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DNA Modifications
DNA Modifications

Cy® Fluorophores

Cy® dyes exhibit excellent spectroscopic performance with high quantum yields, high extinction coefficient, and good stability of fluorescence signal against changes in pH in various buffer conditions. In addition to labeling oligonucleotides chemical during synthesis, we can also attached Cy3, Cy3.5, Cy5, Cy5.5 and Cy7 fluorescent DNA probes by chemically by preparing 5'-amino-end-labeled oligonucleotide probes on a DNA synthesizer. The amino-group containing probes are then labeled with a fluorescent tag containing an isothiocyanate group or a succinimidyl active ester. Contact your Account Representative for pricing on Cy dye labeled oligonucleotides.

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Price/labeling, purification and synthesis is an additional charge

Dyes Scales Scales
5' Int 3'
Cy3Tm 250 nmol $235 $295* $235
1.0 µmol $375 $450* $375
Cy3.5Tm 250 nmol $395 $450* $395*
1.0 µmol $350 $450* $350*
Cy5Tm 250 nmol $235 $295* $235
1.0 µmol $375 $450* $375
Cy5.5Tm 250 nmol $265 $395* $265*
1.0 µmol $485 $496* $485*

* 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

260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

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