MOLECULAR BIOLOGY METHODS

2.91 G enom ic DNA isolation

A) Isolation of genomic DNA from cell lines

Genomic DNA was prepared using a variety of m ethods. In general, tw o different m ethods w ere utilised for the isolation of high m olecular w eight genomic DNA from cell lines. These were as follows:

M ethod 1: Cells growing in tissue culture flasks were w ashed twice w ith cold PBS w hich was aspirated off after each wash. Ten mililitres of fresh PBS were added to the flask and the cells were scraped off the bottom of the flask w ith a cell scraper into a centrifuge tube. The

resultant cell suspension was centrifuged at 1,000 rpm for 8 m inutes at 4°C in order to pellet the cells. The cell pellet was resuspended in 3 mis of an ice cold solution consisting of 150 mM NaCl and 25 mM EDTA. Fifteen m icrolitres of a solution of 10% (w /v ) SDS w ith 300 pg of

Proteinase K w ere added to the cell suspension w hich w as subsequently incubated at 50°C for betw een 1 and 4 hours.

After incubation at 50'C, the solution w as extracted twice w ith Tris-buffer equilibrated phenol followed by tw o extractions w ith chloroform: iso-amyl alcohol (24: 1). The sam ples being extracted w ere mixed for 5 m inutes on a vertical rotor in each case. The tubes containing the respective samples were sp u n for 5 m inutes at 5,000 rpm to separate the tw o phases, after which the aqueous phase was rem oved into a fresh tube using a 10 ml wide-bore pipette. After the final extraction, 2.0

volum es of ice cold 100% ethanol w ith 0.1 volumes of 0.4 M NaCl were added to the sample. The sam ple w as mixed by hand at w hich stage DNA became visible as a stringy w hite precipitate. A pasteur pipette was

fashioned w ith a small hook at the tip, and this w as used in order to retrieve the DNA precipitate from solution. The DNA was spooled o u t onto the pipette and transferred to a 1.5 ml m icrocentrifuge tube

containing 70% ethanol in order to w ash the precipitate. The DNA, still on the pipette, w as allowed to air-dry then transferred to a further m icrocentrifuge tube containing 50 pi sterile distilled w ater, in w hich it

w as dissolved. The concentration of the DNA was estim ated through m easurem ent of the optical density (OD) of a 1 in 200 dilution at 260 nm (assum ing a 50 |ig /m l solution of DNA to have an OD26O value of 1.0),

and the purity w as determ ined through m easurem ent of the OD at 280 nm and subsequent calculation of the ratio OD26O to OD280 (assum ing

th at this ratio is 1.80 for a pure solution of DNA). The integrity of the DNA w as checked by running a small am ount out on a 0.7% (w /v ) agarose gel, alongside ^H in d lll m olecular w eight markers.

M ethod 2: This m ethod largely superceded m ethod 1 and w as initially used in order to isolate genomic DNA from m ouse em bryonic stem cells grow ing in 24-well plates. Cells w ere w ashed twice w ith PBS. The buffer was aspirated off and DNA extraction buffer was added. In general, cells grow ing in 24-well plates received 500 pi of extraction buffer. Those growing in 6-well plates received 1 ml of extraction buffer, w hereas cells grow ing in, for instance, a 75 cm2 (T75) flask received

betw een 3 and 5 mis of extraction buffer. Cells were digested overnight at 37“C, rem oved to a m icrocentrifuge or 15 ml tube, then extracted once w ith an equal volum e of Tris-buffered phenol: chloroform: iso-amyl alcohol (25: 24: 1). Tubes were mixed well, allowed to stand for 5 m inutes then centrifuged at a m inim um of 3,000 rpm for 10 m inutes in the

benchtop or microcentrifuge. The aqueous phase w as rem oved to a fresh tube and the DNA precipitated by the addition of 0.6 volum es of ice cold propan-2-ol. At this stage the DNA became visible as a stringy w hite precipitate which was collected by centrifugation. The resultant DNA pellet was w ashed once w ith 70% ethanol, air-dried then dissolved in an appropriate volum e of sterile TE buffer pH 8.0, or sterile distilled water. From a single well of a 24-well plate the yield of DNA was sufficient for one restriction endonuclease digestion (approxim ately 10 to 20 pg total yield). From cells grow ing in larger areas the concentration, purity and integrity of the DNA preparations was determ ined as described above.

