[PDF] Role of the RNA polymerase trigger loop in catalysis and pausing

What is the relative ease of RNA hydrolysis?

The relative ease of RNA hydrolysis is an effect of the presence of the 2' hydroxyl group . A phosphodiesterase is an enzyme that catalyzes the hydrolysis of phosphodiester bonds, for instance a bond in a molecule of cyclic AMP or cyclic GMP . An enzyme that plays an important role in the repair of oxidative DNA damage is the 3'-phosphodiesterase.

What is the rate of hydrolysis?

The rate of hydrolysis depends on the concentration of silane, the pH of the solution (pH > 10 and pH < 5 give a high rate, pH near 7 gives the slowest rate), and the character of the functional groups of silanes and alkoxy groups [ 20 – 22 ]. Hydrolysis is catalyzed by hydronium ions H 3 O +, hydroxyl ions OH ?, Lewis bases, and some metals.

Why is RNA not susceptible to base-catalyzed hydrolysis?

RNA is susceptible to this base-catalyzed hydrolysis because the ribose sugar in RNA has a hydroxyl group at the 2’ position. 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. Mechanism of base catalyzed RNA hydrolysis.

Where does RNA hydrolyze in an alkaline environment?

The hydrolysis occurs at the phosphodiester bond of the backbone. Hence, RNA rapidly hydrolyzes in an alkaline environment into cyclic 2',3'-monophosphate nucleotides, which undergo further hydrolysis in water to form a mixture of 2'- and 3'-nucleoside monophosphates. This breaking of the backbone of RNA is known as a strand break.