1-Dimethoxytrityloxy-2-(N-acridinyl-4-aminobutyl)-propyl-3-O-succinoyl- long chain alkylamino-CPG
Coupling: This support should be used in a manner identical to normal protected nucleoside support since it contains the DMT group.
(Acetyl-protected Cytidine should be used to avoid deamination when methanolic sodium hydroxide is used for deprotection.)
Deprotection: Cleavage and deprotection should be carried out using a mild deprotection: 0.4M methanolic sodium hydroxide (methanol:water 4:1) for 17 hours at room temperature. Pipet off support, neutralize with 1.5 volumes of 2M TEAA and desalt.
Note: NaOH is not compatible with dmf protecting groups.
QUESTION: Does AMA or methylamine cause any degradation to fluorescein or fluorescein-type dyes such as FAM or FITC?
RESPONSE:Response: While AMA (Ammonium hydroxide/40% Methylamine 1:1 v/v) is considered compatible with fluorescein, the use of methylamine when deprotecting a Fluorescein-labeled oligo does lead to a small amount of degradation, which is characterized by a the appearance of a late-eluting peak by RP HPLC that shows no visible fluorescein absorbance. With standard deprotection conditions (AMA 10 minutes at 65 C) the amount of degradation is approximately 5%