Solved it. Using similar logic to what @Palaniyappan suggested. For future reference:
I loop through columns, by using a for loop:
For Each col in DT.Columns
And then inside the loop, I have an assign activity:
col.ColumnName = GeneratedDT.Rows(1).Item(col.ColumnName.tostring).tostring
then I just drop the rows I do not need.
Thank you both for the suggestions.