"

From 2010.igem.org

B-Galactosidase Activity Assay -- Marian Price-Carter, 9/7/00

Modified From Protocols Online 10/15/10 (htt p://rothlab.ucdavis.ed u/proto cols/beta-galactosidase-3 .html)

Day 1: Start overnight lactose-free broth culture. Negative control: cells lacking 13-galactasidase, such as Agrobacterium positive control: cells with high enzyme activity E.coli.

Day 2: Dilute cells 1/100 in fresh medium now containing lactose, grow to mid-log.1 Prepare solutions: Z buffer, phosphate buffer, ONPG2. Preparation of Cells

Incubate cultures 20’ on ice to stop grnwth and wash:

¯ Pellet at least 2 mL of cells at 4 C by centrifuging 10’ at 6,000 rpm in a Sorval SS34 rotor.

¯ Pour off the supematant.

¯ Resuspend the cell pellet in the same volume of chilled Z buffer.

¯ Measure the ODr0o of the resuspended cells (blank against Z buffer)

Dilute cells in Z buffer to I mL (most easily done with a pippeter). For most activities, 0.5 mL cells + 0.5 mL Z buffer will produce a desirable amount of yellow color in !-2 hours. For higher levels (>500 Miller units), try 0. I mL cells + 0.9 mL Z buffer.

Permeabilize the diluted cells by adding 100 lal chloroform and 50 ~1 0.1% SDS (sodium dodecyl sulfate, sodium laurel sulfate). Chloroform is easier to pippete if the air in the pippete tip is saturated by dm~ving up and releasing chloroform several times. Vortex; equilibrate the tubes 5’ in a 28 C water bath.

Assay

Start reaction by adding 0.2 mL substrate, o-nitrophenyl-13-D-galactoside (ONPG; 4 mg/mL)

¯ Vortex - Record the time of addition precisely with timer or stopwatch.

¯ Incubate the cells at 28 C.

¯ Stop the reaction after sufficient yellow color has developed3 by adding 0.5 mL 1M Na2CO34.

¯ Vortex. - Note time of addition precisely.

¯ Transfer 1 mL to an eppendorftube, spin 5’ at maximum to remove debris and chloroform.

¯ Record the optical density at 420 nm and at 550 nm for each tube. 5

¯ Calculate the units of activity6"

This is basically the assay described by J.H. Miller in "Experiments in Molecular Genetics" 1972 Cold Spring Harbor Laboratories pages 352-355, with an extra step added. In the assay described here, the cells are pelleted and resuspended in assay buffer (Z buffer) to eliminate error due to the effects of different carbon sources in the growth medium on the [3-galactosidase enzyme activity.

B-Galactosidase is able to hydrolyze (cleave) ~-D-galactosides. This enzyme facilitates growth on carbon sources like lactose by cleaving it into a molecule of glucose and a molecule of galactose which the cells can catabolize and grow on. In the assay described above, the substrate o-nitrophenyl-I]-D-galactopyraniside (ONPG) is used in place of lactose. When the 13- galactosidase cleaves ONPG, o-nitrophenol is released. This compound has a yellow color, and absorbs 420 nm light. To measure ~-galactosidase activity the accumulation of yellow color (increase’420 nm absorbance)/minute is monitored.

Footnotes ~ In Sahnonella (which is naturally l]-galactosidase minus) this assay is used to monitor transcription from insertion elements (that encode the [~-galactosidase enzyme) that have inserted into different genes. The assay is usually performed on cells in the mid-log phase of growth. On rich carbon sources like glucose, the OD6oo of a culture of wild-type Salmonella in mid-log phase ranges from 0.28-0.7. On poorer carbon sources or in strains that have mutations in genes that are important for groxvth, the OD6oo at mid-log phase may be lower, since the cells may enter stationary phase at a lower density. Therefore, before doing the assay, it is important to follow the growth of the strain of interest in each type of medium that will be used, plot a groxvth curve, and determine when the cells are in mid-log phase in that particular medium. Solutions for I]-galactosidase assays Z buffer, per 50 mL:

¯ O.80g Na2HPO.~.7H20 (0.06M)

¯ 0.28g NaH2PO4.H20 (0.04M)

¯ 0.5 mL 1M KC1 (0.01M)

¯ 0.05 mL IM MgSO~ (0.001M)

¯ 0.135 mL iB -mercaptoethanol (BME) (0.05M)

¯ bring to approximately 40 mL with H20, dissolve all the salts

¯ adjust the pH to 7.0

¯ use a graduated cylinder to bring the buffer to 50 mL

¯ store at4 C.

