer shouldbe added to tubes every 10 seconds.
9. Place tube in a luminometer. Inject 300ul of GUS Accelerator. After a 2 to 5 second delay followinginjection, count the sample for 5 seconds. If manual injection is used, then the Accelerator should be addedin the same consistent time frame as the addition of Reaction Buffer.
REFERENCES
1.Callagher, S.R. ifl "GUS Protocols: Using the GUS Gene as a Reporter of Gene Expression", Ed. S.R.Callagher, 1992, Academic Press, 47-59.
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Fulton, R., and B. Van Ness. Luminescent reporter Gene Assavs for Luciferase and B-galactosidase Using aLiquid Scintiliation Counter. BioTechniques 14(5): 762-763 (1993).
3. Nguyen, V.T., M. Morange, and OBensaude. Firefly Luciferase Luminescence Assays Using ScintillationCounters for Quantitation in Transfected Mammalian Cells. Anal. Biochem. 171, 404-8 (1988).
1) grow 20ml cells O/N 37 C, dilute 50X into prewarmed LB, grow to 0.6 OD or about 1hr. Induce w/ 2mMIPTG (238mg/0.5l), grow 3hr, spin 6k GS3 10', freeze at -70 C.
2) resuspend cells (from 500ml) in fliptop in 25 mls. UPB8.0, freeze lN2.
same as PB but100ug/ml tRNAPolyadenylic acid10-20 ul Poly A+ mRNA/filter
IMMUNOPRECIPITATION FROM IN VITRO TRANSLATION
1) count net inc (TCA filters)
2) total product lanes require 100kcpm for 2-3 day exposure. Total product aliquots can be cleared ofcharged globin as follows:
make up to 10 or 20ul w/ TE
add 2 vols sated AmSO4
mix, stand on ice 30'
spin 5' 4C, aspirate sup
resuspend pellet in SDS-sample buffer
3) aliquot 200k-5x 106 cpm for imm.ppt. depending upon antigen. 500kcpm good for starters. Dilute to600ul w/ Tris-triton buffer (TTB). Other buffers better for membrane proteins (see Anderson & Blobel,Methods in Enzymol. vol 93, 111).
4) + 10-15ul first antibody, usually pre-immune or normal sera (Dako #902-3) to bind non-specific proteins.
5) inc w/ slow mixing 1h RT
6) + 50ul 1:1 Protein A Sepharose (PAS) in TTB. resuspend before pitteting with cut-off p200
7) inc 30' RT
8) spin 1' RT
9) transfer sup to new tube, + 15ul 2nd antibody (specific for antigen), inc 1hr RT.
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10) pellet (proteins bound non-specifically to pre-immune serum and Sepharose) is washed 3 x w/ TTB and3 x w/ tris buffer (TB). aspirte final pellet to dryness w/ hamilton, resuspend in 45ul SDS-sample buffer
11) specific antigen in supernatant from step 9 is adsorbed after 1h w/ PAS for 30' as before, then washedand prepared for SDS-PAGE as before (steps 7-10)
Note: depending upon antigen, it is possible to continue specific immunoprecipitations w/ a third (secondspecific) antibody. In this case, the supernatant obtained in step 11 is adsorbed again w/ PAS beforeimmunoprecipitating out the second antigen
see Contreras et al. (1982) NAR 10: 6353-63 and Stratagenes Bluescript (pSK) protocols. Stratagene's invitro transcription kit with protocols works fine. Use CsCl purified plasmids with T7 and/or T3 promoter(s).ORF should have a 5' ATG with a good ribosome-binding site (Joshi (1987) NAR 15: 6643-53) and a 3'stop codon. If plasmid lacks T3/7 terminator, linearize at 3' end of ORF with a 5' overhang enzyme 0CHCl3ext., and EtOH ppt.
