Labelling

JOE phosphoramidite for oligonucleotide synthesis, pure 6-isomer (6-JOE).Fluorescent dye JOE is a fluorescein derivative containing two chlorine atoms and two methoxy groups. Its absorption and emission maxima are at 503 nm and 525 nm, respectively.

R6G phosphoramidite for oligonucleotide synthesis, pure 6-isomer. R6G (rhodamine 6G) is a xanthene dye of the rhodamine family with high fluorescence quantum yield and high molar extinction coefficient. Relative to those of fluorescein, the absorption (518 nm) and emission (542 nm) maxima of 6-R6G are shifted into the long-wave region.

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.

SIMA phosphoramidite (hydroxyprolinol), 6-isomer contains xanthene dye dichloro-diphenyl-fluorescein (SIMA) with spectral characteristics similar to those of HEX but it is considered to be more resistant to deblocking under alkaline conditions.

SIMA-dT phosphoramidite is used to introduce SIMA in the sequence during oligonucleotide synthesis, usually as a substitute for the native dT linkage.

This phosphoramidite is used for synthesis of oligonucleotides 5’-labeled with TAMRA. TAMRA (carboxytetramethylrhodamine) is a xanthene dye from the rhodamine family with emission in the orange spectrum range (maximum at 563 nm).

TET phosphoramidite for synthesis of fluorescently labeled oligonucleotides, pure 6-isomer. TET (tetrachlorofluorescein) is a green-fluorescent fluorescein derivate (absorption maximum at 519 nm, emission maximum at 535 nm).

After the condensation of the trebler, three DNA branches begin to grow simultaneously with each step of the synthesis. Deblock of this construct gives rise to DNA containing a branching point. One arm (stem) is attached to the branch point with its 5'-end, and other arms (branches) are attached with their 3'-ends. Reverse amidites can be used to prepare constructs with different branch orientations.

Perylene is a bright and extremely photostable fluorescent polycyclic aromatic hydrocarbon (PAH) label with a quantum yield approaching quantitative. Due to the low lifetime of fluorescence, this probe does not form excimers.With this phosphoramidite, perylene can be introduced into DNA by automated oligonucleotide synthesis.