Question
How did Hershey and Chase differentiate between DNA and protein in their experiment while proving that DNA is the genetic material?

Answer

A.D. Harshey and M.J. Chase conducted experiments on $T _2$ viruses that infect bacteria called bacteriophage and concluded that DNA was the genetic material. Only the DNA of bacteriophage infecting the host enters the bacterial cell which transport the genetic information resulting into the formation of new phase particles.
Hershey and Chase based their experiment on the fact that DNA but not the protein contains phosphorus and similarly Sulfur is present in protein but not in DNA. They then incorporated radioactive isotopes of phosphorus P-32 into phage DNA and that of S-35 into proteins of a separate phage culture.
These phage types were used independently to infect the bacterium E. coli. After some time this mixture was agitated on a blender to separate the empty phage caprices or ghost off the bacterial cells and the two were separated by centrifugation. Hershey and Chase showed that when P-32 was used, all radioactivity was associated with bacterial cells and if followed appeared in the progeny phage. However when S-35 was used, all radioactivity material was limited to phage ghosts. The conclusion was simple and straight forward DNA alone is able to impart all the characteristics to the phage progeny and protein did not play any role in this process.

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