5 ul 5x TB (250mM Tris 7.9, 30mM MgCl2, 10mM Spermidine, 50mM NaCl)
X ul water to 24 ml total
1-5 ug digested plasmid DNA
1 ul 10mM rATP
1 ul 10mM rUTP
1 ul 10mM rCTP
1 ul 0.1mM rGTP
3 ul 2mM 7mGpppG (Pharmacia 27 4635 01)
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1 ul 0.75M DTT
1 ul RNAsin (40U/ml)
1.5 ul T3 or T7 Polymerase
inc 37 C 5', then add
1 ul 10mM rGTP
inc 37 C 20'. This mix can be frozen away for extended periods and aliquots used to program in vitrotranslation. For RNA probes, DNAse the plasmid, 0CHCl3 and EtOH ppt.
IN VITRO TRANSLATION
Use Promega's nuclease-treated -Met (L4210) or -Cys (L4240). The lysate is the same, just the amino acidmixes differ. The Promega protocols work fine as follows, although it is often best to scale them down.
35 ml lysate
7 ml H2O (50 ml final depending on mRNA)
1 ml RNAsin
1 ml 1mM amino acid mixture
2 ml mRNA (1 mg or less)
4 ml Met or Cys (1200Ci/mMol, 10mCi/ml)
inc 37 C 60', place on ice
spot 1 ml on Whatman 1MM, air dry on tin foil
boil in 10% TCA 10', sink filters with ice, rinse 2 x quickly in tap water, once in EtOH and once in acetone,air dry. Count with 5ml Econofluor.
SDS-PAGE ANALYSIS
Take desired volume of mix and dilute to 20 ml w/ water. Add 40ml of cold, saturated AmSO4 (66% final),mix, spin and inc on ice at least 30'. Spin 10' at 4 C, aspirate supernatant completely off and resuspend pelletin SDS sample buffer. This ppt. reduces background significantly. Follow SDS-PAGE protocol (see note forCys translations).
LAMBDA DNA BY PLATE LYSATE
for 4 large plates, 50-100kpfu/plate:
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1) pool 12ml o/n washes
2) spin out cells 10k, 15' RT
3) + to sup: 20ul DNAse 1 (10mg/ml) and 50ul RNAse (10mg/ml)/ 10ml sup
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15g difco agar
top agarose is for 200ml
1.6g NaCl
1.2g agarose litex
2g tryptone
LAMBDA DNA BY LIQUID LYSATE
1) Add cored single plaques (1 plaque = 107 phage) to 0.5ml fresh cells (ON culture in LB w/ 10mMMgSO4 & 0.2% maltose) in 50ml copolymer tubes. Make also mock - plaque.
2) inc. 15' 37C
3) add 5ml LB + 5mM CaCl2
4) Shake hard 37C 4-5hrs until cleared w/ cell debris -compare to control
5) add 100ul ChCl3, shake 5' 37C
6) spin 3000rpm table top 10'
7) transfer sup to corex, add 4ml 20% PEG,2M NaCl, invert well, inc 60' on ice.
8) spin 3000rpm tabletop 20min, drain and wipe tube dry.
9) resuspend pellet in 750ul LB, transfer to eppi, add 750ul LB/DE52, invert 20- 30x.
10) spin 5', transfer sup, spin again, transfer sup.
13) transfer 800ul and add 800ul -20C isopropanol, inc -70C 15', spin 10'
14) decant well and briefly speedvac pellet, resuspend in 20ul TE.
LB/DE52
Wash (mix/settle/aspirate) 50g Whatman DE52-cellulose in 100ml blue cap with 0.05
N HCL till pH under 4.5. Add 10n NaOH dropwise w/ stirring till pH 7. Wash 3x w/ LB. Add LB to 25%final vol w/ 0.2% NaN3. store 4C
LEAF PCR PROTOCOL
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(Klimyuk et al., 1993, TPJ 3: 493-494)
1) Samples are harvested in 1.5 ml tubes and stored on ice.
2) 40ul of 0.25N NaOH was added and the samples boiled for 30 sec.
