Thrombospondin-1 cDNA construct

2.5.1 Thrombospondln-1 preparation and transformation

Thrombospondin-1 cDNA cloned into the Hindlll and Xbal sites of

pcDNAI/Neo plasmid vector (Figure 4) was kindly supplied by Dr NR Bouck, Department of Microbiology-lmmunology and Robert H. Lurie Cancer Center, Northwestern University Medical School, Chicago, Illinois,

USA. The transformation of TSPI/pcDNAI/Neo into competent Escherichia

coli bacteria, DH5a strain (Gibco-BRL, Life Technologies) was performed

Sac II

■ P vul

pcDNAI/

7.0 kb

Bglll

Figure 4. pcDNA1/Neo plasmid vector

2.5.2 Bacterial transformation

Bacterial transformation is the process by which bacterial cells take up naked DNA molecules. If the foreign DNA has an origin of replication recognised by the host cell DNA polymerases, the bacteria will replicate the foreign DNA along with their own DNA. When transformation is coupled with antibiotic selection techniques, bacteria can be induced to uptake certain DNA molecules, and those bacteria can be selected for that incorporation.

The DH5a strain of E.coli competent cells were thawed on ice, and 50 pi aliquots were placed in cold 1.5 ml-microcentrifuge tubes. One microlitre of DNA was added to the competent cells and gently mixed, then incubated on ice for 30 minutes. Cells were heat-shocked in a 37°C water bath tank for 45 seconds exactly, immediately placed on ice for 2 minutes, and 950 pi of Luria-Bertani (LB) medium (5 g/l bacto yeast extract, 10 g/l bacto tryptone, 10 g/l NaCI pH 7.0) were added. Cell mixture was placed in an

orbital shaker at 250 rpm at 37°C for 1 h. 150 pi cell mixture was plated out on an LB agar plates (5 g/l bacto yeast extract, 10 g/l bacto tryptone, 10 g/l NaCI, 15 g/l bacto agar) containing 100 pg/ml ampicillin. After incubation at 37°C overnight, only bacteria which possess the plasmid DNA will have the ability to metabolise ampicillin and form colonies. Single bacterial colonies were inoculated in 10 ml of LB medium containing 50 |xg/ml ampicillin and incubated overnight in a shaking incubator at 37°C. Plasmid DNA was prepared using kits supplied by Qiagen and followed the manufacturer’s guidelines.

2.5.3 Plasmid DNA preparation

Plasmids are small circular double-stranded DNA molecules of bacterial origin which replicate independently of the host cell chromosome. Plasmid DNA exists in a covalently closed circular form and is smaller than bacterial chromosomal DNA. The lysis of bacterial cells in the preparation of plasmid DNA may be achieved by boiling the bacterial culture or by treatment with alkali (which denatures chromosomal and plasmid DNA) and SDS (which denatures bacterial proteins). The mixture is then neutralised with potassium acetate, which causes the covalently-closed plasmid to reanneal. The chromosomal DNA and proteins precipitate along with a potassium-SDS complex and are removed by centrifugation. The plasmid DNA may be concentrated from the supernatant by ethanol precipitation.

2.5.3.1 Small scale preparations of plasmid DNA

Plasmid DNA was prepared from small cultures of bacteria using a QIAprep plasmid minipreparation kit (QIAGEN). This procedure was based on the alkaline lysis method for rapid extraction of plasmid DNA from bacterial cells followed by the adsorption of DNA onto silica in the presence of high salt. Three millilitres of the overnight cultures were centrifuged at 10,000 g for 1 minute and the bacteria were then resuspended in 250 pi of resuspension buffer PI (50 mM Tris.CI pH 8.0, 10 mM EDTA, 100 pg/ml Rnase A). 250 pi of lysis buffer P2 (200 mM NaOH, 1% SDS) was then added and mixed gently, followed by adding 350 pi of neutralisation buffer N3 (3 M potassium acetate pH 5.5) which adjusts the sample to high salt binding conditions and causes precipitation of denatured proteins, SDS, cellular debris and chromosomal DNA. The samples were then centrifuged at 10000 g for 10 minutes and the supernatants were then transferred to individual columns. Further centrifugation at 10000 g for 2 minutes caused flow through the silica membrane which forms the floor of the columns. After washing with 0.75 ml of buffer PE (200 mM NaCI, 20 mM Tris.CI pH 7.5, 5 mM EDTA, 95% ethanol) to remove salts, the DNA was eluted by applying 50 pi of sterile-distilled waster to the silica membrane.

2.5.3 2 Large scale preparation of plasmid DNA

The Qiagen Plasmid Maxi kit was used which was based on the modified alkaline procedure followed by binding of plasmid DNA to an anion- exchange resin. A single bacterial colony was used to inoculate a 5 ml

shaking incubator at 37°C. Then 1 ml of this culture was used to inoculate 250 ml of L-broth containing ampicillin which was then incubated overnight. The bacteria were pelleted by centrifugation at 6000 g for 20 minutes (J2- H2 centrifuge, Beckman) and resuspended in 10 ml of resuspension buffer PI. Ten millilitres of lysis buffer P2 was then added and left at room temperature for 5 minutes. Ten millilitres of neutralisation buffer N3 pre­ chilled to 4°C was added and the sample was centrifuged at 20000 g for 30 minutes. The resulting cell lysate was then filtered onto a QIAGEN-tip which had been pre-equilibrated with 10 ml buffer QBT (750 mM NaCI, 50 mM MOPS pH 7.0, 15% ethanol, 0.15% TritionX-100) and allowed to enter the anion-exchange resin by gravity flow. Under these conditions, the plasmid DNA binds to the anion-exchange resin. The resin was then washed with 60 ml of medium salt buffer QC (1 M NaCI, 50 mM MOPS pH 7.0, 15% ethanol) to remove RNA, proteins and low molecular weight impurities. The DNA was eluted with 15 ml of high salt buffer OF (1.25 M NaCI, 50 mM Tris.CI pH 8.5, 15% ethanol), and was then desalted by precipitation with

10.5 ml isopropanol. The DNA was pelleted by centrifugation at 15000 g for 30 minutes at 4°C, washed with 70% v/v ethanol, air-dried and then dissolved in sterile distilled water.

2.5.4 Digestion of DNA with restriction enzyme

Plasmid DNA was digested in volumes of 30 pi using 1-2 units of enzyme per pg of DNA for 60 minutes at 37°C. Appropriate buffers supplied by the manufacturer were used. Then DNA electrophoresis was carried out on 1 %

agarose gel with ethidium bromide. The correct band of TSP1 cDNA was purified using Qiagen’s gel extraction kit (section 2.3.3).