Product Introduction

Excitation wavelength (nm): 548

Emission wavelength (nm): 566

Cyanine dyes have been used for many years in textiles and other fields. Their use in nucleic acid labeling was first driven by an increase in the commercial supply of succinimide esters and later by an increase in their use as phosphamides. Today, their fluorophore based labeling and detection is a core part of many diagnostic platforms and tests. Cyanine dyes are used as fluorescent markers in oligonucleotide synthesis, primarily for molecular diagnostics, such as the preparation of probes for monitoring quantitative real-time PCR, fluorescence in situ hybridization (FISH), and surface-enhanced resonance Raman spectroscopy (SERRS) based DNA detection assays. Their emission spectra can be adjusted by varying the length of the polyacetylene chain, and their solubility in organic or aqueous solvents can be altered by substituents on the aromatic ring. The most commonly used classical phosphamide dyes are Cyanine-3 and Cyanine-5 (structurally equivalent to Cy™ 3 and Cy™ 5). They are usually attached to the 5' end of the oligonucleotide during synthesis, but are readily incorporated into the sequence. The hydroxyl group protected by MMT is removed in the same manner as protected by DMTr. Because of the lack of heterocyclic bases in their structure and their inability to participate in base pairing, incorporation into sequence interiors is uncommon. This makes double-strand formation unstable. For 3' -ligation, an equivalent 3' -modified CPG vector can be introduced. Previously, this was done by adding the dye to an amino modified oligonucleotide after synthesis or by adding a phosphonide to a carrier with a functional modification that did not interfere with the use of the oligonucleotide (e.g., phosphate ester, linker spacer). 3' -labeling is particularly useful in FRET, where FRET matching pairs are labeled at the 5' end or incorporated into oligonucleotide sequences. Quasar series dyes can replace Cy 3, Cy 5 and Cy 5.5; The maximum emission wavelengths of Quasar570, Quasar670 and Quasar705 are 570, 670 and 705 nm, respectively. Quasar dye increases fluorophore selection and helps eliminate potential crossover issues associated with multiplex qPCR. They are efficiently quenched by BHQ-2 or BHQ-3 and can be used in many different probe forms. Quasar CPG and phosphite amide can be used for direct labeling of oligonucleotides. Active esters can be used to couple amine groups on substrates such as proteins, peptides, and oligonucleotides. Carboxylate variants are used to label peptides, oligonucleotides, or functionalized amines.