3) 40ul of 0.25N HCl then 20ul Tris mix was added and the samples boiled for another 2 min.
-tissue samples can then be used immediatly or stored at 4 C for several weeks.
-The amount of tissue used in each PCR reaction should not exceed 2mm2 or the reaction will not work. Asmall amount of treated material can be excised for use in a PCR reaction with a sterile Gilson tip.
PCR reaction conditions are as follows:
total volume= 50ul
for 5.5 reactions
10X buffer 5ul 27.5uls
10mM dNTPs 1.25uls 6.875uls
primer A 2.5uls 13.75uls
primer B 2.5uls 13.75uls
dH2O 38.75uls 213.1uls
taq poly 1.0ul 5.5uls
95 C 10min 1X
95 C 30sec
55 C 30sec
72 C 45sec 30X
72 C 10min 1X
run 15ul on a 2% agarose gel
note: 2.5 times more primer is used and 2 times more taq polymerase in the leaf PCR protocol. If you couldget by with less, Jonathan Jones would have done so!
Stocks
0.25N HCl
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0.25N NaOH
Tris buffer:
0.5M Tris pH 8.0
0.25% Nonidet P-40
LEAF PCR ON ARABIDOPSIS TISSUE WITHOUT ALKALINE TREATMENT
Preparation of Master mix:
1 x Taq-buffer
1.5 mM MgCl2
200 mM of each dNTP
1 mM each primer
0.5 ml 20 x Taq polymerase
The mix is stored on ice until use.
Preparation of leaf tissue:
Put the leaf in a small Petri-dish. Make a hole in a leaf with the narrow end of the Pasteur pipette (a forcepsmight be helpful) and place the leaf in a PCR-tube, if necessary by blowing. On ice, add 50 ml the Mastermix.
Running the cycles:
Transfer the tubes directly from ice to the prewarmed 94 C block on the Robocycler and run the followingcycles:
94 C for 3 min 1 x
94 C for 30 s; Tann.* for 1 min; 72 C for 1 min-1 min 30 s 35 x
72 C for 10 min (optional) 1 x
Appropriate controls:
Positive Negative
For screening transgenics: plasmid ColO
ColO with endogenous primer-set gDNA
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gDNA with endogenous primer-set - DNA
*The annealing temperature (Tann.) should be 2-3 C below the calculated Tann..
5) resuspend in 7ml total of nuclear lysis buffer NLB, transferto Beckman ti70
polycarbonate tubes (16x76mm, Cat # 355603)
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6) add 770ul 4M AmSO4
7) rock 20', should see viscosity increase
8) spin 1h, 35krpm ti70. The pellet is hardish, supernatantviscous w/ DNA
9) add 0.3g/ml AmSO4 to supernatant w/ stirring in a 25ml beaker.It takes at least
0.5h to dissolve
10)spin 15', 10krpm in 15ml corex. The supernatant containshistones, the pellet primarily binding proteins.Decant thoroughˆly, proteins in supernatant can be ppted w/ 80% AmSO4
Set up cold room daybefore, all solutions at 4C, all tubes on ice.
1) 2.5l (15-20 trays) of seed is grown 7 d in the dark (givesless starch) in vermiculite w/ occassional H2O.Harvest w/ scisˆsors to yeild approx. 1kg leaves.
After weighing, leaves arefurther cut to approx. 2 cm length.
2) wash half in 4l H2O
3) rinse w/ 1.5l homogenization buffer HB
4) transfer to large razor blender, add 2l HB
5) smash w/ 3 1" bursts, then 15" low speed
6) filter thru 1000u and 80u nytex screens (see diagram)
1) 8x106 protos in cellwells, collect and spin in 2x 15ml APM at 500rpm for 5' in bench fuge to pellet.decent supernatant. Subsequent steps at 4 C. Examine cells here, and after next step to check lysis.
2) Lyse by resuspending in 50ml ice cold NIB.
3) Filter through a 20m screen, rinse sreen w/ 50ml NIB, pool in 3x 30ml corex tubes, 1 tube balance.
