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5' fluorescein labeled oligonucleotides have become indispensable tools for genomic research and molecular biology. 5,6 Carboxy Fluorescein amidite is used for the 5' labeling of fluorogenic probes used in 5' nuclease assays. This amidite does not contain a DMT protecting group and can only be added to the 5' terminus of the oligo. This product was prepared using a mixture of 5 and 6-carboxy fluorescein isomers.
Properties:
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Chemical Name:
[(3',6'-dipivaloylfluoresceinyl)-5 and 6-carboxamido-hexyl]-6-O-(2-cynoethyl)-(N,N-diisopropyl)- phosphoramidite
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Formula:
C46H58N3O10P
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Molecular Weight:
843.95
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Appearance:
white solid
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Absorption Maximum (Lambda Max):
495
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Extinction Coefficient at Lambda max:
71300
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Extinction Coefficient at 260 nm:
26900
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Fluorescence Maximum:
520
Spectral properties measured in PCR buffer as 5'-labeled poly(T) oligo.
Product usage:
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Synthesis conditions:
Prior to dilution ensure that all product is at the bottom of the vial. Dilute to the recommended concentration and mix thoroughly in the sealed vial to ensure that all contents are dissolved.
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Dilution:
100 µmol/1mL
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Deprotection conditions:
With fast deprotecting amidites (ie. C-Ac, G-DMF, G-PAC) use concentrated NH4OH for 1 hour at 60 °C. With base-sensitive fluorophores (eg. TAMRA) we recommend using t-butylamine/water (1:3) for 6 hours at 65 °C. With standard amidites (ie. C-Bz, G-iBu) use concentrated NH4OH for 5 hours at 60 °C. With base-sensitive fluorophores (eg. TAMRA) we recommend using t-butylamine/water (1:3) for 12-15 hours at 65 °C. The use of methylamine should be avoided with this product.
If all the solution is not used during the synthesis, it can be stored under argon and its functionality maintained up to 48 hours.
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The mass this product adds after conjugation and work-up (the additional mass seen by mass spectrometry) is:
537.46
Image of cleaved and deprotected structure:
Storage and handling:
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Shipping conditions:
Cold
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Storage conditions:
-15 to -30 °C
