SIMA (HEX) Phosphoramidite


Product Specifications

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Dichloro-diphenyl-fluorescein, SIMA (HEX) exhibits virtually identical absorbance and emission spectra to HEX. SIMA (HEX) is much more stable to basic deprotection conditions than HEX and oligonucleotides can be deprotected using ammonium hydroxide at elevated temperatures and even ammonium hydroxide/methylamine (AMA) at room temperature or 65°C for 10 minutes. SIMA absorption maximum was 3 nm blue-shifted compared to HEX at pH 7. The absorbance is broader, so the extinction coefficient is smaller than that of HEX, but when exciting at 500 nm where the absorbance was normalized, the emission was still 90% of HEX and the emission was red-shifted by 5 nm. A second SIMA (HEX) product, SIMA (HEX)-dT, can be used to introduce SIMA (HEX) in the synthetic oligonucleotide sequence, usually as a replacement for the native dT linkage. Again, this product is fully compatible with deprotection schemes using ammonium hydroxide at elevated temperatures or AMA at room temperature and 65°C.

The spectral characteristics of this dye is detailed here.



  • Coupling: 3 minute coupling time recommended.
  • Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°C, dry
Stability 1-2 days, <90% efficient after 4 days

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-5905-02 0.25 g .25grams 2.35 65 39 24.38 17.73 13 3.25
10-5905-90 100 µmol .107grams 1 20 12 7.5 5.45 4 1
10-5905-95 50 µmol .053grams 0.5 3.33 2 1.25 0.91 0.67 0.17


Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-5905-02 0.25 g .25grams 3.5 0.07 63.6 39.75 28.91 3.98
10-5905-90 100 µmol .107grams 1.5 0.07 23.6 14.75 10.73 1.48
10-5905-95 50 µmol .053grams 0.75 0.07 8.6 5.38 3.91 0.54