Create a 11 pages page paper that discusses the molecular marker and the unknown fragments of dna. A gel tank was made by sealing a tray with masking tape and positioned it on the working bench. A comb was placed in the tray ready for making the wells. 0.5 g of agarose was used to prepare 1% w/v agarose gel mixture in a glass Scott bottle with the addition of 50 ml TBE buffer. The agarose – TBE mixture was heated in a microwave for around 30 minutes to ensure the mixing of the components. 1 µl gel Red was added after the bottle had cooled and the gel solution was swirled to mix and poured gently into the gel tray. The gel was left to set for about 30 minutes and the tape and the comb removed. The gel was placed appropriately into the running while ensuring that the sample wells were at the cathode. After the incubation period, 4µl of 6x concentrated DNA loading buffer (B2) into each of the tubes. The contents were mixed gently flicking the tube and tapping gently. This step was repeated while adding 5 µl B2 DNA loading buffer into the PCR tube. The uncut plasmid DNA did not migrate considerably due to its large size as can be observed from the gel image above. However, by digesting the DNA with the two restriction endonucleases short fragments of DNA which could penetrate the gel matrix were able to migrate and their sizes may help in determining the size of the initial plasmid DNA. PCR products as of the red fluorescent gene migrated considerably indicating their small sizes of the products. However, as can be seen in lane 6 of the gel image they formed a smear which may present difficulties when ascertaining the sizes of DNA. In conclusion, agarose gel provides a matrix for separating DNA products and which help in determining sizes of DNA of interest. Short fragments migrate the farthest due to their small sizes towards the positive anode end of the gel. However large fragments suffer a higher frictional force with the gel matrix reducing their migration capability and thus move short distances.
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