Fluorescent Dyes Applications

Fluorescent Dyes Applications

Fluorescent dyes are particularly advantageous in biological research because they combine very high sensitivity and selectivity in target detection with low toxicity. As such, they have now become the detection method of choice for tracing the presence of specific biomolecules in cells, cell culture whole organisms, and in vitro assays.

Single-dye labeled oligonucleotides are routinely used as cytogenetic probes in Fluorescence In Situ Hybridization (FISH) to detect and localize specific DNA sequences on chromosomes. FISH is also used to detect and localize specific mRNAs within tissues, thereby revealing spatial-temporal patterns of gene expression within both cells and tissues (1,2). Besides FISH, other common applications of single-dye oligos are as fluorescence-based sequencing and genotyping primers (3), and as probes for oligonucleotide ligation assay (OLA) systems (4), or for SNP detection on microarrays (5).

Dual-dye labeled oligos are particularly useful in fluorescence resonance energy transfer (FRET) experiments for determination of intra- and intermolecular distances at very high resolution (1-10 nm) (6). In addition, dual-labeled oligos containing fluorescent dye/dark quencher pairs are now routinely used in quantitative and qualitative real-time PCR experiments and assays (5'-nuclease assay, Molecular Beacon, Scorpions, etc.) Details of how such dual-labeled probes work for detection of minute amounts of target are found in the Quenchers modifications category.

Fluorescent modifications can also be combined with non-fluorescent modifications in a wide variety of combinations for use in highly specializing applications or research projects.

Click here for a list of fluorophores pricing.

Dye & Quencher Selection Table

Dye & Quencher Selection Table

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References

(1) Carter, N.P. Fluorescence in site hybridization state of the art. Bioimaging (1996), 4: 41-51.
(2) Maierhofer, C., Jentsch, I., Lederer, G., Fauth, C., Speicher, M.R. Multicolor FISH in two and three dimensions for clastogenic analyses. Mutagenesis (2002), 17: 523-527.
(3) Giusti, W.G., Adriano, T. Synthesis and characterization of 5'-fluorescent-dye-labeled oligonucleotides. Genome Res. (1993), 2: 223-227.
(4) Fluorescence-based oligonucleotide ligation assay for analysis of cystic fibrosis transmembrane conductance regulator gene mutations. Hum. Mutat. (1995), 5: 153-165.
(5) Fan, J.B., Chen, X., Halushka, M.K., Berno, A., Huang, X., Ryder, T., Lipshutz, R.J., Lockhart, D.J., Chakravarti, A. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. (2000), 10: 853-860.
(6) Didenko, V.V. DNA Probes Using Fluorescence Resonance Energy Transfer (FRET): Design and Applications. Biotechniques (2001), 31: 1106-1121.