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What are the deprotection conditions for your amidites?
1.) Rapid Deprotection Conditions (must use amidites with base protection groups designed for these conditions)
Incubate at 60°C for 20 minutes in concentrated ammonia. If the oligonucleotide is greater than 50 bases in length, incubate for 30-60 minutes at 60°C.
2.) Mild Deprotection Conditions (must use amidites with base protection groups designed for these conditions)
Incubate at room temperature for 16 hours in concentrated ammonia. Mild deprotection conditions are required for many dye labels.
3.) Standard Deprotection Conditions (for standard protected phosphoramidites)
Incubate at 55°C for 16 hours in concentrated ammonia.