B) Isolation of high m olecular w eight genomic DNA from tissue

This m ethod was initially developed for the isolation of high m olecular w eight genomic DNA from transgenic m ouse tails (Hogan, 1986), b u t it was found to be an effective m ethod for the isolation of genomic DNA from any tissue.

Seven h u n d red microlitres of tissue DNA extraction buffer w ere ad d ed to the tissue samples (< 1 gram) in 1.5 ml m icrocentrifuge tubes. The tubes were incubated overnight at 55°C. Tubes w ere spun for 1

m inute at m axim um speed in a m icrocentrifuge in order to pellet debris. The supernatant was rem oved into a fresh tube and extracted twice w ith an equal volum e of Tris-buffered phenol: chloroform: iso-amyl alcohol (25:24:1). For each extraction, tubes were m ixed by vortexing, allowed to stand on the bench for 5 m inutes then m icrocentrifuged for 10 m inutes. Point six volumes of ice-cold propan-2-ol w ere ad d ed to each tube which w as then m ixed by vortexing and m icrocentrifuged for 10 m inutes. The resultant pellet was w ashed once w ith 70% ethanol, then allow ed to air- d ry on the bench. The dried pellet w as dissolved in an appropriate

volum e of sterile TE buffer pH 8.0 or sterile distilled water. As above, the concentration, purity and integrity of the DNA was determ ined through m easurem ent of the OD26O and OD28O values and through agarose gel

electrophoresis.

2.92 R estriction endonuclease digestion of plasm id DNA and genom ic D N A

Restriction endonuclease digestion of both plasm id and genomic DNA was typically carried out in a total volum e of 30 pi. lOX buffers for the respective restriction endonucleases were supplied by the

m anufacturer, and used at a final w orking concentration of IX. For digests in w hich m ore than one restriction endonucease w as utilised sim ultaneously the optim al buffer w as determ ined according to the m anufacturer's instructions. If it w as determ ined th at both enzym es w ould not digest completely together, for instance if Smal, w hich cuts best at room tem perature was to be used in com bination w ith an enzym e th at is optim ally active at 37°C, the two respective digests w ere carried o u t sequentially. Genomic DNA digests were of betw een 10 and 20 pg total genomic DNA and proceeded overnight at the optim al tem perature for the particular restriction endonuclease being utilised. Plasm id DNA (typically 1-5 pg) was digested for a m inim um of one hour at the optim al tem perature. W here larger am ounts of plasm id w ere digested, the

reaction was allowed to proceed according to published activity values for the respective restriction endonucleases. All restriction endonuclease digests w ere typically carried out w ith a 3-5 fold excess of enzym e, at a final glycerol concentration not exceeding 10% (v /v ).

2.93 Agarose gel electrophoresis of DNA

Agarose gels were prepared by dissolving agarose at 0.8-3.0% (w /v ) in IX TBE buffer in a microwave oven. The solution w as allow ed to cool, after which ethidium brom ide was ad d ed to a final concentration of 0.1 p g /m l, and the gel was poured into a gel m ould containing a comb well former. Gels were allowed to set at room tem perature. DNA sam ples w ere prepared by the addition of DNA sam ple buffer to l / 5 t h final volum e, and introduced into the wells of the gel subm erged in IX TBE buffer. Electrophoresis was carried o u t in IX TBE buffer prepared from lOX TBE stock solution. Gels were electrophoresed at 5 to 7 V /cm at room tem perature during the day or 1 to 2 V /cm overnight, until the desired range of separation of the DNA fragm ents was achieved. DNA was visualised by illum ination over a long wave UV light box, and

photographed w ith polaroid film. The sizes of fragm ents w ere estim ated by com parison of their mobility relative to m olecular w eight m arkers of know n size. M olecular weight m arkers utilised w ere as follows:

a) H in d lll restriction endonuclease digestion of bacteriophage X DNA; b) H aelll restriction endonuclease digestion of bacteriophage 0X174 DNA; c) BRL 1 kilobase pair ladder.

