DNA Damage/Repair - Epigenetics Products

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Applicable Products

2541 5-Hydroxy-dU-CE Phosphoramidite
2542 5-Hydroxymethyl-dU-CE Phosphoramidite (hmdU)
2543 5-Hydroxy-dC-CE Phosphoramidite
2544 5-Hydroxymethyl-dC-CE Phosphoramidite (hmdC)
2545 5-Carboxy-dC-CE Phosphoramidite
2546 5-Formyl-dC-CE Phosphoramidite
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.

Item

Mol. Formula

Mol. Wt.

Unit Wt.

250mg

500mg

1g

2541 C41H49N4O10P 788.83 306.17 3.17 6.34 12.68
2542 C42H51N4O10P 802.86 320.19 3.11 6.23 12.46
2543 C53H56N5O10P 954.03 305.18 2.62 5.24 10.48
2544 C50H57N6O9P 917.00 319.21 2.73 5.45 10.91
2545 C49H56N5O10P 905.97 333.19 2.76 5.52 11.04
2546 C47H58N5O12P 915.96 317.19 (Formyl), 349.23 (Diol) 2.73 5.46 10.92
2547 C41H48N5O9P 785.82 319.21 3.18 6.36 12.73
2548 C51H60N5O11P 950.02 317.19 (Formyl), 375.27 (Acetal) 2.63 5.26 10.53

Coupling

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.

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