RNA hydrolysis
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RNA hydrolysis is a reaction in which a phosphodiester bond in the sugar-phosphate backbone of RNA is broken, cleaving the RNA molecule. RNA is susceptible to this base-catalyzed hydrolysis because the ribose sugar in RNA has a hydroxyl group at the 2’ position.[1] This feature makes RNA chemically unstable compared to DNA, which does not have this 2’ -OH group and thus is not susceptible to base-catalyzed hydrolysis.[1]
RNA hydrolysis occurs when the deprotonated 2’ OH of the ribose, acting as a nucleophile, attacks the adjacent phosphorus in the phosphodiester bond of the sugar-phosphate backbone of the RNA.[1] There is a transition state (shown above), where the phosphorus is bonded to five oxygen atoms.[2] The phosphorus then detaches from the oxygen connecting it to the adjacent sugar, resulting in ester cleavage of the RNA backbone. (This mechanism is also referred to as RNA cleavage.) This produces a 2’,3’-cyclic phosphate that can then yield either a 2’- or a 3’-nucleotide when hydrolyzed. This process is shown in Figure 1.[1]
Auto-hydrolysis
The hydrolysis or cleavage of RNA can occur spontaneously, without the presence of a catalyst or enzyme. This process is known as an auto-hydrolysis or a self-cleavage reaction. Spontaneous cleavage in an RNA molecule is much more likely to occur when it is single-stranded.[2] Auto-hydrolysis or self-cleavage reactions take place in basic solutions, where free hydroxide ions in solution can easily deprotonate the 2’ OH of the ribose. This deprotonation makes the reaction base-catalyzed and increases spontaneity of the reaction.[2]