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DNA Modifications
Fluorescein Dye Oligo Labeling

Fluorescein Dye

There are different possibilities for labeling fluorescein dye to an oligonucleotide:

All of our dyes can be attached post synthetically to the 5'- terminus of an oligonucleotide via an amino- or thiol- linker with a 6-Carbon spacer arm. This method is available for JOE .

Another possibility for labeling an oligonucleotide at the 5' or internal terminus is to couple the dye directly during synthesis via its phosphoramidite. This method is available for 6-FAM, Fluorescein, Fluorescein dT, 6-Fluorescein, HEX, TET .

Post synthetic labeling of oligonucleotides at internal sites of the sequence is possible by substituting any thymidine with 5-C6-Amino-2'-deoxythymidine. All dyes available for 5'- labeling can also be attached internally.

It is also possible to label the 3'- end of oligonucleotides post synthetically via an amino link. This method is available for all dyes. For the 3'- labeling with fluoresce in , BSI has special solid supports [CPGs] with the dyes already attached. This is very useful for high quality production of labeled probes.

Contact your Account Representative for pricing on Epoch dye and Quenchers labeled oligonucleotides. For additional information, please Contact us.

Price/labeling, purification and synthesis is an additional charge

Dyes Scales Label position
5' Int 3'
Fluorescein (6-FAM) 250 nmol $85 $180* $85
1.0 µmol $165 $250* $165
Fluorescein 250 nmol $185 $155 $220*
1.0 µmol $210 $210 $210*
6-Fluorescein 250 nmol $185 $185 $150*
1.0 µmol $210 $210 $200*
Fluorescein dT 250 nmol $195 $195 $120
1.0 µmol $275 $275 $120
3'-(6-FAM) PS 250 nmol NA NA $75
1.0 µmol NA NA $75
JOE 250 nmol $195* $295* $295*
1.0 µmol $295* $395* $395*
Hexachloro-Fluorescein (HEX) 250 nmol $95 $200* $200*
1.0 µmol $170 $240* $240*
Tetrachloro-Fluorescein (TET) 250 nmol $195 $255* $255*
1.0 µmol $295 $320* $320*

* Product Note - This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2'-deoxythymidine for internal labeling, a double HPLC purification is required.


A wide variety of modifications can be incorporated into an oligonucleotide at the time of synthesis, using aspecialized phosphoramidite chemistries for labeling. However, certain modifications require the use of post-synthetic conjugation strategies in which a primary amine modified oligonucleotide is covalently attached to a dye via NHS ester chemistry. Other cross-linking chemistries are also available depending on particular project specifications. Single HPLC purification is recommended when using phosphoramidite oligo chemistry, otherwise dual HPLC is required for post-synthetic labeling.

Minimum Guarantee Purified Yield

Due to the chemistry of many modifications, yield will be approximately 40 - 60 % less than a standard oligo.

Please see our yield chart for details.

Quality Controls

Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

For additional information, please Contact us.

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