12/19/2012

     On this day, I learned about the various other methods of DNA seperating other then capillary electrophoresis. Of these several methods that I learned about, I was particularly interested about the method of gel electrophoresis.

     Gel electrophoresis is a method that is used to separate and then analyze DNA, RNA, and proteins on the basis of their size and charge. Particularly in the interest of my internship, it is often used to separate a mixed group of DNA and RNA fragments by length and to separate proteins by their charges. This process occurs in an agarose matrix. Agarose is a gelatinous mixture and it has a neutral charge and a lower degree of complexity--thus making it less likely to interact with biomolecules. Gels made from purified agarose have a relatively big pore size, making them useful for separating large molecules like DNA fragments. DNA is overall negatively charged and so when they are placed in a gel, an electric field is created across the very gel and so the negative DNA approaches the positive electrode while moving further away from the negative cathode. Shorter molecules move faster and travel further than the longer ones because they are able to move more easily through the pores of the gel. After the process, one will find that the different sized molecules have created distinct bands on the gel.  

    This method of DNA separation, however, is not commonly used by mentor as it is limited. For instance, the gel may melt during electrophoresis from the heat caused from passing a current across. In addition, comparing the relative quantity of the various molecules rely on the band darkness of the different spots in the gel. It's method consequently has a substantial degree of error. (That is why experiments are usually run several time to get viable results.) 

     Hopefully by the week I come back from winter vacation, my real mentor, Yolanda, will be back as well so that I may be able to start testing the various samples of DNA for myself!

http://m.youtube.com/?reload=9&rdm=mfca6b1q0#/watch?v=9f2VSyVhsGI&feature=related

<Above is a YouTube link demonstrating a slab gel separation.>

December 12

I was not able to go to my internship as my mentor Yolanda went home for the holidays.
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        Although I was not able to go to my internship on Wednesday, I decided to research more about the particular field of analytical science and about DNA separation, both in which my mentor (and thus I) is involved in.
        DNA isolation is an process that extracts DNA from other sources. There are different methods for doing this but what they all have in common is that they aim to separate DNA present in the nucleus of the cell from other cellular components. While researching online, I found that this process is crucial for genetic analysis, which is used for medical, scientific, or forensic purposes. In the field of medicine, this application is used for diagnostic purposes. To my fascination, I found that this process of DNA separation is important in the field of forensics as it allows investigators to recover DNA for identification of criminals, and the likes. While the area of my internship deals with the primary step of separating two DNA strands of similar length into separate pieces, I found it very fascinating to see how this type of research benefits the real world outside the long white coats and enclosed space called the laboratory.

reference: http://www.enotes.com/dna-isolation-methods-reference/dna-isolation-methods

December 5: Getting Started

Today, I learned all about DNA separation through the use of capillary electrophoresis.

The separation of DNA (not a double but a single strand) of the same length starts with synthesized DNA that is dyed so that the capillary machine detector can detect the separated DNA at the end of the process. Scientists are aware of how to separate DNA with different lengths, but what they do not know and what my internship is focused around is how to separate DNA of the same length. This can simply not be done by adding common separating polymers to the tube, but by adding one of the four bases (adenine, guanine, thymine, and cytosine) which helps to differentiate the speed at which the DNA sample hits the cathode end (due to the phosphate group attached to the DNA which gives it a negative charge). Why adding the bases helps separate the genes is unknown and there is currently a limit to how many parts the DNA can be separated into—as of now, it can be separated into 7 pegs.

After understanding all this, I was then explained to about the lab procedures that I would be performing. The graduate student that helped me, Yolanda, walked me through and we prepared the DNA test samples that will go in the machine for analysis. At the end of my time, I was amazed at how far I had come (and it was only the 2^nd time here) as just 2 weeks ago, I had no idea what capillary electrophoresis was and as to me, it sounded like something in another language. I am looking forward to my next meeting, as I will be able to apply what I have learned today and play an even greater role in preparing the test samples for the lab.

November 28

Was not able to go to internship due to schedule change.