Understanding Cyanine Dyes: Structure & Mechanism, Channel Selection, Troubleshooting Essentials, and a Product Selection Roadmap (with 6 Category Tables)

1. What are cyanine (Cyanine) dyes?

Cyanine dyes are a classic class of polymethine-conjugated dyes: they typically contain nitrogen-containing heterocycles at both ends (e.g., indoline / benzoindoline), connected by a polymethine conjugated bridge in the middle. Because the π-electrons are delocalized over the entire backbone, cyanines exhibit strong absorption and often substantial fluorescence.

Analogy: Think of it as a “tunable-length electronic highway.” The longer the highway, the more the absorption/emission shifts toward the red end (longer wavelength).

2. Why do cyanines come in different colors?

The core “switch” is: the length of the polymethine bridge.

(1) Longer polymethine bridge → red-shifted spectra (longer wavelength)

(2) This is why the common series progresses from Cy3 (orange-red) → Cy5 (far-red) → Cy7 (near-infrared) toward longer wavelengths.

Note: In addition to chain length, the terminal heterocycles, substituents, rigidification (locking), charge, and solvent/protein-binding state can all significantly affect peak position and brightness. Therefore, even for the same “Cy5,” different brands/structures can show small to moderate shifts—often more noticeable in the NIR region.

Common names and “color/channel” mapping

Common representative	Approx. channel	Typical excitation/emission	Typical use
Cy3	Orange-red channel	~555/570 nm	Antibody/nucleic-acid labeling, microscopy/flow cytometry, multicolor assays
Cy5	Far-red channel	~650/670 nm	Lower autofluorescence in biological samples; suitable for tissues/complex samples
Cy7 (and similar heptamethine cyanines)	Near-infrared channel	~740–770 / ~770–800 nm (system-dependent)	NIR imaging, low-background detection
ICG (indocyanine green)	Clinical NIR	Clinical/in vivo imaging often uses ~780–808 nm excitation setups	Clinical/intraoperative vascular & lymphatic imaging, perfusion assessment
JC-1 (a carbocyanine/cyanine-type dye)	“Green ↔ Red” ratiometric	Monomer green (~530); aggregate red (~595)	Mitochondrial membrane potential (ΔΨm) ratiometric readout

Notes:

(1) Ex/Em can change with solvent, salt form, aggregation, and whether the dye is bound to proteins/membranes; values above are common ranges/typical values.

(2) JC-1 extra note: The red signal arises from J-aggregates and is sensitive to dye concentration/loading. Follow recommended concentrations and controls strictly.

3. Why can the same cyanine look “much brighter” in some experiments than others?

Cyanines have a very characteristic feature:

Fluorescence efficiency (quantum yield) strongly depends on the microenvironment—for example, whether the dye is constrained by macromolecules, whether it aggregates, whether it enters a membrane phase, and the local viscosity/rigidity. Many reviews note that a common cause of “loss of brightness” in cyanines is nonradiative decay pathways such as backbone twisting / cis–trans isomerization in the excited state. These pathways can be strongly amplified or suppressed by how “constrained” the environment is—the more the dye’s backbone motion is restricted, the brighter it often becomes.

Three keywords to understand brightness changes in cyanines

1. “If it can twist, it gets dimmer” (more constrained environments often look brighter)

Cyanines can readily follow a nonradiative route of “twisting/isomerization → heat dissipation.” In free solution this route is more accessible, so fluorescence may be weaker. When the dye is constrained by protein/nucleic-acid structures or placed in a more viscous/rigid microenvironment, rotational motions are suppressed and fluorescence often increases.

2. “Aggregation ≠ always self-quenching” (H- vs J-aggregation behave differently)

Cyanines do tend to aggregate, but “aggregation always makes it darker” is not universally true—the key is the aggregation geometry:

(a) H-aggregates: often show blue-shifted absorption and more frequently lead to fluorescence reduction/quenching.

(b) J-aggregates: often show red-shifted absorption with a narrow J-band; emission may decrease, or under some ordered stacking conditions can become stronger and/or narrower (and “super-quenching” can also occur depending on packing geometry and environment).

