Oligo synthesis reagents, labelling reagents and dye technologies FAQs

Our Black Hole Quencher™ (BHQ) 10 succinimidyl ester (BHQ-10S), is a water soluble BHQ dye specifically engineered for conjugating to proteins. BHQ-10 will function as a FRET quencher for fluorophores located up to 100 angstroms away. All other BHQ products are insoluble in aqueous solutions and are not appropriate for protein labeling.

CAL Fluor™ dyes and BHQ™ dyes are very stable when conjugated to peptides in solution and their pH stability is similar to that of the peptide in which they have been incorporated. Please note however that BHQ dyes are susceptible to reduction in certain solutions. DTT, TCIP, and other scavengers will reduce the azo bonds in the BHQ structure and should be avoided in peptide synthesis protocols that involve BHQ dyes.

The Quasar™ dyes may be used as direct replacements for the Cy™ dyes and are anticipated to perform equivalently to their Cy dye counterparts. They share the same chromophore structure and spectral properties, differing principally in their linkage chemistry. Quasar 570 replaces Cy3, Quasar 670 replaces Cy5 and Quasar 705 replaces Cy5.5 dye. Quasar dyes are slightly more hydrophobic and therefore soluble in the reagents of DNA synthesis. Importantly, the Quasar dyes are available as amidites and may be incorporated during oligonucleotide synthesis, thus avoiding the post-synthesis dye conjugation required with Cyanine dyes.

LGC, Biosearch Technologies offers modified oligos with many common fluorophores including FAM, HEX and TAMRA, as well as our own proprietary dyes. Please refer to our Black Hole Quencher™ and Dye Selection Chart for a complete list of various dyes/fluorophores we carry at Biosearch Biosearch Technologies.

Biosearch Technologies makes available many of these same dyes as reactive precursors for others to synthesize their own modified oligos. A full list of dyes and quenchers formulated for that purpose can be found in on our webpage for DNA/RNA Synthesis Reagents.

To manually label oligos and other biomolecules, Biosearch Technologies also offers carboxylic acid and succinimidyl ester formulations of certain dyes and quenchers. A complete list can be found on our Labeling Reagents webpage.

If you have any questions regarding the availability of particular products, please contact our Technical Support team.

Biosearch Technologies recommends the use of FAST deprotection amidites such as: Adenosine-benzoyl,A(Bz;) Cytidine-acetyl,C(Ac); Guanosine-dimethylformamide, G(Dmf). For ultra-FAST deprotection, use the phenoxyacetyl (Pac) amidites: A (Pac), C (Pac) and G (Pac). Thymidine does not need a protecting group. The FAST deprotecting amidites are used when dye-labeled oligonucleotides are expected to be sensitive to basic conditions, especially when long time periods of incubation are involved. This is true for the CAL Fluor™ dyes which are known to degrade in concentrated NH4OH.

The use of a tetrazole activator is in concurrence with our chemistry practices. Biosearch Technologies uses ethylthioltetrazol (ETT) for all amidite productions. Be advised that the 4,5-dicyanoimidizole (DCi) activator, while less acidic, more soluble and more nucleophilic than tetrazol or ETT, does NOT work with our CAL Fluor chemistries.

Biosearch Technologies' dyes have not been tested for compatibility in DNA sequencers or instruments for fragment analysis. While the potential is there, many DNA sequencers are engineered for use with “Big Dye” FRET constructs, such as FAM/NED, to compensate for the limited excitation provided by the laser. LGC Biosearch does not offer these constructs. We encourage users to test our dyes in their instrument prior to designing an assay.

Biosearch Technologies dyes are principally intended for use in probe-based studies such as qPCR and SNP genotyping.