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Cyanine dyes

Cyanine dyes are molecules containing polymethine bridges between two nitrogen atoms with a delocalizedcyanine_dyes charge which have been used for many years as dyes in life science. Since the Cy3, Cy5 and Cy7 were made commercially available as succinimidyl esters in the early 1990s, cyanine dyes began to be used widely as labels for nucleic acids. Because of the good properties of low non-specific binding to biomolecules and bright fluorescence owing to their huge extinction coefficients and good quantum yields, the Cy dyes have been widespread used in DNA and RNA labelling. Cyanine dyes can be divided into two groups based on water solubility: non-sulfonated cyanines and sulfonated cyanines.

Non-sulfonated cyanines
Available non-sulfonated dyes include Cy3, Cy3.5, Cy5, Cy5.5, Cy7, and Cy7.5. Cy stands for 'cyanine', and the first digit identifies the number of carbon atoms between the indolenine groups. The suffix .5 is added for benzo-fused cyanines. Most derivatives of non-sulfonated cyanines have low aqueous solubility except for hydrochlorides of hydrazides and amines. They are organic co-solvent soluble (5-20% of DMF or DMSO). When these molecules are used for biomolecule labeling, they should be dissolved in organic solvent first, and added to a solution of biomolecule (protein, peptide, amino-labeled DNA) in appropriate aqueous buffer. Fluorescent properties of non-sulfonated cyanines have little dependence on solvent and surrounding.

Sulfonated cyanines
Available sulfonated cyanines include sulfo-Cy3, sulfo-Cy5, and sulfo-Cy7, which have additional sulfo-groups that facilitate dissolution of dye molecules in aqueous phase. Charged sulfonate groups decrease aggregation of dye molecules and heavily labeled conjugates. Sulfonated cyanines are highly water soluble, and they do not use organic co-solvent for the labeling in aqueous environment.

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  1. Cy5 carboxylic acid (non-sulfonated)
    A8133 Cy5 carboxylic acid (non-sulfonated)
    Summary: Non-reactive fluorophore, for control experiments, and for calibration
      ≥51.9 mg/mL
      ≥89 mg/mL
      <2.15 mg/mL
  2. Cy3 carboxylic acid (non-sulfonated)
    A8132 Cy3 carboxylic acid (non-sulfonated)
    Summary: Non-reactive fluorophore, for control experiments, and for calibration
      ≥49.3 mg/mL
      ≥99 mg/mL
      <2.48 mg/mL
  3. Cy7.5 azide (non-sulfonated)
    A8116 Cy7.5 azide (non-sulfonated)
    Summary: used for Click chemistry to label alkyne-modified oligonucleotides
      soluble in organic solvents (dmso
      low solubility in water
  4. Cy7 azide (non-sulfonated)
    A8115 Cy7 azide (non-sulfonated)
    Summary: used for Click chemistry to label alkyne-modified oligonucleotides
      soluble in organic solvents (dmso
      low solubility in water
  5. Cy5 alkyne (non-sulfonated)
    A8131 Cy5 alkyne (non-sulfonated)
    Summary: used for Click chemistry to label any molecule bearing azide group.
      ≥55.6 mg/mL
      ≥50 mg/mL
      <2.5 mg/mL
  6. Cy5.5 azide (non-sulfonated)
    A8114 Cy5.5 azide (non-sulfonated)
    Summary: used for Click chemistry to label alkyne-modified oligonucleotides
      ≥70.1 mg/mL
      ≥46.2 mg/mL
      <2.43 mg/mL
  7. Cy5 azide (non-sulfonated)
    A8113 Cy5 azide (non-sulfonated)
    Summary: used for Click chemistry to label alkyne-modified oligonucleotides
      ≥60.1 mg/mL
      ≥49.1 mg/mL
      <2.36 mg/mL
  8. Cy3 alkyne (non-sulfonated)
    A8130 Cy3 alkyne (non-sulfonated)
    Summary: used for Click chemistry to label any molecule bearing azide group.
      dmso
      insoluble in water
  9. Cy3.5 azide (non-sulfonated)
    A8112 Cy3.5 azide (non-sulfonated)
    Summary: used for Click chemistry to label alkyne-modified oligonucleotides
      ≥71.7 mg/mL
      ≥44.2 mg/mL
      <3.43 mg/mL
  10. Cy3 azide (non-sulfonated)
    A8111 Cy3 azide (non-sulfonated)
    Summary: used for Click chemistry to label alkyne-modified oligonucleotides
      ≥28.75 mg/mL
      ≥77.2 mg/mL
      ≥14.77 mg/mL

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