Quick tip: If absorption develops a clear blue-shifted shoulder and brightness drops sharply, it often resembles H-aggregation. If you see a red-shifted, very narrow absorption band, it often resembles J-aggregation—but whether it becomes brighter must be measured and should not be generalized.

3. “Too close causes self-quenching” (high labeling density / high DOL)

In covalent labeling of proteins/antibodies, if the degree of labeling (DOL) is too high, multiple cyanines may be too close, leading to dye–dye interactions, self-quenching, abnormal spectra, and even altered biomolecule behavior (e.g., affinity/in vivo distribution).

So for covalent labeling, it’s not enough to confirm “it labeled”—optimizing DOL is a key variable for brightness and reproducibility.

 

4. What does “Sulfo-” mean?

Many product names include sulfo-Cy3, sulfo-Cy5, etc.

Sulfo- typically means sulfonate groups are introduced into the dye, making it more soluble in water, generally less prone to hydrophobically driven stacking, and potentially reducing some nonspecific adsorption. However, whether aggregation occurs still depends on structure and concentration. The optimal coupling pH is still mainly determined by the reactive handle (e.g., NHS/SE often uses pH 7.2–8.5; maleimide–thiol often uses pH 6.5–7.5).

Summary:

(1) For aqueous antibody/protein conjugation: typically prioritize sulfo- versions (better solubility, less “clumping”).

(2) For membrane insertion/cellular entry/hydrophobic environments: non-sulfonated or specifically lipophilic cyanines (e.g., DiI-type) are often more aligned with the design goal.

5. Cyanine application “family tree” and typical use cases

Application family	Representative dyes/series	Typical use	Key mechanism/structural feature	Selection keywords
A. Covalent labeling	NHS ester / Maleimide / Azide–Alkyne / Tetrazine–TCO forms of Cy3/Cy5/Cy5.5, etc.	Covalent fluorescent labeling of proteins/antibodies/peptides/oligonucleotides, etc.	Same “Cy5” = same color backbone; different linker/handle = different “plug,” with completely different reactive sites	Prioritize the interface: amine/thiol/click; then consider wavelength/brightness
A1. NHS ester (amine-reactive)	Cy3-NHS, Cy5-NHS…	Random-site labeling of antibodies/proteins (often Lys)	Reacts with primary amines; suitable for most protein labeling	“protein/antibody labeling,” “Lys/amine”
A2. Maleimide (thiol-reactive)	Cy5-maleimide…	More site-specific labeling at cysteine residues	Preferential for thiols; often used for site-specific strategies	“Cys/thiol,” “site-specific”
B. Membrane/cell tracking (lipophilic cyanines)	DiI / DiD / DiR, etc.	Cell membrane/neural tracing, membrane-structure tracking, exosome/vesicle visualization (system-dependent)	Long alkyl chains “anchor” into lipid bilayers and diffuse within the membrane to fluoresce	“membrane dye,” “cell tracking,” “lipophilic”
C. Potential-sensitive / ratiometric (mitochondria, etc.)	JC-1 (representative) and other ΔΨm probes	Indicating changes in mitochondrial membrane potential (ΔΨm)	Aggregates vs monomers emit different colors → red/green ratio is more robust	“ΔΨm,” “ratiometric,” “mitochondrial state”
D. NIR & in vivo imaging	ICG (indocyanine green) and NIR cyanines (extendable to Cy7, etc.)	Vascular/lymphatic tracing, perfusion, instrument-matched imaging (research/compliance-dependent)	Lower background and better penetration in NIR; ICG is clinically mature	“NIR,” “in vivo/tissue,” “low autofluorescence”
E. Nucleic-acid binding/staining	SYBR/TO/YO, etc.	DNA/RNA staining, gel/amplification readouts, etc.	Strong fluorescence upon binding/intercalation with nucleic acids	“nucleic-acid staining,” “gel/amplification readout”

