Technical Brief - Amino-Modifiers and Summer Shipping
Fortunately, phosphoramidites are very stable products and generally require no special protection even for summer shipping since domestic and international packages are usually delivered very promptly. However, one significant exception is our amino-modifiers with trifluoroacetate (TFA) protecting groups. These products are viscous oils and trace impurities seem to be able to cause some degradation if transit times are extended especially during summer shipping. These products also have no DMT or MMT group and so confirming coupling efficiency is more difficult. We ship these products in containers containing blue ice to help protect them from degradation. However, occasionally international shipments can be held up in the customs clearance process so we advise international customers to place an order for projected summer needs in late spring before high temperatures are encountered in their area.
How do you detect if some degradation has occurred in transit?
As noted above, these products are clear oils and this can be verified by holding the vial up to the light. If any crystals are observed in the clear oil, significant degradation has occurred and the vial should not be used. Indeed, complete degradation of these products to the corresponding H-phosphonate analogue leads to complete crystallization of the product.
How can you avoid this situation?
These products are all stable in freezer storage so, as noted above, we advise our overseas customers to place an order for projected summer needs in late spring before high temperatures are encountered.
An alternative is to use the equivalent amino-modifiers protected with phthalic diamide (PDA) protecting groups. 5’-PDA-Amino-Modifiers1, which were developed by Stefan Pitsch along with Stefan Berger of ReseaChem in Switzerland, were introduced by Glen Research in the spring of 2012. In contrast to the other protected amino modifiers which are viscous oils, the analogous PDA protected compounds are granular powders. This important property of these compounds allows straightforward handling, storage and aliquoting and leads to a significant increase in stability.
These products are, therefore, fully stable even for extended summer shipping. They are also priced equivalently so there would be no additional cost involved in using the PDA products.
It has to be noted that PDA protection is rapidly removed with methylamine and mixtures like AMA. In fact, 20 minutes at room temperature is sufficient to remove >95% of the PDA protecting group with AMA. However, deprotection with ammonium hydroxide does not proceed to completion and a significant percentage of the protected amine will remain.
Our TFA amino-modifiers are shown in Figure 1 along with the PDA products. At this point, we do not offer the C3 version of the PDA-Amino-Modifiers but we do offer a C12 option.
Key Points for PDA-Amino-MOdifiers
- Oligonucleotides containing PDA-amino-modified oligonucleotides must be treated with aqueous methylamine or AMA for complete deprotection.
- If ammonium hydroxide must be used, reaction at 55°C will yield around 80% of the deprotected amino group, even with extended deprotection times.
1. Developed by Stefan Pitsch and ReseaChem GmbH (S. Berger), Patent pending.