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dR-DDQ-1 (alpha) CPG Column

dR-DDQ-1 (alpha) CPG Column

CPG column can be used for 3'-labelling an oligonucleotide with the non-fluorescent DDQ-1 quencher moiety.
  • Used to add a non-fluorescent quencher to the 3' end of an oligonucleotide.
  • Quenches in green region. Alternative to dabcyl and BHQ-1 in certain applications.
  • 1000 Å CPG suitable for highly modified oligonucleotides (> 20mers).
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Product information

Deep Dark Quencher 1 is a non-fluorescent molecule (so called Dark Quencher) quenching the lower wavelength dyes such as FAM (absorption max. ca. 440 nm). As such, its quenching properties are very similar to that of dabcyl and overlaps, to some degree, with BHQ-1. Thus, for dual-labelled probes, DDQ-1 is not suitable for quenching fluorescent dyes that emit at a higher wavelength, e.g. Cy5®. This modification is available as a 3'-modifier CPG 1000 Å support or internal phosphoramidite. The quencher is attached to the anomeric position of dRibose. This removes the possibility of losing the label during deprotection, a problem often associated with dabcyl due to the 1,2-diol configuration. Additionally, incorporation of DDQ-1 results in preservation of the natural sugar-phosphate backbone meaning there is no adverse effect on the structure of the oligo.

Applicable Product

LK2349 3'-DDQ-1 SynBase™ CPG 1000/110

Physical Data

Item

Unit Wt.

LK2349 546.57

Coupling

This product is used as per standard nucleosidic supports. Non-nucleosidic CPG supports do not detritylate as rapidly as nucleosidic ones, therefore an additional detritylation step is recommended. It is therefore necessary to use a cycle that does not contain an initial capping step.

Cleavage & Deprotection

UltraFAST conditions can be used and provide the best results: a 1:1 mixture of aqueous ammonium hydroxide and aqueous methylamine (AMA) for 10min at 65°C.

Purification & Analysis

Purification by RP-HPLC or cartridge purification is recommended. IE-HPLC or PAGE for high purity oligos also works very well, however FPLC tends not to give a good separation. This is thought to be due to the zwitterionic nature of this modification.

Note that if analysing oligos after purification by MS, an additional peak at M-134 is observed. This is attributed to fragmentation within the MS through the diazo bond.

Storage & Stability

The support is stored in the fridge or freezer and protected from exposure to light. Similarly, modified oligos are also protected from light.

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