Endy:General Western Blot

Transfer and Incubations

 * After running gel, cut away stacking gel, cut a corner to mark orientation, and soak in transfer buffer for 45 minutes.
 * Cut PVDF and 3mm Whatman blotting paper to correct size.
 * Cut corner on PVDF and wet with methanol, then soak 5 minutes in H20, followed by 10 minutes in transfer buffer. Wet 4 pieces of blotting paper in transfer buffer.
 * Set up transfer bottom to top: 2 pieces blotting paper, gel, PVDF, two pieces blotting paper. Be sure to preserve orientation of blot and avoid bubbles.
 * Transfer 2 mA/cm^2 until transfer is complete (i.e. rainbow marker is fully transferred to PVDF membrane). For one 8.5 X 5 blot, this works out to 85 mA for about 2 hours.
 * Block membrane for 1 hr with 5% milk/TBS-Tween (0.1 %). Use the lid of a pipette tip box and 15 mL fluid to cover blot. (for two blots, use a large tip box and 25 mL fluid for all incubations/washes) Place blot on shaker table for all incubations.
 * Incubate overnight with 1:10000 dilution of anti-GFP in 2% milk/TBS-Tween (0.1%)
 * Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.
 * Incubate 30 minutes with 1:10000 dilution of ECF secondary antibody in TBS-Tween (0.1%)
 * Wash 3X in 15 mL TBS-Tween (0.1%) for 10 minutes.

Analyzing Western

 * Turn on Fluorimager 30 minutes before use. Put in 570 filter.
 * Settings are PVDF 488/570 df 30, PMT = 500.  Select area to scan.
 * Place 1 mL/gel of ECF substrate on a transparency. ECF substrate in buffer is stored in 1 mL aliquots at –80C.
 * Using forceps, lay blot face down on top of substrate (no bubbles) for about one minute (less if bands become visible). Transfer blot face down to fluorimager plate.
 * Insert plate into machine. Scan image.  Remove plate immediately.
 * Remove plate before shutting down scanner. Leave software open if anyone is signed up within two hours.
 * Clean plate with dI and kim wipes, then with ethanol from the glass bottle.

Quantification in ImageQuant
volume = (average pixel value – background value) * object area
 * Use rectangle tool to draw object around band. Copy and paste object so that all objects have the same area.
 * It is not necessary to define a background in ImageQuant. Do volume report without background correction, and set the negative control equal to 0 ng/lane for your standard curve. Alternatively, make a new object to define background and set background on all lanes equal to “object ave” for this object. (analyze>>”background correction” to set background correction, then analyze>>”volume report”) (“local average” sets background equal to the average pixel value of the object perimeter.  This will be problematic if bands are not well separated.)
 * Double click report to make it an excel file. Save images and excel volume report.
 * Use standard curve to estimate ng gfp/lane for samples and calculate gfp/cell. The     molecular weight of GFP-SsrA is about 28.3 kDa.

2X Tricine Sample Buffer

 * 2 mL 4X Tris-Cl/SDS, pH 8.8
 * 6 mL 40% glycerol (24% final)
 * 0.8 g SDS (8% final)
 * 0.31 g DTT (0.2 M final)
 * 2 mg Coomassie blue G-250 (0.02% final) (used C. Blue G)
 * to 10 mL with MilliQ H2O and mix
 * aliquot 500 uL/tube and store at –20 C

4X Tris-Cl/SDS pH 8.8

 * 91 g Tris
 * dissolve in 300 mL H2O
 * pH to 8.8 with 1N HCl (about 120 mL)
 * to 500 mL with H2O
 * filter 0.45 um
 * add 2g SDS and store 4 C

Lysis Buffer (12.5 mM Tris pH 6.8, 4% SDS

 * 1.25 mL 1M Tris (pH 8)
 * to 80 mL with st. H2O
 * pH if necessary
 * to 100 mL with st. H2O
 * add 4g SDS

TBS-Tween (0.1%)

 * 100 mL 10X TBS
 * 900 mL H2O
 * 1 mL Tween (Polyoxyethylene sorbitan monolaurate)

10X TBS (500 mM Tris, 1.5 M NaCl)

 * 150 mL 5M NaCl
 * 250 mL 1M Tris, pH 7.5
 * to 500 mL with H2O

1M Tris-Cl, pH 8 (or 7.5)

 * 121 g tris base
 * 700 mL MilliQ H2O
 * to pH 8 with 6N HCl (about 100 mL)
 * to 1 L with MilliQ H2O
 * filter 0.45 um or autoclave (fluid, 20 psi, 250 F, 20 min)

Transfer Buffer (“Towbin Buffer”)

 * 3 g Tris
 * 14.4 g glycine
 * 800 mL dI
 * 200 mL methanol

note: anti-GFP is Assay Designs 915-059, rabbit (store one aliquot at 4 C to avoid freeze/thaw, rest at –20C) ECF Western Blotting kit is Amersham RPN5783 (rabbit) To connect to Bionet from fluorimager: \\18.79.1.147\endy   DNA-NET\username