4) Pellet nuclei in HB4 swingbucket at 2470rpm (1000g), 20', 4 C.
5) Gently resuspend in 40ml NIB, pool in 2x 30ml corex.
6) Spin to pellet starch and debris in HB4 at 110rpm (1g), 3', 4 C.
7) Transfer supernatant containing nuclei to new tubes. Pellet at 1750rpm (500g)
15'. Decant completely, quickly wipe tube dry.
8) Resuspend nuclei in 5ml HEN-5. Transfer to ultra tube.
at 0.4M NaCl, 1% formamide decreases Tm 0.65C, and 1% mismatchdecreases Tm 1.5C
8)leave to anneal at Tm several hr
9) EtOH ppt w/ 0.2 vol NaOAc
10) resuspend in:
2ul reverse transcriptase buffer RTB
2ul 10mM dNTPs
0.5ul 14.5 ul H2O
1ul BSA
14.5ul H2O
1ul MMV RT (BRL) or AMV
11)inc 1h, 37C
12)1ul 200mM EDTA
13)PCHCL3 ext
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14)EtOH
15) run sequencing gel on products depending upon extension length
solutions:
PAB RTB, see BRL catalogue
0.4M NaCl
40mM Pipes 6.9
1mM EDTA
PROGENY ANALYSIS OF PLANTS CARRYING 35S SENSE/ANTISENSE GENES
1. Transform plants by infiltration, grow to seed (F1). Transgenes should be dominant (expressedconstitutively), therefore phenotypes possible in these seeds although there are so relatively fewtransformants that they would be virtually impossible to see.
2. Plate F1 seeds on KAN and select for transformants. Examine these plants carefully during their growth.Transfer the plants to soil and grow to F2 seed. The plants are hemizygous (heterozygous for transgene).Now is the time to take leaf material for Southerns and northerns/RNAse protection. The former areperformed on DNA digested, for example, with one and with two polylinker enzymes. Northerns for foreigngenes require only random-primed DNA probes. To measure sense/antisense transcripts, strand-specificprobes are required. A protocol is described in Curent Protocols (4.7.1) and good kits are available from invitrogen, or Stratagene. Collect F2 seed of all F1 plants. Seed from plants showing good mRNAaccumulation and/or single copy integration are most interesting. The alleles look like this: all hemizygous
R r
R RR Rr
r Rr rr
3) Plate F2 seed on KAN: 25% should be sensitive (rr), 75% resistant (Rr or RR). Of the 75% resistant,66% should be hemizygous, 33% homozygous. These F2 resistant individuals should be studied forphenotypes, and various assays can be performed with them. Transfer to soil and grow these plants to F3seed. The alleles coming out of these plants should look like this:
66% hemizygous 33% homozygous
R r R R
R RR Rr R RR RR
r Rr rr R RR RR
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4) Plate 50 F3 seed from each F2 line on KAN and score sensitive/resistant.
F3 single copy homozygotes should all be resistant. These are the most important lines for further crosses.Homozygous, KAN-resistant plants can be transferred to soil and used for crosses.
5)pipette off supernatant to 50ml screw cap tubes and add 0.15gCsCl/ml. Do not worry about small amountsof material floating around
6)layer solution carefully onto 8ml 5.7M CsCL (w/5ul EtBr stock)cushions in sw28 open tubes. Tubesshould have been inced w/0.1MNaOH/1%SDS for 30', then rinsed thoroughly in H2O pror to use
7)spin sw27 22h, 24krpm 18C
8)aspirate top solution w/ interface junk to cushion, then quickˆly aspirate cushion around red RNA pellet
9) immediately add 3ml sarcosyl/urea SU, transfer to 15ml corex.vigorous pipetting required to dissolvegelatinous flakes
10)add 1.5ml P to fully dissolved RNA, vortex, then 1.5 ml CHCl3,vortex
11)spin 5', 7.5krpm
12)back ext PCHCl3 phase w/ 1.5ml SU, vortex, spin, add SU phaseto first SU phase
13) resuspend RNA in 20 ml. GTB, rinse tubes, transfer to 50ml screw cap. re-rinse with 8 ml GTB, add0.15g CsCl/ml. Do not worry about small amounts of material floating around. Final volume should be30ml.
