Use of Universal-Q SynBase™ CPG & Polystyrene (2300/2410/2411/2458) in Oligonucleotide Synthesis
This updated protocol replaces the information on pages 97 & 98 of the 2010 Product Guide.
Deblocking
An initial additional detritylation is recommended as this step is much slower on universal supports than on standard base supports. This prevents N-1 oligos from the 3'-end.
Coupling
No changes are required from the standard synthesis method recommended by synthesiser manufacturer.
Oxidation
The linker is stable to capping mixtures, but is slightly labile in oxidiser solution (8% cleavage overnight which is the equivalent of approximately 2000 synthesis cycles on an average program).
Cleavage & Deprotection
Contrary to previously published mild methods, the best conditions we have found to completely remove the Q linker during deprotection are AMA at 70°C for 2.5h or AMA at 80°C for 2h. For this reason it is inadvisable to use this support with modifications that require mild, ultramild or room temperature deprotection. Compatibilty with RNA is therefore mixed. We would not recommend the use of the support with TBDMS chemistry. For TC chemistry we have found that cleavage is possible using neat EDA, overnight at room temperature to give around 70-80% full length product. EDA salt adducts are formed but these are removed during the purification process. The cleavage and deprotection conditions are not compatibile with 2'-F chemistry.
For TC chemistry, to carry out the deprotection between syringes, pass the EDA onto the column such that it only just appears at the other side of the column. Do not pass the EDA back and forth otherwise you will lose some of the oligo. Leave the reaction to stand at room temperature overnight, by which time the oligo will be associated with the resin and the EDA can be washed from the resin. Further details on the EDA method, including vacuum manifold instructions, can be found in the document RNA synthesis using 2’-thiomorpholine-4-carbothioate (TC) protection.
Storage & Stability
Refrigerate at 2-8°C. Material is stable for several years.