dR-DDQ-1 (alpha) CPG Column
dR-DDQ-1 (alpha) CPG Column
Key features
Show- 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).
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.
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Synthesizer
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Column
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Type/Description
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Notes
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MerMade 6,12
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MerMade, syringe (all scales)
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Pipette type column
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A MerMade column is also known as a Supercolumn
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MerMade 4, 48X, 96E, 192E, 192X
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MerMade, Syringe (up to 1.3 mL)
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Pipette type column
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A MerMade column is also known as a Supercolumn
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ABI 384 / 394
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Luer
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Barrel column with luer fitting at either end
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Also known as ALL-FIT or Standard
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Expedite 8909
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Luer
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Barrel column with luer fitting at either end
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Also known as ALL-FIT or Standard
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ABI3900
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MerMade
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Pipette type column
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A MerMade column is also known as a Supercolumn
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K&A H4, H8, H8SE, H2, H32, H64
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Luer
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Barrel column with luer fitting at either end
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Also known as ALL-FIT or Standard
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K&A S4CL/S8CL
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Luer
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Barrel column with luer fitting at either end
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Also known as Standard. For this instrument, we recommend the Luer (Standard) column as the ALL-FIT columns have a wider barrel.
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Dr Oligo 48
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MerMade
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Pipette type column
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A MerMade column is also known as a Supercolumn
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Dr Oligo 192XLc, 768XLc just plates
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MerMade, Syringe (up to 1.3 mL)
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Pipette type column
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A MerMade column is also known as a Supercolumn
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OligoMaker X12, 48, 192, X192, X96
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MerMade, Syringe (up to 1.3 mL)
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Pipette type column
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A MerMade column is also known as a Supercolumn
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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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