Preparation and analysis of proteins

1mM EDTA 10mM KCl 0.2% Nonidet P-40

freshly added 0.1mM PMSF and 1mM DTT

Buffer B: 20mM HEPES, pH 7.9

420mM NaCl 1mM EDTA 10mM KCl

freshly added 0.1mM PMSF

Buffer C: 20mM HEPES, pH 7.9

10mM KCl 1mM EDTA

2.2.4.5.3 Measurement of protein concentrantion

Bradford Assay (Bradford, 1976) is a rapid and accurate method commonly used to determine the total protein concentration of a sample. The method is based on the observation that the absorbance maximum for an acidic solution of Coomassie Brilliant Blue G-250 shifts from 465nm to 595 nm when binding to protein occurs. Within the linear range of the assay (~5-25 mg/ml), the more protein present, the more Coomassie bind. The concentration of given samples were measured by mixing 1-5 µl proteins extract with 800 µl 0.25 M Tris/HCl (pH 7.8) and 200 µl Roti-Quant (Roth). Then the mixture was incubated for 5 minutes at RT. The absorbance was read in the photometer at 595nm, and the concentration was caculated with the following formula: protein concentration (µg/μl) = OD595nm × 19.89 (μg) / volume of protein extract (μl).

and the protein pellet was recovered by centrifugation at 14000rpm for 5 minutes. This step was repeated two times. The pellet was air-dried for 10-15 minutes and dissolved in the appropriate buffer. If the color of sample turns into yellow, add 1-5 drops of 1M NaOH until the color of sample turns into blue again.

2.2.5.2. SDS polyacrylamide gel electrophoresis and Western blotting analysis

SDS polyacrylamide gel electrophoresis (SDS-PAGE) was carried out as described from Laemmli (Laemmli, 1970)on acrylamide slab gels. The glass plate sandwich mold were assembled according to the manufacturer’s instruction using 1mm thick spacers. Acrylamide gels was prepared (Table 2.8).

Separating gel 7.5% 10% 12%

ddH2O 5.0ml 4.1ml 3.5ml

1.5M Tris-HCl, pH 8.8 2.5ml 2.5ml 2.5ml Acrylamide/Bis (30/0.8, 37.5:1) 2.5ml 3.4ml 4.0ml

10% (w/v) SDS 100µl

40% (w/v) APS 30µl

TEMED 20µl

Stacking gel 5%

ddH2O 6.2ml

0.5 M Tris-HCl, pH 6.8 2.5ml Acrylamide/Bis (30/0.8, 37.5:1) 1.3ml

10% (w/v) SDS 100µl

40% (w/v) APS 30µl

TEMED 20µl

Ingredients were mixed gently, and APS and TEMED were added just before pouring the gels.

The separating gel was poured to an appropriate level and the top of gel was slowly covered with a layer of ethanol to ensure a flat surface and to exclude air. After the gel was polymerized, the ethanol was poured off. The stacking gel was then poured above the separating gel with a comb inserted. After the stacking gel was polymerized, the comb was carefully removed and the gel slots were rinsed with ddH2O and excessive gel debris were removed. The gel slabs

Table 2.8 compositions of separating gel and stacking gel

were assembled into the electrophoresis chamber and the chamber was filled with Laemmli buffer. Protein samlpes were denatured by boiling in SDS-loading buffer or Roti-Load 1 (Roth) for 5 minutes. Samples and prestained protein molecular mass markers were loaded and empty slots were filled with equal volume loading buffer to prevent spreading of adjoining lanes. For electrophoresis, a constant current of 20-25mA/gel was used for stacking gels and 30-35mA/gel for separating gels.

After SDS-PAGE, proteins on the gel were transferred to PVDF membrane using a semi-dry blotting system. The transfer sandwich was assembled on the bottom of anode electrode by laying, one after the other, 6 pieces of whatman paper (soaked in anode buffer I), 3 pieces of whatman paper (soaked in anode buffer II), a piece of PVDF membrane, the gel and 6 pieces of whatman paper (soaked in cathode buffer III). Air bubbles were extruded by gentle rolling with a glass pipet. Finally, the cathode electrode was placed on top of the transfer sandwich. The transfer was performed at a constant current of 1mA/cm² for 1-2 hours.