6. A “five-step” decision checklist for cyanine dye selection

Step	Decision point	How to judge quickly	Recommended direction	Key cautions
1	What lasers/channels/filters does the instrument have?	Check the configuration table for microscope/flow cytometer/imaging system; confirm excitation lines and emission windows	Lock the broad class first: e.g., “Cy3-like channel,” “Cy5-like channel,” “NIR channel”	Channel definitions vary across platforms; follow the instrument
2	Is sample background high? Do you need to go longer-wavelength?	Tissues, blood, thick samples often have higher background; run a blank sample first	High background → prioritize far-red/NIR; low background → visible-range options may be brighter and/or more economical	Longer wavelength is not “always better”: detector sensitivity, filter matching, and bleed-through matter
3	What “chemical interface” is available on the target?	Are there amines/thiols? Can you introduce click handles?	Amine → NHS; thiol → maleimide; modular assembly → click/tetrazine, etc.	Buffers/additives may “steal” the reaction (amine-containing buffers, reducing agents, etc.); wrong interface = no labeling
4	Is it mainly an aqueous protein/antibody system? Do you need a more hydrophilic version?	Antibody/protein labeling, high nonspecific binding, aggregation-prone → usually yes	For aqueous/protein labeling, prioritize sulfo/water-solubilized versions to reduce aggregation/nonspecific binding	More hydrophilic often means less membrane permeability; clarify “do you need cellular entry?” upfront
5	Are controls and troubleshooting “exits” ready?	Write controls into the experimental plan: unlabeled, dye-only, free-dye removal verification	Design “can you explain the result?” first, then apply to real samples	Suggested three-piece set: unlabeled control, dye-only control, free-dye removal verification; especially critical for membrane/vesicle systems

7. Most common cyanine experimental issues and cautions

1. Over-illumination → photobleaching: reduce excitation intensity, shorten exposure, use antifade systems; objective differences in photostability across dyes do exist.

2. Dye aggregation → reduced brightness / higher background / abnormal spectra: reduce local dye concentration, increase solubility (sulfo-), optimize coupling ratios and purification.

3. “If it’s water-soluble, it definitely won’t insert into membranes” is a misconception: many water-soluble fluorophores can still interact strongly with lipid bilayers, causing interpretation bias.

4. False positives when labeling vesicles/EVs with lipophilic dyes: lipophilic dyes can self-assemble into micelles/particles and be taken up by cells, creating the illusion that “vesicles entered cells.”

5. Same oligonucleotide type, different sequence → different brightness: Cy3/Cy5 brightness may change with the local nucleic-acid microenvironment. For strict quantitation, use same-sequence standards/internal references; avoid comparing brightness directly across different sequences.

8. Cyanine Dye Product Selection Overview: Navigation Table + Six Category Product Tables (Free Dyes | Reactive Conjugates | Membrane Stains | Nucleic-Acid Stains | Application-Ready Products & Tools)

