Team:CIDEB-UANL Mexico/Test/Protocol
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<h2>Use of plates with BioBrick lyophilazed</h2> | <h2>Use of plates with BioBrick lyophilazed</h2> | ||
- | <li>Search in the Part Registry web site for the desired BioBrick and look forward its exact position in the DNA´s plate.</li> | + | <p> |
- | Position correctly the lyophilizated DNA´s plate. | + | <li>1. Search in the Part Registry web site for the desired BioBrick and look forward its exact position in the DNA´s plate.</li> |
- | Using a 10 μl micropipette, take a white tip and drill the aluminum cover in the well where is located the BioBrick piece. | + | <li>2. Position correctly the lyophilizated DNA´s plate. </li> |
- | Using the same micropipette, throw away the tip, take another one to take 10 μl of mQ water and introduce this tip in the well. | + | <li>3. Using a 10 μl micropipette, take a white tip and drill the aluminum cover in the well where is located the BioBrick piece. </li> |
- | Up and down the liquid using the micropipette a couple of times until the DNA is completely resuspended (when dissolving the DNA, it will give to the water a reddish coloration, so, the more reddish the solution means that the resuspension was well done. | + | <li>4. Using the same micropipette, throw away the tip, take another one to take 10 μl of mQ water and introduce this tip in the well. </li> |
- | Pour the liquid in a 0.6 μl centrifuge tube, label and store at -20°C. | + | <li>5. Up and down the liquid using the micropipette a couple of times until the DNA is completely resuspended (when dissolving the DNA, it will give to the water a reddish coloration, so, the more reddish the solution means that the resuspension was well done.)</li> |
+ | <li>6. Pour the liquid in a 0.6 μl centrifuge tube, label and store at -20°C. </li> | ||
+ | </p> | ||
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<p><li><b>Transformation of Ca+ Competent cells</b></li> | <p><li><b>Transformation of Ca+ Competent cells</b></li> | ||
- | <li>1.In a 1.5mL | + | <li>1.In a 1.5mL centrifuge tube pre-cooled, add 50 μl of competent bacteria. (It’s very important to keep the materials at 4°C).</li> |
<li>2.Add 2 μl of DNA and mix giving some light hits among the tubes.</li> | <li>2.Add 2 μl of DNA and mix giving some light hits among the tubes.</li> | ||
- | <li>3.Stand | + | <li>3.Stand on ice from 20 to 30 minutes.</li> |
- | <li>4.Give the thermal shock by immersing the | + | <li>4.Give the thermal shock by immersing the centrifuge tubes inside a beaker with water at 42°C for a minute.</li> |
- | 5.Put the tubes back in the ice for 2 minutes.</li> | + | <li>5.Put the tubes back in the ice for 2 minutes.</li> |
<li>6.Add 200 μl of LB medium and incubate at 37°C from 20 to 30 minutes.</li> | <li>6.Add 200 μl of LB medium and incubate at 37°C from 20 to 30 minutes.</li> | ||
- | <li>7. | + | <li>7.Plate in Petri dishes with LB agar and their respective antibiotic and incubate at 37°C all night long.</li></p> |
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<p><li><b>Stria in plate</b></li> | <p><li><b>Stria in plate</b></li> | ||
- | <li>1.Take the bacteriological handle and introduce in the flame of the burner until the point of the handle gets red, so it can be sterilized.</li> | + | <li>1.Take the bacteriological handle and introduce in the flame of the burner until the point of the handle gets red, so it can be sterilized.</li> |
<li>2.Take it away from the flame and wait until it’s a little bit cooled.</li> | <li>2.Take it away from the flame and wait until it’s a little bit cooled.</li> | ||
<li>3.Introduce the sterilized handle inside the tube that contains the bacteria and take a drop of the culture.</li> | <li>3.Introduce the sterilized handle inside the tube that contains the bacteria and take a drop of the culture.</li> | ||
- | <li>4.Take it away from the tube and inoculate the plate by stria forming parallel lines, spreading it over the agar. 5.First, inoculating a corner, sterilize the handle again and spread from a corner the bacteria previously inoculate, sterilize again and finish with wide movements.</li> | + | <li>4.Take it away from the tube and inoculate the plate by stria forming parallel lines, spreading it over the agar.</li> |
+ | <li>5.First, inoculating a corner, sterilize the handle again and spread from a corner the bacteria previously inoculate, sterilize again and finish with wide movements.</li> | ||
<li>6.Incubate the plate at 37°C from 18 to 24 hours.</li></p> | <li>6.Incubate the plate at 37°C from 18 to 24 hours.</li></p> | ||