After transfering, membranes were blocked in PBST containing 5-10% non-fat milk at RT for at least 2 hours or at 4°C overnight with regular shaking and then incubated with the corresponding primary antibodies overnight at 4°C or at RT for 1.5 hour. After 3×10 minutes washing with PBST, membranes were incubated with secondary antibodies at RT for 1 hour.

All the secondary antibodies are coupled to horseradish peroxidase and can be visualized by enhanced chemoluminescence (ECL). Membranes were washed 3×10 minutes with PBST after the incubation with the secondary antibodies, and ECL solution (Amersham/Millipore) was added to membranes according to manufacturer’s instructions. The membranes were then sealed in plastic bags. X-ray films were laid over the membrane and different exposure time was chosen. Films were finally developed in an X-ray film processor.

Membranes were stripped in a stripping buffer I at 65°C for 40 minutes or a stripping buffer II for 30 minutes at RT with frequently shaking. This strips the bound antibodies from the membrane so that it can be re-immunoblotted with different antibodies. After stripping, membranes were washed 3× 10 minutes with PBST and were blocked and immunoblotted as described above.

SDS-loading buffer: 62.5 mM Tris, pH 6.8 3% SDS

2% 2-mercaptoethanol 0.01% bromophenol blue 15% glycerol

Laemmli buffer: 192mM glycine 25mM Tris-base 0.1% (w/v) SDS

Do not adjust the pH with acid or base

Anode buffer I: 0.3M Tris, pH 10.4

10% methanol

Anode buffer II: 25mM Tris, pH 10.4

10% methanol

Cathode buffer: 40mM 6-amino-n-caproic acid

pH is not adjusted

PBST: 1× PBS

0.1% (v/v) Tween^® 20

Stripping buffer I: 62.5mM Tris-HCl, pH 6.7 2% (w/v) SDS

100mM 2-mercaptoethanol

Stripping buffer II: 25mM glycine, pH 2.0 1% (w/v) SDS

2.2.5.3. Detection of proteins on the PVDF membrane by Coomassie blue staining

The membranes were incubated in Coomassie staining buffer for 2 minutes and were then destained in destaining buffer I for 10 minutes. Afterwards, the membranes were washed in destaining buffer II until no background was left. The membranes were then kept in ddH2O or air-dried between two pieces of Whatman paper.

Coomassie staining buffer: 0.1% Coomassie brilliant blue R250

50% methanol

7% acetic acid

Destaining buffer I: 50% methanol

7% acetic acid

Destaining buffer II: 90% methanol

10% acetic acid

2.2.5.4 Mammalian pulldown

HEK293 cells were transiently cotransfected with mammalian expression vectors pCMV-GST, pCMV-GST-MBD2/MBD3, pCMV-GST-HDAC1 or pCMV-GST-RbAp46/RbAp48 with Gal, hp66α, four single mutant forms of hp66α (K30R, K149R, K451R, K487R), Gal-hp66β or two single mutant forms of Gal-Gal-hp66β (K33R, K454R). Cells were collected 48 hours after transfection and nuclear extracts were prepared as described above. 400μg of nuclear extract was incubated with 40μl glutathione-Sepharose 4B beads (Amersham Biosciences) for 30 minutes at room temperature. The beads were washed six times with washing buffer NTEN-100. Bound proteins were eluted with SDS sample buffer, fractionated together with the corresponding input fractions on SDS-PAGE and subsequently detected by Western blotting using the anti-Gal4 polyclonal IgG antibody. The membranes were stripped as described above.

Blots were subsequently reprobed with mouse anti-GST polyclonal IgG at a dilution of 1:3000 and subsequentlywith horseradish peroxidase-conjugated goat anti-mouse IgG at a dilution of 1:10000. The ECL^TM kit was used to visualize the proteins on the membrane following the manufacturer’s protocol.

NTEN-100: 20mM Tris, pH 8.0

100mM NaCl 1mM EDTA 0.5% Nonidet P-40 freshly added 1mM DTT