Navigation Table

Scenario / Goal	Tables to check first	Typical product types in the table	Quick selection tips
Want to fluorescently label proteins/antibodies/peptides (do the conjugation yourself)	Table 1	Bio-conjugation / Functionalized Cyanines (NHS/SE, Mal, N₃, Sulfo, etc.)	Cy3/Cy5/Cy7 NHS/SE (amine labeling), maleimide (thiol labeling), azide (click), water-soluble Sulfo versions
Need better water solubility / lower background conjugation (reduce aggregation, improve aqueous compatibility)	Table 1 + Table 5 (PEG5000 / solubilization)	Sulfo-Cy (sulfonated) reactive dyes; Cy-PEG5000 “ready linker” products (NHS/Mal/SH/NH₂/COOH)	For aqueous conjugation, prioritize Sulfo; for “longer spacer / stronger hydrophilicity,” prioritize PEG5000
Want click chemistry (Click) to attach dye to a target	Table 1 + Table 5 + Table 6	Cy-N₃, Cy-alkyne, Cy-PEGn-N₃ and other click handles/intermediates	If you already have an alkyne, choose N₃; if you already have N₃, choose an alkyne; to reduce steric hindrance, consider PEGn versions
Only want free dyes (no reactive group) for spectra/imaging/tracing (especially NIR)	Table 2	NIR/Far-Red Imaging Dyes & Basic Cyanine Salts	ICG, IR-820, IR-780, IR-775, HITC and other “free dyes / basic salts”
Membrane staining & tracking for cells/liposomes/exosomes (membrane-inserting dyes)	Table 3	Membrane Staining Probes (DiI/DiD/DiR, etc.)	Long-alkyl-chain lipophilic membrane-inserting dyes such as DiI/DiD/DiR
Nucleic-acid gel staining / nucleic-acid quantification (SYBR, PicoGreen, etc.)	Table 4	Nucleic-Acid Dyes & Cellular Functional Probes	SYBR Green I, PicoGreen, TO/YO series nucleic-acid dyes
Cellular nucleic-acid staining / live–dead exclusion / post-fix nuclear staining (e.g., TO-PRO, TOTO)	Table 4	TO-PRO 1, TOTO-3, thiazole orange / oxazole yellow, etc.	For dead-cell indication (“enters only when membrane integrity is lost”), prioritize TO-PRO; for fixed/strong nuclear staining, consider TOTO
Mitochondrial membrane potential (ΔΨm)	Table 4 + Table 6	JC-1 (ratiometric), DiOC5(3) (membrane potential probe)	For more robust relative quantification, JC-1 (red/green ratio) is common; for alternative membrane-potential readouts, see DiOC5(3)
Don’t want to conjugate yourself; want ready-to-use labeled products (proteins/peptides/affinity systems/controls)	Table 5 + Table 6	Cy5-streptavidin, Cy5.5-BSA, Cy5-Aβ, Cy3-transferrin, Cy3-Protein A, negative controls, etc.	For “ready-to-use / reproducibility,” prioritize finished products; also saves time for method validation
Oligonucleotide probe synthesis (solid-phase) to attach Cy dyes onto DNA/RNA	Table 5 + Table 6	Phosphoramidite, CPG (1000 Å), and other solid-phase synthesis reagents	For solid-phase synthesis, prioritize CPG / Phosphoramidite; choose 3′/5′ introduction based on your synthesis route
PCR / enzymatic incorporation for nucleic-acid labeling (dUTP incorporation)	Table 6	Dye-labeled nucleotides such as Sulfo-Cy3-E-dUTP	For aqueous compatibility / reduced nonspecific adsorption, prioritize Sulfo (sulfonated) versions
Tracing & building delivery/lipid/nanoparticle systems (DSPE, microspheres, drug conjugates)	Table 6	Cy3 iRGD-PEG-DSPE, Cy5-PS 100 nm microspheres, Cy7-paclitaxel, Cy3-cisplatin, etc.	For “carrier tracing / method calibration / drug-behavior studies,” this table is most direct; complements Table 2/3

Summary: Protein/antibody → Table 1; membrane/liposome → Table 3; nucleic-acid detection/staining → Table 4; free-dye imaging → Table 2; ready-to-use products / system tools → Table 5/6. Then, within the relevant table, narrow down by channel (Cy2/Cy3/Cy5/Cy7…) + connection strategy (NHS/Mal/Click/PEG/nucleic-acid synthesis).

Table 1 | Bio-Conjugation / Functionalized Cyanines (NHS/SE, Maleimide, Azide, Acid/Acid Chloride; incl. Sulfonated/Water-Soluble Versions)