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6) layer solution carefully onto 8ml 5.7M CsCL (w/5ul EtBr stock) cushions in sw28 open tubes. Tubesshould have been inced w/ 0.1M NaOH/1%SDS for 30', then rinsed thoroughly in H2O pror to use.
7) spin sw27 22h, 24krpm 18C
8) aspirate top solution w/ interface junk to cushion, then quickly aspirate cushion around red RNA pellet
9) immediately add 3ml sarcosyl/urea SU, transfer to 15ml corex. vigorous pipetting required to dissolvegelatinous flakes
10)add 1.5ml Phenol to fully dissolved RNA, vortex, then 1.5 ml CHCl3, vortex
11)spin 5', 7.5krpm
12)back ext PCHCl3 phase w/ 1.5ml SU, vortex, spin, add SU phase to first SU phase (4.5ml total)
13)EtOH ppt, -20C
14)resuspend in 100ul DEPC-treated H2O
15)2ul for OD 260/280. ratio should be about 2 for good RNA
REB, autoclave stock/500ml
100mM Tris, pH 9.0 50ml 1M
100mM NaCl 13ml 3M
10mM EDTA 100ml 0.5M
1% SDS 50ml 10%
5mM DTT 2.5ml 1M
GTB, filter sterilized stock/500ml
5M guanidinium thiocyanate 295g
25mM Na citrate 3.67g
0.5% sarcosyl 12.5ml 20%
2mM EDTA 4ml 250mM
5% Bme 25ml
5.7M CsCl/0.1M EDTA 84.185g CsCl/100ml
7M urea/2% sarcosyl 42g urea,10ml 20%sarc/100ml
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RNA MINIPREP 1
1) grind 0.5-2g material in lN2 to fine powder
2) pour 6 large spatulafulls into 30ml corex tubes w/ 10 ml RNAextraction buffer
23.add 100-200ul depc water (2g of tissue gives 200ul water)
24.transfer to a epp. take 4-5ul forOD 260
End -80c
RT-PCR
Total RNAs should have been isolated with a protocole compatible with the RTase
step (chloroforme extraction following a phenol extraction for instance).
Contamination of RNAs by genomic DNA should not be too important (almost invisible on a gel). TheDNase treatment is performed with a RNase-free DNase in the RTase buffer. Prior to the RTase step, theDnase is heat inactivated and therefore does not require a phenol/chloroforme extraction.
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1. DNase treatment of total RNAs
On ice, mix the following :
RNAs 10 ug (not more than 29.5 ul)
10xRTase buffer 5 ul
RQ1 DNnase 2 ul
H20 up to 36.5 ul
Mix well, spin down and incubate at 37 C for 15‚
Inactivate the DNase at 65 C for 10‚ then transfer the tubes on ice
2. RTase (synthesis of the first strand of cDNAs)
on ice, add the following to the DNase-treated RNAs :
0.1 DTT 5 ul
10 mM dNTPs 5 ul
0.5 ug/ul oligo-dT 2 ul
MMLV-RTase 1 ul
RNase-inhibitor 0.5 ul
Incubate the tubes 1 hour at 37 C then 2‚ at 92 C
For long storage, store the cDNAs at -80 C, otherwise at -20 C.
3. PCR
Perform the PCR by using 1 ul of cDNAs for a 50 ul PCR reaction. The optimal number of cycles should bedetermined in order to stop the reaction during the exponential part of the amplification, before reaching theplateau phase, otherwise the PCR will not be quantitative. Remember to include appropriate positive andnegative PCR controls.
