Nucleic Acids in Chemistry and Biology

162 Chapter 4

4.4.3.4 Phosphoramidates. Phosphoramidatesare internucleotide linkages in which either the

3
- or 5
-oxygen of the phosphodiester is replaced by an amino group. Much of the work with 3
-phospho-
ramidates was pioneered by Sergei Gryaznov.^32 In general these are now prepared by coupling a nucleoside
5
-phosphoramidite to a solid support-bound 3
-deoxy-3
-amino nucleoside to form an N3
-P-phosphorami-
date linkage (Figure 4.23b).^33 Oligomers with phosphoramidate linkages show enhanced resistance to snake
venom phosphodiesterases and give significantly higher Tms for duplexes with complementary DNA and
RNA strands. The internucleotide phosphonamidite linkage can be sulfurised to form a phosphoroth-
ioamidate and oligodeoxynucleotides with N3
-P5
-amidate linkages are useful steric block antisense
reagents because their duplexes with RNA are not recognised by RNase H (see Section 5.7.1).

4.4.3.5 Other Internucleotide Modifications. One interesting analogue involves the use of bora-

nophosphateinternucleotide linkages first described by Barbara Shaw.^34 In the boranophosphate linkage,

a non-bridging oxygen atom is replaced by a borano group (BH 3 ) (Figure 4.23c). This also creates a P-chiral

centre. A boranophosphate is isoelectronic and isosteric with a natural phosphate, but it has increased

lipophilicity. Boranophosphate-modified oligonucleotides can induce RNase H-mediated cleavage of com-

plementary RNA and they have enhanced resistance to nucleases.

2 

–5

linked oligoadenylates(Figure 2.39) are an important class of naturally occurring oligoribonucleotide

in which consecutive nucleotide units have 2
–5
linkages. 2
–5
Oligoadenylates are prepared by 2–5A syn-

thetase from ATP in interferon-treated cells, and play a key role in mediating the antiviral effect of interferon.

4.4.3.6 2
-Modifications. Of the many 2
-modifications,^35 the 2

-O-methyl ribonucleosideis the

most well known (Figure 4.24). 2
-O-Methyloligoribonucleotides are more stable in binding complemen-

tary DNA or RNA than are oligodeoxyribonucleotides because the 2
-O-methyl sugar adopts a C3
-endo

B

O

O

O

B

O

O

P

O

H 3 C O

B

O

O

HN

B

O

O

P

O

O O

B

O

O

O

B

O

O

P

O

H 3 B O

abc

Methylphosphonate Phosphoramidate Boranophosphate

Figure 4.23 Structures of (a) the methylphosphonate internucleotide linkage, (b) the N3
-P phosphoramidate

internucleotide linkage, and (c) the boranophosphate linkage

B^2

HO O

O

B^2

O

O

B^1

DMTO O

O

SOP

S

PhCOS

B^1

DMTO O

O

P N

S

SCOPh

+ i, tetrazole/acetonitrile

ii, S 8 /pyridine/CS 2

B^2

O

O

B^1

DMTO O

O

SOP

S

NH 4 OH

Figure 4.22 Solid-phase synthesis of oligonucleotide phosphorodithioates

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