Category	CAS No.	Aladdin Cat. No.	Product Name	Specs / Purity	Key Features & Applications
Bio-conjugation dye | Maleimide (thiol labeling)	1593644-50-8	C171357	Cy5.5 Maleimide	Ex: 678 nm, Em: 695 nm, ≥95%	Maleimide selectively couples to thiols (Cys, -SH on reduced antibodies). Far-red/NIR channel; suitable for protein/peptide labeling, in vivo imaging, and multicolor detection.
Bio-conjugation dye | NHS ester / SE (amine labeling)	146368-14-1	C288764	Cyanine 5, SE, red fluorescent dye	Ex: 647 nm, Em: 665 nm, ≥95% (HPLC)	SE/NHS ester reacts with primary amines (Lys, N-terminus). Cy5 far-red channel; widely used for antibody/protein labeling, immunofluorescence, flow cytometry, and imaging.
Bio-conjugation dye | NHS ester / SE (amine labeling)	956579-01-4	C596040	800CW NHS (equivalent to IRDye 800CW NHS)	≥98%	800 nm NIR-channel NHS ester; suitable for antibody/protein labeling for deep-tissue in vivo imaging, intraoperative fluorescence guidance, small-animal imaging (research use).
Bio-conjugation dye | NHS ester / SE (amine labeling)	477908-53-5	C1454842	Cy7-SE	≥98%	Cy7 (NIR channel) SE/NHS ester; commonly used for protein/antibody labeling, in vivo imaging, and multicolor NIR detection.
Bio-conjugation dye | NHS ester / SE (amine labeling)	1393363-07-9	C651286	Cy3 NHS ester	≥98%	Cy3 orange-red channel NHS ester; used for immunofluorescence, FISH/probe labeling, flow cytometry, and microscopy imaging.
Bio-conjugation dye | NHS ester / SE (water-soluble Sulfo / sulfonated)	1424150-38-8	S595796	Sulfo-Cy3 Succinimidyl Ester	≥96%	Sulfonation improves water solubility; NHS ester enables more convenient amine labeling in aqueous buffers (less need for organic co-solvent), suitable for aqueous protein/antibody conjugation.
Bio-conjugation dye | Maleimide (water-soluble Sulfo / sulfonated)	1656990-68-9	S595919	Sulfo-Cy3 Maleimide	≥96%	Water-soluble thiol labeling (maleimide); suitable for coupling to Cys in aqueous systems, reducing hydrophobic aggregation and nonspecific adsorption.
Bio-conjugation dye | NHS ester / SE (amine labeling)	186205-33-4	C649855	Cy2-SE (iodine)	≥95%, Em: 510 nm; Ex: 492 nm	Cy2 green-channel SE/NHS ester; suitable for multiplex labeling (commonly paired with Cy3/Cy5); used for protein/antibody labeling, fluorescence imaging, and quantitative detection.
Bio-conjugation dye | NHS ester / SE (amine labeling)	1032678-42-4	C171426	Cy5 N-hydroxysuccinimide ester	≥95%	Cy5 NHS ester (amine labeling); commonly used for antibody/protein labeling. Far-red channel with lower background; suitable for flow cytometry, immunofluorescence, and in vivo/tissue imaging.
Bio-conjugation dye | Click chemistry (azide)	1267539-32-1	C196719	Cy5 Azide	≥95%	Azide for click chemistry (with alkynes/DBCO systems); suitable for bioorthogonal labeling, metabolic labeling, and probe construction (choose CuAAC vs SPAAC based on your click system).
Bio-conjugation dye | NHS ester / SE (amine labeling)	2408482-09-5	C171360	Cy7 N-hydroxysuccinimide ester (Cy7 NHS ester)	≥95%	Cy7 NIR NHS ester; used for antibody/protein labeling, deep-tissue imaging, and NIR multicolor experiments.
Bio-conjugation dye | NHS ester / SE (amine labeling)	2632339-91-2	C276360	Cyanine3 NHS ester	≥95%	Cy3 NHS ester (amine labeling); used for immunofluorescence, FISH probe labeling, microscopy/flow cytometry, etc.
Bio-conjugation dye | Maleimide (thiol labeling)	2755154-93-7	C276411	Cyanine3 maleimide tetrafluoroborate	≥95%	Cy3 maleimide (thiol labeling), suitable for site-directed labeling of proteins/peptides at Cys; used for imaging, conjugated probes, and quantitative detection.
Bio-conjugation dye | NHS ester / SE (amine labeling)	1263093-76-0	C276024	Cyanine5 NHS ester	≥95%	Cy5 NHS ester; widely used in far-red channels for protein/antibody labeling, immunofluorescence, flow cytometry, and multicolor co-localization.
Bio-conjugation dye | NHS ester / SE (amine labeling)	2375105-86-3	C276343	Cyanine5.5 NHS ester	≥95%	Cy5.5 far-red/NIR-channel NHS ester; used for protein/antibody labeling and in vivo imaging (more red-shifted than Cy5).
Bio-conjugation dye | Maleimide (water-soluble / highly hydrophilic)	2242791-82-6	S275842	Water-soluble Cy5 Maleimide	≥95%	More hydrophilic Cy5 maleimide formulation; suitable for aqueous thiol labeling, reducing nonspecific adsorption/aggregation; used for site-directed protein/antibody conjugation and imaging.
Bio-conjugation dye | NHS ester / SE (water-soluble Sulfo / sulfonated)	1603861-95-5	S595924	Sulfo-Cy7 Succinimidyl Ester (Sulfo-Cy7 NHS ester)	≥95%	Water-soluble Cy7 NHS ester; enables amine labeling in aqueous buffers; suitable for in vivo imaging, antibody conjugation, and multicolor NIR detection.
Bio-conjugation dye | NHS ester / SE (water-soluble Sulfo / sulfonated)	2230212-27-6	S276215	Sulfo-Cyanine 5 NHS ester	≥95%	Water-soluble Cy5 NHS ester; suitable for aqueous protein/antibody labeling; used for immunofluorescence, flow cytometry, tissue imaging, and reduced aggregation vs hydrophobic dyes.
Bio-conjugation precursor | Carboxylic acid (re-activatable)	1032678-01-5	C1492397	Cy3 Acid	—	Cy3 precursor with a carboxyl group: can be re-activated via EDC/NHS for amine coupling, or used to synthesize more functional derivatives (linkers/probe construction).
Bio-conjugation dye | NHS ester / SE (amine labeling, high-brightness version)	228272-52-4	C1454879	Cy3B NHS ester	—	Cy3B is typically brighter and more photostable (for demanding imaging such as single-molecule/super-resolution); NHS ester for amine labeling of proteins/antibodies.
Bio-conjugation precursor | Acid chloride (high reactivity; moisture-sensitive)	1803099-44-6	C1453275	Cyanine7.5 carboxylic acid chloride	—	Acid chloride is highly reactive and can rapidly react with amines/alcohols to build Cy7.5 conjugates; moisture-sensitive—requires dry handling, and fresh preparation/use is recommended.

