6-SIMA phosphoramidite

6-SIMA phosphoramidite is widely used in oligonucleotide synthesis to create fluorescently labeled primers and hybridization probes for quantitative PCR. SIMA, or Dichloro-diphenyl-fluorescein (HEX), is a xanthene dye with spectral characteristics analogous to HEX but with a higher quantum yield and improved chemical stability under basic deprotection conditions. Unlike HEX, SIMA (HEX) demonstrates exceptional stability when subjected to ammonium hydroxide at elevated temperatures or to AMA (a 1:1 mixture of concentrated aqueous ammonium hydroxide and 40% aqueous methylamine) at room temperature or 65°C for 10 minutes. At neutral pH (pH 7), SIMA (HEX) exhibits a minor 3 nm blue shift in its absorption maximum relative to HEX. Although the absorption band is slightly broader, leading to a modest reduction in the extinction coefficient, SIMA (HEX) retains high fluorescence efficiency. When normalized and excited at 500 nm, its emission intensity reaches 90% of that of HEX, with a 5 nm red-shifted emission peak, providing subtle but significant spectral differentiation.