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 nonhistone proteins, and placed in an appropriate buffer, the chromatin decondenses to the 10-nm fiber structure. Suppose researchers mix a sample of 10-nm–fiber chromatin with a large amount of the enzyme DNase I that randomly cleaves DNA in regions not protected by bound protein. Next, they remove the nucleosomes, separate the DNA fragments by gel electrophoresis, and stain all the DNA fragments in the gel. 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?

Key Concepts

Nucleosome Structure

Nucleosomes are the fundamental units of chromatin, consisting of a segment of DNA wrapped around a core of histone proteins. Each nucleosome typically contains about 145 base pairs (bp) of DNA, which is crucial for the organization and compaction of eukaryotic genomes. Understanding nucleosome structure is essential for predicting how DNA is protected from enzymatic cleavage and how it contributes to the overall architecture of chromatin.

DNase I Activity

DNase I is an enzyme that cleaves DNA at sites that are not protected by bound proteins, such as histones in nucleosomes. When chromatin is treated with DNase I, the enzyme will cut the linker DNA and any exposed regions, resulting in fragments of varying sizes. This concept is vital for interpreting the results of gel electrophoresis, as the size of the resulting DNA fragments will depend on the locations of the nucleosomes and the extent of DNase I digestion.

Gel Electrophoresis

Gel electrophoresis is a laboratory technique used to separate DNA fragments based on their size. When DNA is subjected to an electric field in a gel matrix, smaller fragments migrate faster than larger ones, allowing for the visualization of different sized fragments. The number of bands observed on the gel corresponds to the sizes of the DNA fragments generated by DNase I digestion, providing insights into the organization of chromatin and the positions of nucleosomes.