Using Non-Fluorescent (Dark) Quenchers - Dabcyl & Dabsyl Labelling

Follow

Applicable Products

2085 5'-Dabcyl-CE Phosphoramidite
2144 Dabcyl-dT-CE Phosphoramidite
2374 3'-Dabcyl CPG
2426 3'-Dabsyl CPG

Physical & Dilution Data

Dilution volumes (in ml) are for 0.1M solutions in 10% THF in dry acetonitrile (4059) for 2144, and 0.1M solutions in dry acetonitrile (4050) for 2085. 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

2085 C30H45N6O3P 568.69 430.18 4.40 8.79 17.58
2144 C63H76N9O10P 1150.32 707.90 2.17 4.35 8.69
2374 - - 462.44 - - -
2426 - - 498.49 - - -

General

Today, the most commonly used dark quenchers are all azo based. It must be noted that as a result it is not uncommon to observe fragmentation during mass spectrometry analysis by MALDI-TOF. Dabcyl and DDQ-1 will show a fragment of M-134, BHQ™-1 shows M-298 and BHQ™-2 shows M-300.

Dissolution

Dabcyl-dT-CE Phosphoramidite (2144) is dissolved in 10% THF in acetonitrile (4059, provided free upon request), 5’-Dabcyl-CE Phosphoramidite (2085) in anhydrous acetonitrile.

Coupling

A 6min coupling time is recommended for the phosphoramidites. 3’-Dabcyl CPG (2374) and 3'-Dabsyl-CPG (2426) are used as per standard nucleoside supports. However, since non-nucleosidic modifications detritylate at a slower rate it is recommended to carry out an initial additional detritylation. In this case it is important not to carry out any additional capping.

Deprotection

Standard oligonucleotide deprotection conditions can be applied when deprotecting an oligo containing this modification; typically AMA, 55oC, 35min.

Storage & Stability

All compounds are stored in a freezer at -10 to -30°C. Stability of the phosphoramidites in solution is 2-3 days.

Have more questions? Submit a request

Comments

Powered by Zendesk