Note: BME is added to the reaction buffer to stabilize the ~-galactosidase enzyme. The important part of BME is a reactive thiol (SH group). Thiols react with oxygen in the air and oxidize (inactivate) over time. Therefore, try not to make much more Z buffer than you will use in a few days. Store the unused portion at 4 C. ONPG should be dissolved fresh each day. Dissolve 1.5X as much as you think you will need, because you may have to repeat one or more of the assays Le. for a different amount of time or with a different cell dilution. Dissolve the ONPG to a final concentration of 4mg/mL in 0. IM

phosphate buffer pH 7.0.

Phosphate buffer, per 100 mL:

¯ 1.61g Na2HPO4.7H20 (0.06M)

¯ 0.55g NaH2PO4.H~O (0.04M)

¯ adjust the pH to 7.0

¯ phosphate buffer is stable at room temperature and does not need to be made fresh each time.

3 What is sufficient yellow color? To get the most accurate measure of activity, the absorbance at

420 nm (A42o) should range.from 0.6 to 0.9. Readings as low as 0.1 and as high as 1.2 are acceptable. Tubes that have become as yellow as a tube of(unused) LB broth will probably be sufficiently yellow.

If the reading is too low, try the assay again with more cells or longer incubation time. When the element has inserted into a gene that is not expressed much, it will probably take hours to develop enough yellow color. If your negative control starts to tum yellow (after several or more hours) it means that the substrate is beginning to auto-hydrolyze. The assay can be left overnight.

The auto-hydrolysis is then accounted for by subtracting the A42o and A~oo of the negative control from that of the tests before doing any further calculations.

If the reading is too high, try the assay again with fewer cells¯ Aim to stop the reaction after 15 minutes. For example, if in your first attempt, you added 0.5 mL 0fcells + 0.5 mL of Z buffer, and it was too yellow after 5 minutes, try adding 0.1 mL cells + 0.9 mL of Z buffer. Watch the tube carefully. Some cultures may have to be diluted even further[

~ Adding the 1 M Na~CO3 stops the reaction by raising the pH of the solution to 11. At this pH the enzyme is not active.

5 The reading at 420 nm is a combination of absorbance by o-nitrophenol and light scattering by cell debris. The absorbance at 550 corrects for light scattering. There is no absorbance from onitrophenol at this wavelength. The light scattering at 420 nm is proportional to that at 550 rim: light scattering at 420 nm = 1.75 x OD55o

6 Use the following equation to calculate units of enzyme activity: Miller Units = I000 x [(OD~o - 1.75 x OD~5o)] / (T x V x OD6~o)

¯ OD~o and OD~o am mad from the reaction mixture.

¯ OD6oo reflects cell density in the washed cell suspension.

¯ T = time of the reaction in minutes¯

¯ V = volume of culture used in the assay in mLs.

The units give the change in A4~o/min/mL of cells/OD6oo

Typical values:

a fully induced lac+ operon (+IPTG) = 1500 units

an uniduced lac÷ operon (no IPTG) = 1.5-3 units

10/19/10

Today we are doing large scale DNA extractions from E-Coli Recovering t9002 and lac-z

first taking the OD of each tube

after Blacking spectrometer I will run a sample of each tube.

E-coli w/T9002 from 10/15/10 has an OD of .355 @600um

E-Coli w/LacZ from 10/15/10 has an OD of 3.49 @ 600um

Streaked E-coli w/T9002 from 10/12/10 has an OD of .363 @600um

1. 2 Streaked E-Coli w/LacZ from 10/15/10 has an OD of 3.26 @ 600um

after I took 4 bottles from spec to hood and removed 5ml from each tube placing into 50 cc tubes with LB/Amp and then placed them int 37C inculbator

Then placed the 4 tubes extracted from and placed them into centrefuge to spin down to extract DNA.

Then following protocol from pg 19. After extracting the DNA I placed into fridge in back Room @ 4C.

Then made LB Broth in 3 1Lt flasks weighing 10 g in each LB mix then adding 500 ml to it, placed into microwave one time on beverage setting then into autoclave on liquid setting 121 C @ sw