Purpose: The purpose of this lab was to perform agarose gel electrophoresis of our leaf genomic DNA extract, wheat germ extract, along with two different samples of Lambda
DNA (one that has been cut or digested with the restricted enzyme Hind III from
Haemophilus influenza , and one that has not been cut.)

Data:
Figure 1: Shows the gel electrophoresis the lanes from left to right are 1kb ladder, uncut lambda DNA, cut lambda
DNA, S3 leaf, S3 Wheat, S9 Leaf, S9 Wheat, Cut lambda (just to give symmetry), uncut lambda (just to give symmetry), 2kb ladder (works better than 1kb).
Figure 2: Shows the Rf value verses the log of the number of base pairs
Questions
1. There are many similarities and differences between agarose electrophoresis of nucleic acids and polyacrylamide electrophoresis of proteins. However, because agarose forms a weaker, softer, gel than polyacrylamide, electrophoresis in agarose gels in

generally performed in a horizontal orientation rather than vertical. Another difference is that there is no stacking gel in agarose electrophoresis. This is due to the greater frictional component of nucleic acids in the gel versus in solution, such that they focus very quickly at the buffer-gel interface before entering the matrix. On the other hand, agarose electrophoresis is similar to PAGE in that a loading dye/treatment solution is added to each sample to increase its density, solution properties, and to allow visualizing the progress of the electrophoresis. Similarly one always includes molecular weight standards in one lane for calibration purposes.
2 . Genomic DNA is isolated by being cut into smaller fragments of manageable sizes with one or more specific restriction endonuclease. The RNA initially present has essentially been “digested” by these restriction enzymes; which can take over foreign
DNA that may enter the cell. Ethanol precipitates DNA because DNA is polar and is negatively charged due to its phosphate group whereas ethanol is non-polar. Therefore when ethanol is placed in the presence of DNA it becomes insoluble and precipitates out of the solution. I would estimate there is approximately one hundred micrograms of
DNA in one gram of plant tissue.
3.
4. See Figure 3. a. Hind III restriction enzyme is a type II restriction endonuclease. Unlike type I restriction enzymes, type II restriction endonucleases perform very specific cleaving of DNA. Type I restriction enzymes recognize specific sequences, but cleave DNA randomly at sites other than their recognition site whereas type II restriction enzymes cleave only at their specific recognition site. b . Not all of the fragments were observed, this could be because the gel may not have run for long enough and the sample fragment size was too small or because the fragments were too large to pass through the gel. c. The estimates of the fragment sizes compare pretty well to the known sizes of the fragments.