Table 2 | NIR/Far-Red Imaging Dyes & Basic Cyanine Salts (No Reactive Group / Core Scaffold)

Category	CAS No.	Aladdin Cat. No.	Product Name	Specs / Purity	Key Features & Applications
NIR imaging dye | IR/ICG type (non-reactive)	3599-32-4	I107931	Indocyanine Green (ICG)	Moligand™, ≥75%	Common clinical NIR dye (typical absorption ~780 nm, emission ~820 nm). Widely used for vascular/lymphatic/perfusion imaging and in vivo tracing research; readily binds proteins in aqueous media; store protected from light.
NIR imaging dye | IR/ICG type (non-reactive)	172616-80-7	N119962	New Indocyanine Green (IR-820)	Dye content 80%	An ICG-derived NIR dye; commonly used in in vivo fluorescence imaging/tracing and photothermal/photodynamic-related research (system-dependent).
NIR imaging dye | IR/ICG type (non-reactive)	207399-07-3	I302749	IR-780 iodide	Dye content ≥95%	Heptamethine NIR cyanine; often relatively hydrophobic; used in NIR imaging, mitochondrial/cellular uptake studies, and exploratory photothermal/photodynamic models.
NIR imaging dye | IR/ICG type (non-reactive)	115970-66-6	I157644	IR 783	≥98% (HPLC)	NIR cyanine dye (often used for spectroscopy/imaging research); can be used for labeling-system development and in vitro/in vivo NIR tracing (depends on solubility/formulation).
NIR imaging dye | IR/ICG type (non-reactive)	19764-96-6	H289966	Iodide-1,1ˊ,3,3,3ˊ,3ˊ-hexamethylindotricarbocyanine	≥97% (HPLC)	A common HITC (indotricarbocyanine) type NIR fluorescent dye; used for spectroscopy/imaging and as a starting dye for further functionalization/conjugation.
NIR imaging dye | IR/ICG type (non-reactive)	199444-11-6	I157638	IR-775 chloride	≥90% (N)	NIR cyanine dye (IR-775) for spectroscopy/imaging and materials research; often requires organic solvent stock solutions and strict light protection.
Basic cyanine salt / synthetic intermediate | thia-cyanine	53213-94-8	D131515	3,3'-Dipropyl thiadicarbocyanine iodide	≥98%	A typical thia-cyanine scaffold/salt; often used as a parent core for synthesizing other cyanine derivatives or for spectroscopy/sensing materials research.