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- | <p>< | + | <p><li><b>Extension on surface (When cultivating a transformation)</b></li> |
<li>1.Take the inoculum using a micropipette and place it in the agar surface.</li> | <li>1.Take the inoculum using a micropipette and place it in the agar surface.</li> | ||
- | <li>2.Take the glass | + | <li>2.Take the glass bacteriological loop and introduce it in a beaker with absolute alcohol.</li> |
<li>3.Put it away and quickly pass it by the flame and cool it a little bit.</li> | <li>3.Put it away and quickly pass it by the flame and cool it a little bit.</li> | ||
- | <li>4.Place the | + | <li>4.Place the glass bacteriological loop in the agar without making any contact with the dumped culture.</li> |
<li>5.Spread the inoculum in the plate until it’s dry.</li> | <li>5.Spread the inoculum in the plate until it’s dry.</li> | ||
<li>6.Incubate the plate at 37°C from 18 to 24 hours.</li></p> | <li>6.Incubate the plate at 37°C from 18 to 24 hours.</li></p> | ||
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<p><li>1.Add the correct antibiotic to a test tube with culture medium. </li> | <p><li>1.Add the correct antibiotic to a test tube with culture medium. </li> | ||
- | <li>2.Pick a colony with a | + | <li>2.Pick a colony with a bacteriological loop previously sterilized or pick with the point of the micropipette</li> |
<li>3.Shake by making small circles in the culture (if a handle was used) or up and down the culture a couple of times (if a micropipette was used).</li> | <li>3.Shake by making small circles in the culture (if a handle was used) or up and down the culture a couple of times (if a micropipette was used).</li> | ||
- | <li>4.Incubate at 37°C with vigorous and continuous agitation from 16 to 18 hours.</li></ | + | <li>4.Incubate at 37°C with vigorous and continuous agitation (250rpm) from 16 to 18 hours.</li></p> |
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<p><li>1.Add the correct antibiotic to a test tube containing culture medium.</li> | <p><li>1.Add the correct antibiotic to a test tube containing culture medium.</li> | ||
- | <li>2.Take approx. 20 μL of | + | <li>2.Take approx. 20 μL of culture containing bacteria and introduce them into a test tube with the new culture medium.</li> |
- | <li>3.Incubate at 37°C with vigorous and continuous agitation from 16 to 18 hours.</li></p> | + | <li>3.Incubate at 37°C with vigorous and continuous agitation (250 rpm) from 16 to 18 hours.</li></p> |
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<h2>Minipreps of plasmidic DNA</h2> | <h2>Minipreps of plasmidic DNA</h2> | ||
- | <p><li>1.Add 1.5 mL of culture inside | + | <p><li>1.Add 1.5 mL of culture inside a centrifuge tube. Centrifuge at 14000 rpm for 30 seconds and throw the supernatant away inside a container with chlorine at 0.1% or with liquid soap.</li> |
<li>2.Add 200 μL of Solution I and mix giving vortex until the pill is completely dissolved. (A micropipette can be used if it’s difficult to dissolve).</li> | <li>2.Add 200 μL of Solution I and mix giving vortex until the pill is completely dissolved. (A micropipette can be used if it’s difficult to dissolve).</li> | ||
<li>3.Leave all at room temperature from 5 to 10 minutes.</li> | <li>3.Leave all at room temperature from 5 to 10 minutes.</li> | ||
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<li>5.Add 200 μL of Solution III and mix by inversion. Leave all the samples in ice for about 10 minutes.</li> | <li>5.Add 200 μL of Solution III and mix by inversion. Leave all the samples in ice for about 10 minutes.</li> | ||
<li>6.Centrifuge at 14,000 rmp for 5 minutes.</li> | <li>6.Centrifuge at 14,000 rmp for 5 minutes.</li> | ||
- | <li>7.Pass the supernatant inside a new | + | <li>7.Pass the supernatant inside a new centrifuge tube containing 1mL of ethanol at 100% by using a tip, being careful of not passing any precipitate.</li> |
<li>8.Incubate at 20°C for 10 minutes (From 10 minutes to 2 hours).</li> | <li>8.Incubate at 20°C for 10 minutes (From 10 minutes to 2 hours).</li> | ||
<li>9.Centrifuge at 14,000 rpm for 10 minutes and throw the supernatant away.</li> | <li>9.Centrifuge at 14,000 rpm for 10 minutes and throw the supernatant away.</li> | ||
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<li>11.Centrifuge at 14,000 rpm for 5 minutes and remove the sobrenatant using a tip.</li> | <li>11.Centrifuge at 14,000 rpm for 5 minutes and remove the sobrenatant using a tip.</li> | ||
<li>12.Dry the pill at 37°C for 5 minutes in the incubator.</li> | <li>12.Dry the pill at 37°C for 5 minutes in the incubator.</li> | ||
