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BASIS Chandler Senior Class of 2016

Sunday, March 20, 2016

I completed my first Gel electrophoresis on the extracted DNA samples this week. 
Gel electrophoresis is the method of separating charged molecules of DNA, RNA and Protein according to their size. In this case, I used negatively charged DNA strands and used electric current across the gel to get the strands to travel towards the opposite charge. Smaller strands travel through the gel more quickly than the larger ones, which is how we distinguish that the molecules have been separated by size. 

Protocol
Preparing the Agarose gel:
  -Prepare 50X TAE buffer
  -Prepare 1X TAE buffer
  -Prepare 0.8% agarose gel:
          -0.8 grams agarose
          -100 ml 1X TAE
          -Microwave 2 min. (stop once at 50s, swirl,continue)
          -Add 4 microlitres of Ethidium bromide.
  -All 25-30 min. for the gel to solidify
  -Prepare the genomic DNA samples
    - Based on the concentrations, use 250-350 ng of DNA 
    - Total volume should be 20 microlitres. Using nuclease free water to make up the difference.
    - Add 5 microlitres of 6X loading dye to each of the prepared samples.
  - Fill the gel apparatus with 1X TAE buffer until the wells are completely covered. 
  -Pipette 5 microlitres of the ladder and 25 microlitres of the prepared samples into the wells
  -Add 4 microlitres of Ethidium Bromide to the positive end of the apparatus in the 1X TAE Buffer
  - Run for 1 hr. at 110 volts.
  - Use UV box to image gel 

Results:
The orange bands are the movement of DNA. On the left, is the DNA ladder, that contains a mixture of DNA fragments of known sizes. As we move to the right, we can see the movement of the varying concentration of DNA. By comparing these DNA bands to the DNA ladder, it can be said that the size of these DNA samples is around 7,000 base pairs of nucleotides.



 

6 comments:

  1. Hi Nikita, I am pleased to see the progress you have made. EtBr staining is efficient but be careful when you work with it, as it is a mutagen. Are the samples loaded in the different lanes varying concentrations of DNA? Did you destain the gel with water? That might take off some background to get a clearer image of the DNA bands. After separating DNA bands on agarose gels, what is the next thing you plan to do? Looking forward to your next post.

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    1. Yes, the samples loaded in the different lanes have varying concentrations of DNA, but the overall volume added up to 25 microlitres. This was just a quick run gel to see if I get efficient results. I agree that it was really hard to see the bands, and in the beginning I just thought that the bands were stuck because we took it out a little before an hour. But, my lab manager said that the gel was great, and that was the final results. Hopefully, next time I run a gel, I can leave it in longer, and I'll get a different procedure to get a clearer image. As of now, I just do what I'm told to. I have no idea what I plan to next. I'm sure the lab manager has something in mind, but it hasn't been cleared with me yet.

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  2. Hey Nikhita!This seems really cool. I love making gels and running gel electrophoresis, it's really cool to see the results, so I'm glad you're getting to do this!

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    1. Yes, my favorite part is loading the samples into the wells. It stressed me out in the beginning, but I enjoy the overall process.

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  3. Hi Nikhita!

    I'm sure you remember that we talked about gel electrophoresis for a short while in AP Biology, but what was it like to actually do it? Was it a cool experience?

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    1. Yes, I remember going over this in AP Biology, and the overall experience was really fun. I was stressed out in the beginning, because you have to load the samples inside these little wells and if the sample didn't get inside the well you pretty much have to start over. That's my favorite part, because it's like I'm playing a computer game where if I miss, it's like "Game Over." It's so much fun though, and I look forward to the next time I'll get to run a gel again.

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