SIMA phosphoramidite, 6-isomer

Cat. # Quantity Price Lead time
DE260 250 mg $260.00 in stock
EE260 500 mg $440.00 in stock
FE260 1 g $740.00 in stock
HE260 10 g please inquire 10 days

SIMA (dichloro-diphenyl-fluorescein) is a xanthene dye with spectral characteristics similar to those of HEX but with a higher quantum yield. SIMA has higher stability during deprotection under alkaline conditions, so deprotection can be run with aqueous ammonium hydroxide at higher temperatures or with AMA (1:1 mixture, concentrated aqueous ammonium hydroxide/40% aqueous methylamine) at room temperature for 2 h or 65°C for 10 min. When used for deprotection with aqueous ammonium hydroxide at 55°C overnight, oligonucleotide-bound SIMA does not degrade, while with HEX the fluorophore degrades by at least 10%.

SIMA phosphoramidite is used in oligonucleotide synthesis to produce fluorescently labeled primers and hybridization probes for quantitative PCR.

Recommendations for using the reagent:

Coupling: 3 min.

Deprotection: Standard conditions with 25% ammonium hydroxide; deprotection time depends on the composition of nucleic acids and their protective groups. AMA (1:1 mixture of concentrated aqueous ammonium hydroxide / 40% aqueous methylamine) can be used for 2 hours at room temperature or 10 min at 65°C.

Absorption and emission spectra of SIMA

Absorption and emission spectra of SIMA

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General properties

Appearance: white powder
Mass spec M+ increment: 757.1
Molecular weight: 1065.02
Molecular formula: C58H64N3Cl2O10P
Solubility: Good solubility in acetonitrile and DCM
Quality control: NMR 1H and 31P, HPLC-MS (95%)
Storage conditions: 12 months after receival at -20°C in the dark. Transportation: at room temperature for up to 3 weeks. Avoid prolonged exposure to light. Desiccate.
MSDS: Download
Product specifications

Spectral properties

Excitation/absorption maximum, nm: 531
ε, L⋅mol−1⋅cm−1: 92300
Emission maximum, nm: 555
Fluorescence quantum yield: 0.63
CF260: 0.57
CF280: 0.18

Oligo synthesis details

Diluent: Anhydrous Acetonitrile
Coupling conditions: 3 minute coupling time recommended
Deprotection conditions: identical to protected nucleobases
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