Nucleic Acids in Chemistry and Biology

154 Chapter 4

B

DMTO O

OO

NCCH 2 CH 2 O P

N

O

Si

O

NCCH 2 CH 2 O P

N

B

DMTO O

O

B

O

O O O

O

O

O

O

O

MeO P

N

Si O

O

O

a 2'-TBDMS O

b 2'-TOM

c 2'-ACE

SiMe

Me

Si

Si

Figure 4.13 Standard building blocks used for RNA synthesis, (a) tert-butyldimethylsilyl (TBDMS) phosphoramidite,
(b) triisopropylsilyloxymethyl (TOM) phosphoramidite, and (c) tris(acetoxyethyl) orthoformate (ACE)
phosphoramidite

additional 2
-hydroxyl group in ribonucleosides. Three effective methods for the synthesis of RNA are

now available. Two of the methods involve silyl-type protecting groups at the 2
-position while DMT is

used at the 5
-position. The third utilises silyl protection at the 5
-position and an acid-labile group to pro-

tect the 2
-position.

4.2.1 Protected Ribonucleoside Units

4.2.1.1 Hetereocyclic Base Protection. As with DNA synthesis, the exocyclic amino groups of

adenine, guanine and cytosine need protection. Acyl groups are still the method of choice. Benzoyl and

acetyl protecting groups are commonly used, since they are readily removed during the ammonia deprotec-

tion at the end of the synthesis. However, with the newer 2
-O-protecting group strategies it is often desir-

able to have amino-protecting groups that are removed under milder conditions. Therefore, PAC or

dimethylaminomethylene are often used for adenine and guanine, while acetyl, though more stable than

PAC, is also employed frequently. For coupling using phosphotriester chemistry, additional protection for

the O^6 - and O^4 -positions of guanine and uracil respectively is necessary, since these positions are suscepti-

ble to reaction during phosphorylation.

4.2.1.2 Hydroxyl Group Protection. The 2
-hydroxyl group needs to be protected with a group that

is stable throughout the synthesis and which can be removed selectively at the end without side-reactions.

To introduce a protecting group at the 2
-hydroxyl group, orthogonal protection of both 5
- and 2
-positions

is needed. In addition during such synthesis, there is danger of migration of protecting groups between the

2 
- and 3
-hydroxyl positions, which can occur under both acidic and basic conditions and which makes

the separation and purification of the desired 2
-protected nucleoside difficult.

Currently there are three main types of RNA phosphoramidite building blocks based on different O-2
-

protecting groups (Figure 4.13). After initial 5
-protection, one of these protecting groups is introduced into

a ribonucleoside selectively at the 2
-position and then phosphitylation of the 3
-hydroxyl group is carried

out as described for 2
-deoxyribonucleosides.

4.2.1.2.1 TBDMS. The tert-butyldimethylsilyl (TBDMS) group is moderately stable to the acidic

conditions used during sequential deprotection of the 5
-DMT group that is used in chain assembly, but

http://www.ebook3000.com