Question

Genomic DNA from the nematode worm Caenorhabditis elegans is organized by nucleosomes in the manner typical of eukaryotic genomes, with 145 bp encircling each nucleosome and approximately 55 bp in linker DNA. When C. elegans chromatin is carefully isolated, stripped of non-histone proteins, and placed in an appropriate buffer, the chromatin decondenses. Suppose researchers mix a sample of this chromatin with a large amount of DNase I that randomly cleaves DNA in regions that are not protected by bound proteins. Next, they remove the nucleosomes, separate the DNA fragments by gel electrophoresis, and stain the fragments with ethidium bromide.

a. Approximately what range of DNA fragment sizes do you expect to see in the stained electrophoresis gel? How many bands will be visible on the gel?

b. Explain the origin of DNA fragments seen in the gel.

Answer 1

Answers:

a. We will see DNA fragments with 145-200 bps (only one band)

b. The DNA sequence linked to histones will be protected from the action of DNase I, thereby this enzyme only can cut linker DNA (i.e., 55 bp fragments). In consequence, it is expected to observe a single band with a length of approximately 145 to 200 base pairs