Nucleic Acids in Chemistry and Biology

basic conditions without competing cleavage of the oligonucleotide chain (Figure 3.47). Consequently, it
is the protecting group of choice in oligonucleotide synthesis (Sections 4.1 and 4.2).
-Elimination is also
important biologically in the base excision repair pathway involving the enzymatic cleavage of phosphate
diesters following removal of damaged bases by glycosylase enzymes (Section 8.11.4).

3.2.2.2 Hydrolysis of Aryl Triesters. Because aryl phosphates are much more reactive than alkyl phos-

phate triesters, it is possible to achieve selective, nucleophilic displacement of the phenolic residue in a dialkyl
aryl phosphate on account of its better leaving group ability (pKa 5). One of the best nucleophiles for this
purpose is the oximate anion(Figure 3.48). Although aryl triesters were used historically during oligonu-
cleotide synthesis, they were replaced by the cyanoethyl group, since this group may be removed in a single
step along with the base protecting groups and oligomer cleavage from the solid support (Section 4.1).

3.2.2.3 Hydrolysis of Phosphate Diesters.85,86 At pH 2, phosphate diesters exist as their

monoanions, which are extremely stable kinetically (Table 3.1). Even in strongly alkaline conditions, diesters
hydrolyse with predominant C O cleavage (the extent depending on the nature of the alkyl group) and far
more slowly than triesters, since attack at the phosphorus atom is impeded by anion–anion repulsion. The
spontaneous (pH-independent) reaction of the monoanion is so slow that it is yet to be quantified for simple
phosphate diesters with alkoxy leaving groups. In acidic conditions, their hydrolysis occurs through the neu-
tral species, which are similar to trialkyl phosphates in reactivity. The diaryl esters are rather more reactive
under alkaline conditions, as is to be expected for reactions involving a better leaving group, and also allow
the pH-independent reaction to be observed (which is very sensitive to the pKaof the aryloxy leaving group).
This marked stability of the phosphate diester linkage during hydrolysis is a vital feature of the biological role
of DNA, where maintenance of the primary structure is required to preserve the genetic code. It is dramatically
changed for esters of 1,2-diols, such as the ones found in RNA. Here, the vicinal hydroxyl group enormously
enhances the rate of hydrolysis of di- and triesters. Similarly, the cyclic phosphates of 1,2-diols hydrolyse more
than 10^7 times faster than their acyclic or 6- and 7-membered cyclic relatives. This corresponds to a decrease in
G‡of 36 kJ mol^1. About 60% of this acceleration is attributed to relief of strain in the five-membered cyclic
ester, which has a 98° O P O angle and an enhanced enthalpy of hydrolysis of20 kJ mol^1.

104 Chapter 3

O

O

O

BP

P

O

O

O

O

BP

O

NC

H

O

O

O

BP

P

O

O

O

O

BP

O

B Base (B:)

α

β

P=protecting group

Figure 3.47 Selective deprotection of oligonucleotide phosphate triesters by b-elimination

H

N

NO 2

O

Cl

O

P

O

R'OOR'

H

N

NO 2

O

P

O

R'O OR'

B

O

P

O

R'O OR'

CN

NO 2

Figure 3.48 Selective nucleophilic displacement in an aryl ester

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