Oligo Labeling Modifications

BOC RNA offers a wide range of modifications for DNA oligonucleotides and RNA oligonucleotides, including base modifications, label modifications, fluorescent modifications, phosphorylation, and more. Our custom DNA/RNA modification services are designed to meet your needs through strict quality control and fast turnaround, providing scientists with the tools necessary to meet even the most challenging applications.


  • TAMRA marker

TAMRA is the most commonly used rhodamine dye for oligonucleotide applications. Its fluorescent properties are sometimes used for oligonucleotide labeling, but TAMRA is more commonly used as a quencher.

TAMRA's light absorption properties and spectral overlap with several commonly used fluorophores, including FAM, HEX, TET and JOE, allow it to be used as a quencher for the design of double-labeled probes.TAMRA has been widely used in the design of assay probes, particularly Taqman probes for Real-Time PCR.

  • Dabcyl marker

Dabcyl has been widely used as a quencher in diagnostic probes, such as molecular beacons, due to its light-absorbing properties and lack of residual fluorescence. The absorption properties of Dabcyl limit the range of dyes it can quench to those with an emission wavelength of 400-550 nm (maximum absorption wavelength of 471 nm). However, when used in molecular beacons, Dabcyl and the fluorescent moiety are close enough to each other and in turn can quench dyes of a slightly wider spectrum, thus increasing the versatility of the Dabcyl molecule. Dabcyl has been replaced in most cases by the Black Hole Quencher family of dyes.

  • Black Hole Quencher

Each Black Hole Quencher dye has a high extinction coefficient and broad spectral overlap, resulting in an improved quenching efficiency compared to molecules such as Dabcyl. This means that Black Hole Quencher dyes offer the use of a wider range of wavelengths for different detection purposes, covering the visible to near-infrared region (480-730 nm). This, coupled with the fact that these molecules have no residual background fluorescence (being true dark quenchers), makes Black Hole Quencher dyes a favorable choice for real-time PCR applications.

Of the four Black Hole quenchers, Black Hole Quencher-1 and Black Hole Quencher-2 are preferred, whether 5'-Phosphoramidites, dT-Phosphoramidites, or 3'-CPG. If only excitation and emission values are considered, Cy5, Cyanine-5 and Quasar 670 require Black Hole Quencher-3 for effective quenching, but Black Hole Quencher-2 is recommended because it is not easily degradable. Black Hole Quencher-1 is typically used for quenching in the 480-580 nm range and can be used with commonly used fluorescent groups such as FAM, TET, JOE and HEX. Black Hole Quencher-2 is used for quenching in the 550-650 nm range and is most effective in quenching fluorescent groups such as TAMRA, ROX, Cyanine-3, Cy3, Cy3.5TM and Red 640.

Oligo Labeling Modifications

We Provide the Following Oligo Labeling Modifications

LabelingShort Code Price
3'-DY547 (Cy3 Alternative)DY547-3'Inquiry
3'-Biotin LC3'-LCBiInquiry
3'-Biotin LC LC3'-2LCBiInquiry
5-DY547 (Cy3 Alternative)DY547Inquiry
5'-DY647 (Cy5 Alternative)DY647Inquiry
5'-DY677 (Cy5.5 Alternative)DY677Inquiry


  • Quality guaranteed
  • Affordable price class that fits your budget
  • Flexible synthesis scale
  • Fast delivery
* Only for research. Not suitable for any diagnostic or therapeutic use.
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