Fluorescent Dyes for Oligonucleotide Labeling

Fluorescent oligonucleotide probes are developed for the detection and the quantification of target DNA or RNA sequence with the high sensitivity and specificity along with low toxicity. They have been used in a wide range of applications including, FISH, in situ hybridization, sequencing and genotyping. Fluorescent dye and quencher paired molecular beacon probes are widely used in the field of real–time nucleic acid detection and PCR quantification, SNP detection, and clinical diagnostic assays.

There are two major strategies for chemical incorporation of fluorescent dyes into an oligonucleotides: direct fluorescence labeling during chemical synthesis and post synthetic fluorescence labeling. The direct oligonucleotide labeling during solid phase synthesis can be achieved via the standard phosphoramidite chemistry containing various spacer arm lengths. Direct labeling during solid phase chemical synthesis might afford high yield but also increases the risk of damaging fluorescence tag from acidic deprotection step. Thus certain fluorescent dyes are not compatible with solid phase chemical synthesis, thus their labeling must be conducted post–synthetically through various labeling methodologies.

Post synthetic labeling of a fluorescent dye to an oligonucleotide can be achieved by labeling various activated dyes to modified oligomers having functional groups such as primary amine, thiol, aldehyde, azide, alkyne, or carboxylic acids. Depending on binding target, the fluorophore might be selectively introduced at either the 5′ or 3′ ends of the oligonucleotide as well as randomly incorporated throughout the sequence. BioActs offers fluorescent dye phosphoramidites and fluorescent nucleotide phosphoramidites for direct fluorescence labeling and Flamma NA series dyes for post synthetic fluorescence labeling method.