Glen Report 12.12: TOM-Protected Minor Base RNA Phosphoramidites

RNA synthesis using monomers containing the 2'-O-Triisopropylsilyl-OxyMethyl (TOM) group (TOM-Protecting-Group™) is characterized by very high coupling efficiency along with fast, simple deprotection. High coupling efficiency is achieved because the TOM-Protecting-Group exhibits lower steric hindrance than the 2'-O-t-butyl-dimethylsilyl (TBDMS) group used in our alternative RNA monomers. Fast and reliable deprotection is achieved using methylamine in ethanol/water at room temperature. A further feature of the TOM-Protecting-Group is that during basic steps it can not undergo 2' to 3' migration. This migration under basic conditions leads to non-biologically active 2'-5' linkages when using the TBDMS group. These features allow the TOM-Protected monomers to produce longer oligonucleotides.

I-TOM 5-Me-U-TOM 5-Me-C-TOM 2-aminopurine-TOM
2,6-diaminopurine-TOM 5-Br-U-TOM 5-I-U-TOM 3'-A-TOM
Figure 1: Structures of Minor Bases with TOM-Protecting-Group

The regular TOM-Protected RNA monomers have achieved considerable acceptance by a growing number of our customers. Now we are beginning to offer minor bases with the TOM-Protecting-Group. Although these are intended for use with the regular TOM-Protected RNA monomers, they are also fully compatible with the use of monomers with 2'-O-TBDMS protection. (See our Catalog for the regular RNA monomers and supports with the TOM-Protecting-Group as well as pricing.)

Initially, we have prepared the minor bases most requested by our customers and they are shown in Figure 1 and described in very basic terms below. Inosine, 5-Methyl-Uridine, 5-Methyl-Cytidine, 2-Aminopurine riboside and 2-Amino-Adenosine are useful for analyzing RNA structure and activity relationships, for example, in ribozyme studies. 5-Bromo-Uridine and 5-Iodo-Uridine have been used for crystallography studies and cross-linking experiments. 3'-Adenosine is used to prepare oligonucleotides with non-standard 2'-5' linkages.

We will be happy to prepare further minor bases, so please contact us with your favorite structure.

At the time of this writing, TOM-Protecting-Group is a trademark of Xeragon AG, Zurich and patents are pending.

Product Information 

Some of the TOM-Protected minor bases have been discontinued.  Please see our current listing:

Minor RNA Phosphoramidites (TOM Protected)