I'm assuming you mean "A's B" or "B of A"
They're sort of interchangeable but "B of A" is very formal, and applies to a lot of cases where "A's B" would not. "A's B" implies possession always, while "B of A" is more of an indicator of relation or used to describe a thing.
"John's car" sound much more natural than "The car of John". Even though the latter is technically correct, it sounds very formal and odd.
"The President of the United States" and "USA's President" are interchangeable, but the latter is much more informal.
"College of Science" and "Science's College" are not interchangeable, because in this case "of" is used to show what the college is about, not to imply possession.