- | <li>13.Add 20 μL of mQ water with RNAse ( | + | <li>13.Add 20 μL of mQ water with RNAse (10mg/mL) and resuspend with wortex.</li> |
<li>14.Run a gel or store at 4°C (DNA Electroforesis in agarose gel).</li></p> | <li>14.Run a gel or store at 4°C (DNA Electroforesis in agarose gel).</li></p> | ||
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<h2>Quantification of DNA by Ultra Violet Spectrophotometry</h2> | <h2>Quantification of DNA by Ultra Violet Spectrophotometry</h2> | ||
- | <p><li>1.Take 1ml of mQ water and place it inside a 1.5mL | + | <p><li>1.Take 1ml of mQ water and place it inside a 1.5mL centrifuge tube.</li> |
- | <li>2.Add 1 μL of plasmidic DNA samples of E.coli | + | <li>2.Add 1 μL of plasmidic DNA samples of E.coli (Dilution 1:1,000).</li> |
- | <li>3.Calibrate the spectrophotometer with a | + | <li>3.Calibrate the spectrophotometer with a cuvette containing 1mL of distillated water.</li> |
- | <li>4. | + | <li>4.Transfer the sample of the centrifuge tube to a cell of the spectrophotometer by using a micropipette.</li> |
<li>5.Place the cell in the spectrophotometer.</li> | <li>5.Place the cell in the spectrophotometer.</li> | ||
<li>6.Select the DNA or RNA option in the machine.</li> | <li>6.Select the DNA or RNA option in the machine.</li> | ||
- | <li>7.Select the DNA option in the spectrophotometer.<li> | + | <li>7.Select the DNA option in the spectrophotometer.</li> |
<li>8.Read the absorbance of the sample with the spectrophotometer.</li> | <li>8.Read the absorbance of the sample with the spectrophotometer.</li> | ||
<li>9.Annotate the reading made at 260, 280 and 320 nm, the relation 260/280 and the concentration given by the spectrophotometer.</li> | <li>9.Annotate the reading made at 260, 280 and 320 nm, the relation 260/280 and the concentration given by the spectrophotometer.</li> | ||
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<h2>Plasmidic DNA characterization</h2> | <h2>Plasmidic DNA characterization</h2> | ||
- | <p><li>1.Prepare the mix.</li> | + | <p><li>1.Prepare the digestion mix with the restriction enzymes needed ( Reaction order: mQ water enzyme > Buffer > Enzyme buffer > DNA to get a final volume of 10 μL).</li> |
<li>2.Distribute the mix in equal parts.</li> | <li>2.Distribute the mix in equal parts.</li> | ||
- | <li>3.Add the sample of DNA to the reactions and give a | + | <li>3.Add the sample of DNA to the reactions and give a gently vortex.</li> |
<li>4.Incubate the reactions at 37°C in the incubator from 1 to 12 hours. | <li>4.Incubate the reactions at 37°C in the incubator from 1 to 12 hours. | ||
- | 5.Run the agarose to check the result.</p> | + | <li>5.Run the agarose to check the result.</p> |
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<h2>BioBrick Pieces Assembly</h2> | <h2>BioBrick Pieces Assembly</h2> | ||
- | <p><li>1.Prepare the mix. (Reaction order: mQ water > Buffer > Enzyme).</li> | + | <p><li>1.Prepare the mix. (Reaction order: mQ water > Buffer > Enzyme). Using the NEB enzymes.</li> |
<li>2.Distribute the mix in equal parts.</li> | <li>2.Distribute the mix in equal parts.</li> | ||
- | <li>3.Add the sample of DNA to the reactions and give a | + | <li>3.Add the sample of DNA to the reactions and give a gently vortex.</li> |
<li>4.Incubate the reactions at 37°C in the incubator from 1 to 12 hours.</li> | <li>4.Incubate the reactions at 37°C in the incubator from 1 to 12 hours.</li> | ||
<li>5.Run 10 μL in agarose gel.</li> | <li>5.Run 10 μL in agarose gel.</li> | ||
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<p><li>1.Take in account the concentration of every sample that now contain the fragments which will used bind.</li> | <p><li>1.Take in account the concentration of every sample that now contain the fragments which will used bind.</li> | ||
- | <li>2.Use the Ligation Calculator to obtain the quantities to separate the ligation MIX | + | <li>2.Use the Ligation Calculator to obtain the quantities to separate the ligation MIX with a final volume of 20 μL.</li> |
- | <li>3.Prepare the mix using the quantities given by the calculator in the following order: Agua mQ >Ligation Buffer>Vector/Fragment.</li> | + | <li>3.Prepare the mix using the quantities given by the calculator in the following order: Agua mQ >Ligation Buffer>Vector/Fragment ratio.</li> |
- | <li>4.Distribute the ligation mix if necessary and add the ligase T4 | + | <li>4.Distribute the ligation mix if necessary and add the ligase T4 (NEB ligase)</li> |
- | <li | + | <li>5.Incubate the reactions at 25°C (room temperature) for an 1 hour or all night long.</li></p> |
</div> | </div> | ||
Latest revision as of 22:34, 16 June 2012
Lab Protocols
Use of plates with BioBrick lyophilazed