New dye and quencher products in development - Download the posters from FB3
20 July 2012
Following the very successful FB3 meeting in Gothenburg, the posters presented by us can now be downloaded. Just follow the links below. Both these posters feature products currently in development so watch this space for further news of their availability.
Cyanine dyes are used as fluorescent markers in oligonucleotide synthesis, primarily for molecular diagnostics such as the preparation of probes used in monitoring real-time PCR, fluorescence in situ hybridisation (FISH) and in SERRS based DNA detection assays. Their emission spectra can be tuned by altering the length of the polymethine chain and solubility in organic or aqueous solvents can be altered via the substituents on the aromatic ring.
Cyanine dyes absorbing over 540nm and 650nm have been studied. These dyes are commercially available as phosphoramidites under the names Cy3™ and Cy5™ respectively, usually for incorporation onto the 5' end of an oligonucleotide during solid phase synthesis, although there is the possibility of including it within the sequence of nucleotides as it has a MMTr-protected hydroxyl group in addition to the phosphoramidite. This, however, is not common due to the lack of heterocyclic base in their structure and as such they do not have the ability to participate in base pairing. Internal addition can therefore destabilise any duplexes formed
We have attached these dyes onto CPG supports in order to allow direct incorporation onto the 3' end of an oligonucleotide. Previously this was done by adding the dye post-synthetically onto an amino-modified oligonucleotide or by adding the amidite to a support functionalised with a modification that will not interfere with the use of the oligonucleotide (e.g. phosphate, spacer). This will be especially useful for functions such as detecting DNA-protein interactions i.e. for the production of double-labelled probes for use in fluorescence resonance energy transfer (FRET) studies.
The products featured in this work are now available.
Oligonucleotide probes used for qPCR are typically labelled with a fluorescent dye to enable detection of the target sequence. In most cases the probe is a doubly labelled oligo where one dye acts as a fluorophore and the other as a quencher. In order to increase the sensitivity of the PCR assay, it is desirable for the quencher to have no native fluorescence (dark quencher). To ease preparation of probes for use in assays with different fluorophores it would be advantageous to have a quencher capable of quenching a range of fluorophores; to this end we have developed a new non-fluorescent quencher with a broad absorption range.
A series of double-dye probes have been synthesised to evaluate the efficiency of a new non-fluorescent quencher when paired with FAM-C7, Cy3™, Cy5™ and Cy5.5™ and for use in RT-PCR. The quencher was evaluated when incorporated at the 5' end of the oligonucleotide. The new quencher was compared to existing commercially available quenchers such as Deep Dark Quencher-1 and Black Hole Quenchers™.
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