SDS-PAGE FOR PROTEINS
PA stock made from biorad 2.6% C, add 362 ml. H2O/150g mix. This gives 30:0.8%.
sterile filter.
gradient gel 7.5% 15% standard 12.5%
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30% Acryl stock 11.5ml 22.5ml 37.5ml
resolving buffer 5.6ml 5.6ml 11.2ml
60% sucrose 3.8ml 13ml -
10% SDS 450ul 450ul 900ul
H2O 28ml 4ml 40.0ml
TEMED 15ul 10ul 25ul
10% APS 0.18ml 0.18ml 360ul
5% stacking gel
30% Acryl stock 5.0ml
stacking buffer 7.5
10% SDS 300ul
H20 17.1ml
TEMED 40.0ul
10% APS 0.4ml
8x Resolving buffer, filter, 4 C
363g Tris/l, pH 8.8
4x Stacking buffer, filter, 4 C
60.5g Tris/l pH 6.8
5x Running buffer, 4 C
30.25 g Tris/l
144 g Glycine/l (not HCl salt)
sample buffer, frozen
[final] [stock] /50ml 2x (for dil.)
Tris, 8.8 0.2M 1M 20ml 20
sucrose 0.5M - 18g 36
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EDTA 5mM 0.25M 2ml 4.0
methinone 1% - 0.5g 1g
BPB 0.05% - 2mg 3mg
SDS 2.5% 10% 12.5ml 2.5g
DTT 5mM 1M 250ul 500ug
for samples containing cysteine or free 35-S cysteine, add iodoacetamide 50mM 0.5M 2.5ul/25ul sample
inc 15' 37C, then + 1ul Bme to quench iodoacetamide
2M urea may be used in SDS gels. Allow urea to dissolve fully before adding SDS.
3) aspirate and + denaturing buffer (SWDB), inc RT 1h
4) asp and + renaturing buffer (SWRB), inc RT 1h
5) asp, transfer to sealbag, + plenty of SWRB, inc 4C o/n
6) asp and + 10-15 ml binding buffer (SWBiB) + milk
7) asp, + 3 ml (< as possible) SWBiB + milk + DNA probe, inc RT 1h
8) wash 3 x 5' in SWBiB. expose up to 1 week
Note:
a) milk may inhibit binding. Try 10mg/ml BSA (boiled 10' in 10mM KHPO4 & 50mM Hepes Ph 7.5) inSWBB. If milk is thus replaced, omit from SWBiB.
b) [NaCl] in SWRB and SWBiB can be optimized
c) Other variables - Buffer (Tris, Hepes), MgCl2 (Mn, Zn), EDTA, NP-40
Solutions:
SWBB 5% Non-fat dry milk
30mM Hepes 7.5
SWDB 50mM Tris 8.3
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50mM DTT
1mM EDTA
6M Gua-HCl
SWRB 50mM Tris
1mM EDTA
2mM DTT
0.5M NaCl
10% glycerol
0.1% NP-40
SWBiB 30mM Hepes 7.5
50mM NaCl
5mM MgCl
2mM DTT
0.25%Non fat dry milk
T4 POLYMERASE FILL IN RXN
1) resuspend 40ug DNA in 90ul H2O for bal 31 deletions (see baldel.ptc) Use less
DNA, smaller volumes for normal fillins
2) add 10ul 10 x T4pol buffer
3ul T4 polymerase (BM #1004786100)
3)inc 5' , 37C
4)add 5ul 2mM dNTPs
5)inc 10', 37C
6)add 3ul Klenow enzyme (BM #997463500)
7)inc 5', 37C
8)P/CHCl3 ext.
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9)EtOH ppt.
10x T4 pol buffer
330mM Tris-acetate pH 7.9
660mM K-acetate
100mM Mg-acetate
WESTERN BLOTTING
electroblotting: assure that gel is cut to correct size for S&S BA85 or Millipore GSWP 0.22um membraneafter they have been washed 10' in transfer buffer. Transfer for 3h at 250mM at RT