Catalog Number: 10-3041-xx
Description: Nebularine-CE Phosphoramidite
Diluent: Anhydrous Acetonitrile
|Coupling: 12 minute coupling time is recommended.
|Deprotection: Mild deprotection recommended. 30% Ammonium Hydroxide:EtOH (3:1) for 24 hours at Room Temperature or as required by nucleobases. Complete 2' deprotection per RNA Technical Bulletin. See Technical Bulletin for details (Technical Bulletin).
|Storage: Freezer storage, -10 to -30°C, dry
|Stability in Solution: 1-2 days
MINOR RNA PHOSPHORAMIDITES (TBDMS PROTECTED)
Inosine and 5-Methyl-Uridine are useful for analyzing RNA structure and activity relationships. 5-Bromo-Uridine and 5-Iodo-Uridine have been used for crystallography studies and cross-linking experiments. 6-Thioguanosine (6-thio-G) has applications in ribozyme and siRNA research, as well as in RNA-protein interactions. The removal of the silyl protecting group without interfering with the sulfur is critical. This is removed1 cleanly by triethylamine trihydrofluoride in DMSO but t-butylammonium fluoride (TBAF) leads to degradation of the thio-nucleotide analogue and should not be used. 2-Aminopurine riboside is useful for analyzing RNA structure and activity relationships, for example, in ribozyme studies.
7-Deaza-Adenosine is lacking nitrogen at the 7-position, which is replaced by carbon. The N7 position in adenosine takes part in non-Watson and Crick hydrogen bonding, which may be relevant to RNA folding and subsequent activity. This Adenosine analogue is also known as Tubercidin. 8-Aza-7-deaza-Adenosine is an isomer of Adenosine with virtually identical electron density. Again, the N7 nitrogen is not available for hydrogen bonding. Nebularine or Purine Nucleoside can be viewed as an Adenosine derivative that is lacking the exocyclic amino group. This molecule allows researchers to determine the relevance of the exocyclic amine of Adenosine to RNA structure and function. 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. PseudoUridine is one of the most common modified nucleosides found in RNA. The availability of a phosphoramidite will allow detailed research into the effects of this modified base on RNA structure and activity.
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