2.94 Isolation of DNA fragm ents from gels

A) Isolation of DNA fragments from low m elting point agarose

Low m elting point (LMP) agarose gel purification was utilised for the preparation of all the DNA probes described in this thesis. Low m elting point agarose gels were prepared in IX TBE as for standard agarose gels, except that LMP gels w ere allowed to set at 4°C. As LMP gels tend to be m uch m ore fragile than standard agarose gels, LMP gels of greater than 1.0% (w /v ) were routinely utilised. DNA sam ples w ere loaded into the gel and electrophoresed at 4°C in IX TBE buffer at 5 V / cm. After suitable separation, fragm ents to be isolated from LMP gels w ere cut out of the gel as a thin gel slice. This was carried out over long w ave UV illum ination. Excess agarose was trim m ed from around the DNA w ithin the gel slice, and the slice was transferred to a sterile 1.5 ml m icrocentrifuge tube that had been prew eighed. The tube containing the gel slice was then reweighed and the w eight of the gel slice was

w ater to 1 gram of gel. The tube was subsequently boiled for 10 m inutes after w hich time the probe w as aliquotted into separate tubes, the

concentration of DNA was estim ated and recorded on the tubes in nan o g ram s/p i, and the tubes were stored at -20°C.

B) Isolation of DNA fragm ents using DEAE paper

This m ethod was used for the isolation and purification of DNA fragm ents for cloning purposes. It w as used successfully to isolate DNA fragm ents u p to and greater than 10 kilobase pairs. H ow ever, in general, sm aller DNA fragm ents were m ore efficiently purified by this m ethod.

Using a sterile scalpel, a small cut w as m ade in the gel

im m ediately ahead of the DNA fragm ent to be isolated. This procedure w as perform ed over UV illum ination. Squares of DEAE (NA45) ion- exchange paper (Schleicher and Schuell, Dassell, Germany) w ere cut slightly larger than the w idth of one of the wells, and then soaked in TE buffer p H 8.0. Using forceps and a sterile scalpel, the DEAE paper was carefully inserted into the incision that had been m ade in the gel. The ion-exchange paper was positioned such that once electrophoresis resum ed, the DNA fragm ent to be isolated w ould ru n onto the paper. The correct position of the ion-exchange paper was verified over UV illum ination. Electrophoresis resum ed and the gel w as allow ed to ru n for a further 15-20 minutes. After this period of time, the gel was rem oved and again exam ined over UV light. At this time the DNA fragm ent being isolated w as alm ost invariably entirely located on the ion-exchange paper. If not, the gel w as returned to the electrophoresis cham ber and electrophoresis w as continued. Once it w as confirm ed th at the DNA fragm ent had m igrated onto the paper, the paper w as rem oved from the gel and w ashed briefly in TE buffer p H 8.0. Excess paper w as trim m ed from around the DNA, and the paper was transferred to a 1.5 m l m icrocentrifuge tube containing 400 p.1 1 M NaCl. The tube w as then placed at 70°C for 30 m inutes, vortexing every 5-10 m inutes. After 30 m inutes, the paper was rem oved from the tube, w ashed in TE buffer p H 8.0 and exam ined over UV light to determ ine if the DNA had come off the paper into the salt solution. If this was found to be so, 1.0 ml of ice- cold 100% ethanol w as added to the tube w hich w as subsequently vortexed briefly to mix. For DNA fragm ents know n to be low in

concentration, 10 |ig yeast tRNA (transfer RNA) were added to the tube

prior to ethanol precipitation. The tube was transferred briefly to dry ice or -20°C, after w hich time it was centrifuged for 10 m inutes at top speed in the microcentrifuge. The resultant DNA pellet w as w ashed w ith 70% ethanol and air-dried. The pellet w as dissolved in sterile distilled w ater and one tenth of the total volum e w as analysed by agarose gel

electrophoresis. The concentration of the purified DNA fragm ent w as estim ated through reference to DNA m olecular w eight m arker

fragm ents w hich w ere ru n on the same gel.

