1. Consider two DNA molecules, one 200 base pairs long, the other 800 base pairs long. Assuming that each is a rigid rod of diameter 25 Å, with a length of 3.4 Å per base pair, calculate the ratio of the electrophoretic mobilities of these two molecules using the very approximate equation U = v/E = Ze/f. Note that charge is proportional to the length. (5 points) How is the situation different in gel media compared to in free solution? (5 points)
2. The digestion of chromatin by a nuclease, such as micrococcal nuclease, tends to cleaves the DNA at the junctures between nucleosomes to make a series of oligonucleosomes. To determine the DNA “repeat size”, the DNA from such a digestion is electrophoresed on a polyacrylamide slab gel parallel to a lane of restriction digestion of bacteriophage DNA of known sizes. The following data give the distances migrated on such a gel. Deduce the repeat size of the calf chromatin. (10 points) Phage DNA fragments Size (base pairs) d (cm) 794 11.5 642 13.6 592 14.6 498 16.7 322 22.5 288 24.1 263 25.4 160 33.0 145 34.2 117 37.2 94 40.0
Fragments of calf nuclear DNA Number d (cm) I 30.5 II 19.2 III 14.4 IV 11.5
3. To visualize the effect of dust contamination on light-scattering experiments, perform the following calculation. A solution, containing 4 mg/ml of protein of M=100,000 dalton, is contaminated to the extent of 0.0005% of the protein weight by dust. The dust particles are 0.1m in radius, with density = 2.00 gm/cm3. By what percent will the 90° scattering be changed by this contamination, assuming Rayleigh scattering for all particles? (10 points)
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