The 3' and 5' designations refer to the numbers that chemists assign to the:

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The 3' and 5' designations refer to the carbon atoms in the deoxyribose sugar of DNA. The numbering system starts at the carbon atom that is part of the pentose sugar ring and extends out to the other atoms in the molecule. The 5' end of DNA has a phosphate group attached to the 5' carbon of the sugar, while the 3' end has a hydroxyl (-OH) group attached to the 3' carbon of the sugar.

The 3' and 5' Designations Refer to the Numbers That