|2542||5-Hydroxymethyl-dU-CE Phosphoramidite (hmdU)|
|2544||5-Hydroxymethyl-dC-CE Phosphoramidite (hmdC)|
|2547||5-Hydroxymethyl-dC II-CE Phosphoramidite|
|2548||5-Formyl-dC III-CE Phosphoramidite|
Physical & Dilution Data
Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (4050). Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.
|2546||C47H58N5O12P||915.96||317.19 (Formyl), 349.23 (Diol)||2.73||5.46||10.92|
|2548||C51H60N5O11P||950.02||317.19 (Formyl), 375.27 (Acetal)||2.63||5.26||10.53|
A coupling time of 25-60s is recommended for all amidites, except for 2548 which should be coupled for 180s.
Cleavage & Deprotection
Recommendations are specific to each product, but will also need to take into account the requirements of other bases and modifications in the oligo.
2541 - Use Fast or UltraMILD protection on the nucleobases (plus UltraMILD Cap A, 4210). Cleave and deprotect with ammonium hydroxide at RT for 24h.
2542 - Use Fast or UltraMILD protection on the nucleobases (plus UltraMILD Cap A, 4210). Cleave and deprotect with AMA at 65ºC for 10min (although this is not compatible with Bz-dC), or use ammonium hydroxide at RT for 2h, then deprotect the nucleobases as required.
2543 - Use UltraMILD protection on the nucleobases (plus UltraMILD Cap A, 4210). Cleave and deprotect with 0.05M Potassium carbonate in methanol at RT for 4h, or ammonium hydroxide at RT for 2h.
2544 - Any nucleobase protection can be used, however the product is not compatible with AMA or UltraMILD deprotection methods. Cleavage and deprotection is with 30% ammonium hydroxide at 75ºC for 17h.
2545 - Use a combination of iBu-dG and Ac-dC nucleobase protection, or UltraMILD (plus UltraMILD Cap A, 4210). Cleave and deprotect with 0.4M NaOH in MeOH/water 4:1 (v/v) at RT for 17h.
2546 - Any nucleobase protection can be used, dependent on the deprotection strategy required. Typically, use ammonium hydroxide at 55ºC for 17h, AMA at 65ºC for 10 min, or 0.4 M NaOH in MeOH/water 4:1 (v/v) at RT for 17h. Then oxidise with 50mM sodium periodate at 4ºC for 30min, and desalt (G25).
2547 - Either utilise iBu-dG/Ac-dC base protection and deprotect with 0.4M NaOH in MeOH/water 4:1 at RT for 17h, or use UltraMILD deprotection (plus UltraMILD Cap A, 4210) and deprotect with 0.05M potassium carbonate in methanol at RT for 4h.
2548 - Either utilise dmf-dG/Ac-dC base protection and deprotect with 30% ammonium hydroxide at RT for 17h and immediately evaporate, or employ iBu-dG/Ac-dC or UltraMILD (plus UltraMILD Cap A, 4210) and deprotect with 0.4 M NaOH in MeOH/water 4:1 (v/v) at RT for 17h, desalt (G25) and evaporate. Subsequently, remove the acetal protecting group using 80% acetic acid in water at 20ºC for 6h.
Storage & Stability
All products are stored dry in a freezer at -10 to -30°C, or short term at 2-8ºC (except 2548 where -10 to -30°C is required). Stability in solution is 2-3 days, except for 2546 and 2548 which must be used with 1-2 days.