Ribozyme activity is substantially affected by the substitution of modified pyrimidine bases. Zebularine (pyrimidin-2-one ribonucleoside) may be regarded as a Cytidine derivative lacking the exocyclic amino group. Zebularine and Pyridin-2-one Ribonucleoside, the 3-deaza analogue of Zebularine, are prime candidates for use in evaluating ribozyme activity and function. It should be noted that Zebularine is mildly fluorescent, absorbing at 298nm and emitting at 367nm.
Coupling: 12 minute coupling time is recommended. Monomers that allow for UltraMild deprotection must be used. To avoid any exchange of the iPr-Pac group on the dG with acetyl, use the UltraMild Cap Mix A (40-4210-xx/ 40-4212-xx).
Deprotection: Cleave and remove base protection in 30% Ammonium Hydroxide:EtOH (3:1) for 4 hours at Room Temperature. Complete 2' deprotection per RNA Technical Bulletin. |See Technical Bulletin for details (http://www.glenresearch.com/Technical/TB_RNA_TBDMS_Deprotection.pdf).