Catalog Number: 10-1330-xx

Description: dT-Me Phosphoramidite

METHYL PHOSPHORAMIDITES

For many years, Glen Research has supplied methyl phosphoramidites in addition to þ-cyanoethyl (CE) phosphoramidites for the few situations where the more labile cyanoethyl group is not an advantage. Some of our customers, probably remembering that the methyl group was removed specifically with thiophenol, have tried to use these monomers to prepare the interesting, uncharged, and nuclease-resistant methyl phosphotriester linkage. Unfortunately, this linkage is labile to ammonium hydroxide and the regular phosphodiester linkage is formed (along with a small amount of chain scission). Now we offer UltraMild methyl phosphoramidites for this application. Oligos produced from these monomers can be deprotected with potassium carbonate in methanol to produce methyl phosphotriester linkages. Since these linkages are diastereomeric and uncharged, the oligos may be hard to handle. Consequently, it is likely that chimeras will be produced using these monomers along with the regular UltraMild CE phosphoramidites. If many dG residues are included in the oligonucleotide, we recommend the use of phenoxyacetic anhydride (PAc₂O) in Cap A. This modification removes the possibility of exchange of the isopropyl-phenoxyacetate (iPr-Pac) protecting group on the dG with acetate from the acetic anhydride capping mix.

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Material Safety Data Sheet

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REQUENTLY ASKED TECHNICAL QUESTION

QUESTION: Can Me phosphoramidites (10-1300, etc.) be used to produce methyl triester oligonucleotides?

RESPONSE:Possibly, but we are unaware of a method. Some people remember that the methyl phosphoramidites were used to prepare oligos originally and that thiophenol was used to remove the methyl group prior to ammonium hydroxide deprotection. This might suggest that omitting the thiophenol step would lead to the methyl triesters. Wrong. Thiophenol was used to remove the methyl group specifically prior to the ammonium hydroxide step to avoid chain scission. If the methyl triesters are treated with ammonium hydroxide, they are predominantly hydrolyzed to the phosphodiesters but a small percentage of the linkages are also hydrolyzed to eliminate either the 3'or 5' alcohol (chain scission).

While working with dT-Me Phosphoramidite and deprotecting under UltraMild conditions, it was clear that the methyl triester group was essentially unreacted over 24 hours in potassium carbonate in methanol. We have now introduced UltraMild Me Phosphoramidite monomers and, finally, methyl triester oligonucleotides can be simply produced.

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DILUTION/COUPLING DATA

The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures. Please link for more detailed usage information with the various synthesizers.

If you cannot find the answer to your problem then please contact us or telephone +44 (0)1954 210 200

If you cannot find the answer to your problem then please contact us or telephone +44 (0)1954 210 200