Analysis # 1 - Nabeel Siddiqui nhs256 Bio 206L Wed....

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Nabeel Siddiqui nhs256 Bio 206L Wed. 9:00-1:00 (49530) 2/3/2010 Transformation and PCR Exercise # 4: Analysis 1. Agarose gel works as a semi permeable membrane that works to differentiate the sizes of ions and molecules. It works when a gradient is formed due to an electrical field. The larger ions and molecules take longer to permeate through the gel and are closer to the top of the gel. The gradient also helps the ions and molecules migrate to a pole based on the net charge of the ion or molecule. DNA is negatively charged due to the phosphate located on the deoxyribose sugar. This means that in electrophoresis, the DNA fragments would move toward the positive pole, or the anode. 2. Agarose gel can be used as a semi permeable membrane to sieve out larger molecules or smaller molecules from a solution. Its concentration correlates to the size of the molecules it allows through. For instance agarose solutions with a concentration of .7 % are ideal for sorting out larger molecules of about 5-10 kb because the resulting bands are more separated and easy to spot. For smaller molecules, a concentration of 2% or higher should be used so that there is distinction between a smaller range of molecule size. In order to form agarose gel from solution, you must first bring the solution to a boil using a microwave oven.
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When the solution is heated then you can pour the gel into the mold and wait for it to form. 3. If you wanted the gel to run faster, you would have to decrease the ionic strength of the buffer so that there are less negatively charged ions in the solution. Because DNA is negatively charged, it would adapt better to a less concentrated buffer which would cause it to separate out more evenly and run through the gel quicker. 4.
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Analysis # 1 - Nabeel Siddiqui nhs256 Bio 206L Wed....

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