2.95 Labelling DNA fragm ents

A) Labelling DNA fragments to high specific activity by random prim ing

This m ethod was used for the preparation of all labelled DNA probes described in this thesis and follows the m ethod of Feinberg, 1984. DNA w as isolated in low melting point agarose as described above and aliquotted at a final concentration of betw een 2 and 5 n an o g ram s/|il. A pproxim ately 50 nanogram s of DNA in low m elting point agarose w ere boiled for 10 m inutes, centrifuged briefly to bring dow n any condensate, and placed at 37°C for 5 to 10 m inutes. Ten microlitres of OLB buffer and 2 |il BSA (10 m g /m l solution) were ad d ed to the tube and the volum e w as raised to 44.5 |il. Two point five units of Klenow DNA polym erase w ere added to the tube followed by 50 |iCi [a32p]dCTP (5 pi volume). Labelling was carried out for at least 4 hours at room tem perature, b u t w as generally allowed to proceed overnight. The reaction w as term inated by the addition of 2 pi of 0.5 M EDTA pH 8.0. Labelling by this m ethod typically resulted in probes labelled to a specific activity of > 1 X 108 d p m /p g .

The level of incorporation of radioactivity w as m easured as described (Maniatis, 1982). Five microlitres of the labelled probe were diluted up to a total of 50 pi w ith sterile distilled water. Five m icrolitres of the diluted probe were spotted onto the centre of a W hatm an glass fibre disc. An equal volume of the diluted probe w as added to a tube containing 100 pi of a solution of salm on sperm DNA (500 p g /m l in 20 mM EDTA p H 8.0). Five mililitres of a solution of ice-cold 10% (w /v ) trichloroacetic acid (TCA) were added to the tube. The resultant

precipitate was collected by filtering through another glass fibre filter disc w hich w as subsequently w ashed several additional times w ith 5 ml ice-

cold 10% (w /v ) TCA. After wasliing w ith TCA, the filter w as w ashed w ith 95% ethanol. Both filters were dried under a heat lam p. Filters w ere counted by liquid scintillation, the first filter giving a m easure of the total radioactivity in the sample, and the second a m easure of the radioactivity specifically incorporated into the probe.

B) Preparation of radioactively labelled m olecular w eight m arkers;

Radioactively labelled DNA m olecular w eight m arkers were

p rep ared for reference purposes on Southern blots. Bacteriophage X DNA w as digested w ith the restriction endonuclease, H indlll. Klenow DNA polym erase specifically incorporates nucleotides into 3' recessed ends. The first available nucleotide of the 3' recessed end created by the restriction endonuclease H in d lll is an adenosine (A). In order to label H in d lll digested X DNA, 1 pg of DNA in a total volum e of 44 pi, was heated to 65°C for 10 m inutes then cooled on ice. Five microlitres of lOX m edium salt buffer, 5 pCi of [a35S]dATP, and 2.5 units of Klenow DNA polym erase were added to the tube and the labelling reaction was

incubated at 37°C for a m inim um of 30 m inutes. After 30 m inutes, 2 pi of 0.5 M EDTA pH 8.0 were added to the tube to term inate the labelling reaction. For Southern blots, 5 pi of labelled X H in d lll DNA w ere ad d ed to 2 pg cold (unlabelled) X H in d lll DNA.

2.96 S o uthern blotting

A) Blotting onto nylon m em branes

Gels were ru n until the desired range of separation w as achieved, as described above. At this time gels were docum ented by photography over long w ave UV illum ination. For reference, a ruler was placed alongside the gel which could be com pared in the photograph to the respective positions of the molecular w eight w arkers utilised. Gels w ere agitated for 30 m inutes in a solution of 0.5 M N aOH, 1.5 M NaCl in order to d en atu re the DNA. DNA was transferred overnight onto Biodyne B nylon m em branes by capillary elution in the presence of 20X SSC, as described in M aniatis, 1982. After overnight transfer, the positions of the wells w ere m arked onto the nylon m em brane w ith pencil, the efficiency