# What happens to the third hydroxyl group in a phosphodiester linkage?

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds.

But what happens to the third hydroxyl group; i.e. why is it an oxygen and not hydroxyl?

At physiological pH it is simply deprotonated, i.e. it becomes $\ce{-O-}$ instead of $\ce{-OH}$. That's why DNA is said to have a negative charge.