Alkaline Hydrolysis of RNA

Question 1

RNA vs DNA

Answer 1

RNA treated with 0.1 M NaOH at room temperature is degraded to a mixture of 2’- and 3’ nucleoside monophosphates within a few hours whereas DNA is stable under the same conditions.

The 2’ hydroxyl group of ribose can form hydrogen bonds in some RNA moleucles.

Alkaline hydrolysis of RNA requires a 2’- hydroxy group.

Question 2

Step 1

Answer 2

A hydroxide ion abstracts the proton from the 2’- hydroxyl group of a nucleotide residue. The resulting 2’-alkoxide is a nucleophile that attacks the adjacent phosphorus atom, displacing the 5’-oxygen atom and generating a 2’-3’-cyclic nucleoside monophosphate

Question 3

Step 2

Answer 3

The cyclic intermediate is not stable in alkaline solution however and a second hydroxide ion catalyzes its conversion to either a 2’- or 3’- nucleoside monophophate.