Table 3 | Membrane Staining Probes (Lipophilic Cyanines | Membrane-Inserting Type)

Category	CAS No.	Aladdin Cat. No.	Product Name	Specs / Purity	Key Features & Applications
Membrane stain probe | Lipophilic cyanine (membrane-inserting)	41085-99-8	D131225	1,1'-Dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI)	For fluorescence analysis, ≥98%	Classic lipophilic carbocyanine membrane dye; long hydrophobic chains insert into lipid bilayers; commonly used for cell membrane/liposome/exosome labeling, cell tracking, and neural tracing.
Membrane stain probe | Lipophilic cyanine (membrane-inserting)	34215-57-1	D131213	3,3'-Dioctadecyloxacarbocyanine perchlorate	≥98%	Ultra-long alkyl chains, strongly hydrophobic, stably embeds in lipid membranes; suitable for membrane/liposome/hydrophobic-phase tracing, membrane dynamics, and particle labeling.
Membrane stain probe | Lipophilic cyanine (membrane-inserting)	127274-91-3	D266406	DiD perchlorate	≥98%	Lipophilic far-red membrane dye (DiD) with stable membrane insertion; used for membrane/exosome/liposome labeling, cell tracking, and membrane fusion studies.
Membrane stain probe | Lipophilic cyanine (membrane-inserting)	100068-60-8	D131031	DiR' [DiIC18(7)], for membrane staining	≥95%	NIR lipophilic membrane dye (DiR/DiIC18 type), suitable for deep in vivo tracing; commonly used for cell tracking, exosome/liposome labeling, and in vivo imaging.

Table 4 | Nucleic-Acid Dyes & Cellular Functional Probes (Nucleic-Acid Staining/Quantification/Counterstaining + Mitochondrial Membrane Potential)

Category	CAS No.	Aladdin Cat. No.	Product Name	Specs / Purity	Key Features & Applications
Nucleic-acid dye | Intercalation/binding-enhanced fluorescence	107091-89-4	T131378	Thiazole Orange	Dye content ~90%	TO (Thiazole Orange)-type dye shows strongly enhanced fluorescence upon nucleic-acid binding; used for DNA/RNA staining, nucleic-acid probe/aptamer systems, cellular nucleic-acid imaging, and method development.
Nucleic-acid dye | Gel staining / quantification	163795-75-3	S171397	SYBR Green I Gel Stain Solution	10,000× in DMSO	High-sensitivity dsDNA fluorescent dye widely used for gel staining and nucleic-acid detection; supplied as a concentrated DMSO stock—dilute to working concentration and protect from light throughout.
Nucleic-acid dye | Nuclear/chromatin counterstaining	143413-85-8	Y275655	YODi-1, DNA & Chromatin Counterstain	≥97%, 5 mM DMSO solution	YO-family nucleic-acid binding dye (commonly used for counterstaining/contrast staining); suitable for nuclear/chromatin staining and imaging (typically provided as a DMSO stock—dilute appropriately for your system).
Nucleic-acid dye | Intercalation/binding-enhanced fluorescence	152068-09-2	O598365	Oxazole Yellow, 1 mM in DMSO	—	YO (Oxazole Yellow)-type nucleic-acid binding dye with fluorescence enhancement upon binding; commonly used for nucleic-acid staining and probe systems (DMSO stock; protect from light).
Nucleic-acid dye | High-sensitivity dsDNA quantification	177571-06-1	P1505322	PicaGreen (~PicoGreen)	—	PicoGreen-type dsDNA quantification dye; suitable for trace DNA fluorescence quantification (plate reader / solution-based assays); widely used for sample quantification and QC in library prep/purification workflows.
Nucleic-acid dye | Cell-impermeant (dead-cell / nucleic-acid staining)	157199-59-2	T1427933	TO-PRO 1	—	TO-PRO dyes generally do not enter cells with intact membranes; commonly used for dead-cell indication/nucleic-acid staining, live–dead exclusion in flow cytometry, or nuclear staining after fixation.
Nucleic-acid dye | Dimeric high-affinity (far-red)	166196-17-4	T1454133	TOTO-3	—	TOTO (dimeric) nucleic-acid dye with strong dsDNA signal in the far-red channel; commonly used for nucleic-acid staining in fixed cells/tissues, FISH/microscopy imaging (often membrane-impermeant).
Cellular functional probe | Mitochondrial membrane potential (ΔΨm)	47729-63-5	J335286	JC-1 iodide	≥95%	Classic ratiometric mitochondrial membrane potential dye: high ΔΨm favors red-emitting aggregates, low ΔΨm favors green-emitting monomers; used for apoptosis/mitochondrial function assessment and pharmacology screening.
Cellular functional probe | Mitochondrial membrane potential (ΔΨm)	3520-43-2	J125134	JC-1, mitochondrial membrane potential dye	≥95%	Another JC-1 ΔΨm probe; suitable for flow cytometry/microscopy, often analyzed as a red/green ratio to reduce impacts from dye loading and cell-number differences.

