Cy3-dCTP 

Cy3-dCTP is a directly fluorescently labeled deoxyribonucleotide, in which Cy3 is a cyanine fluorescent dye. Cy3-dCTP is used for direct enzymatic labeling of DNA and cDNA: with the aid of DNA polymerases, this modified nucleotide is incorporated into the extending DNA strand during processes such as reverse transcription, PCR, nick translation or random primer labeling^[1][2].

Guide (The following is our recommended protocol. This protocol is only a guide and should be modified according to your specific needs).
While specific steps vary by application, a standard direct labeling protocol (e.g., for microarrays or FISH) generally follows these stages:
1. Reaction Setup
1.1 Mix the DNA or RNA template with primers (e.g., oligo dT or random hexamers).
1.2 Prepare a dNTP mix where a portion of the natural dCTP is replaced by Cy3-dCTP.
1.3 Recommended Ratio: A common ratio is 30–50% Cy3-dCTP to 50–70% unlabeled dCTP to balance labeling efficiency with enzyme processivity.
2. Enzymatic Incorporation
2.2 Add the appropriate enzyme (e.g., Klenow fragment for DNA, Reverse Transcriptase for RNA, or Taq polymerase for PCR).
2.3 Incubate at the enzyme's optimal temperature (e.g., 37°C for Klenow/RT or cycling for PCR).
3. Stopping and Purification:
3.1 Stop the reaction using EDTA (HY-Y0682) or heat inactivation.
3.2 Crucial Step: Remove unincorporated nucleotides using a spin column, ethanol precipitation, or centrifugal filters. This is essential to minimize background fluorescence during downstream applications.
4. Analysis:
4.1 Measure the concentration and labeling efficiency (dye incorporation) using a spectrophotometer like a NanoDrop.
4.2 Read absorbance at 260 nm (DNA) and 550 nm (Cy3).

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

1156.71

C₄₃H₅₁Li₄N₆O₂₀P₃S₂

Liquid

Pink to red

O=S(C1=CC2=C(C=C1)C(C)(C)C(/C=C/C=C3N(CCCCCC(NCC#CC4=CN(C5OC(COP(OP(OP(O[Li])(O[Li])=O)(O[Li])=O)(O[Li])=O)C(O)C5)C(N=C4N)=O)=O)C6=C(C=CC(S(=O)(O)=O)=C6)C/3(C)C)=[N+]2CC)([O-])=O

Room temperature in continental US; may vary elsewhere.

Solution, -20°C, protect from light, 2 years

• [1]. Yurov YB, et al. High resolution multicolor fluorescence in situ hybridization using cyanine and fluorescein dyes: rapid chromosome identification by directly fluorescently labeled alphoid DNA probes. Hum Genet. 1996;97(3):390-398.  [Content Brief]

  [2]. Li K, et al. Highly Ordered DNA Framework Interface Enables Efficient Enzymatic Oligonucleotide Synthesis. Adv Sci (Weinh). 2025;12(44):e05868.  [Content Brief]