Chapter 11, Problem 27P

Summary Introduction

To review:

DNase I is a restriction endonuclease which cuts the DNA but cannot cut the DNA that is protected by bound proteins. Human DNA is isolated, exposed of its non-histone proteins, and mixed with DNase I. Removal of samples carried after 30 minutes, 1 hour, and 4 hours and allowed to run separately in gel electrophoresis. The resulting gel is stained to make all DNA fragments in it visible, and the results are shown in the figure. The size of DNA fragment in base pairs (bp) is estimated by the scale to the left of the gel.

On the basis of the above information, following questions are asked:

a. Based on the gel results, speculate why longer DNase I treatment produces different results.

b. To conclude about the organization of chromatin in the human genome from this gel.

Introduction:

When DNA interacts with enzyme (proteins), it induces changes in the DNA. This interaction can be analyzed by the biochemical methods such as gel electrophoresis. DNase I is an endonuclease. It cleaves the DNA at the phosphodiester bond which is adjacent to pyrimidine nucleotide and mostly produces tetranucleotides with $\text{5'}-\text{P}$ and $\text{3'}-\text{P}$. It can cleave double stranded DNA, single stranded DNA, and chromatin. It is encoded by the human gene DNA $\text{SE1}$. It is also important in DNA fragmentation during apoptosis. DNA footprinting assay can be done using DNase I. Also, we can study the interaction between proteins and DNA both within as well as outside the cell.