Table 5 | Functionalized Cyanine (Cy3/Cy5/Cy7) Products & Functional Derivatives (PEG Conjugation | Click Chemistry | Oligo Synthesis | Pre-Labeled Biomolecules)

Category	CAS No.	Aladdin Cat. No.	Product Name	Specs / Purity	Key Features & Applications
Cy3/Cy5-PEG5000 functional product | Amine conjugation (NHS)	—	C163510	Cy5 PEG N-hydroxysuccinimide ester	MW 5000 Da	PEG5000 long spacer + NHS ester for rapid coupling to primary amines on proteins/antibodies; improves water solubility and reduces nonspecific adsorption—ideal for building water-soluble fluorescent probes/conjugates.
Cy3/Cy5-PEG5000 functional product | Thiol conjugation (Mal)	—	C163507	Cy5 PEG Maleimide (Cy5-PEG-Mal)	MW 5000 Da	PEG5000 + maleimide for selective coupling to Cys/thiols; suitable for site-specific antibody labeling, thiol labeling of peptides/proteins, and construction of in vivo imaging probes.
Cy3/Cy5-PEG5000 functional product | Re-functionalizable (PEG-SH)	—	C163492	Cy3 PEG Thiol (Cy3-PEG-SH)	MW 5000 Da	Terminal -SH can be further coupled (e.g., to maleimide/alkenes); often used as an “extendable fluorescent PEG linker” for nanomaterial surface modification and controlled conjugation.
Cy3/Cy5-PEG5000 functional product | Re-functionalizable (PEG-NH₂)	—	C163476	Cy3 PEG Amine (Cy3-PEG-NH₂)	MW 5000 Da	Terminal -NH₂ enables reactions with activated acids/acid chlorides/isocyanates, etc.; used for synthesis of fluorescent polymers, surface modification, and probe construction.
Cy3/Cy5-PEG5000 functional product | Re-functionalizable (PEG-COOH)	—	C163473	Cy3 PEG Carboxylic Acid (Cy3-PEG-COOH)	MW 5000 Da	Terminal -COOH can be activated by EDC/NHS for amine coupling; suitable for conjugation to peptides/proteins/aminated surfaces to build long-spacer fluorescent probes.
Cy3/Cy5-PEG5000 functional product | Affinity system (Biotin)	—	C163479	Cy3 PEG Biotin	MW 5000 Da	Cy3-PEG5000-biotin for fluorescent tracing/enrichment/imaging in the biotin–streptavidin (SA) system; PEG helps reduce steric hindrance and nonspecific adsorption.
Cy3/Cy5-PEG5000 functional product | Targeting ligand (Folate)	—	C163482	Cy3 PEG Folate	MW 5000 Da	Folate is a common ligand for folate-receptor targeting; used for cellular targeting imaging and receptor-mediated uptake studies; PEG improves water solubility and in vivo stability.
Click-chemistry dye | Azide (N₃, NIR)	—	C1499712	CY7-N₃	Moligand™, 10 mM in DMSO	Cy7 NIR azide for click chemistry (with alkynes/DBCO, etc.) to build bioorthogonal labeling probes; supplied as a 10 mM DMSO stock for quick use.
Click-chemistry dye | Alkyne	—	C595828	Cy3 Alkyne	≥96%	Cy3-alkyne handle for click reaction with azide substrates to build fluorescent labels; suitable for probe synthesis, metabolic labeling, and bioorthogonal systems.
Click/linker intermediate | Short PEG spacer (PEG3-azide)	—	C595606	Cy5-PEG3-Azide	≥96%	Cy5 + PEG3 spacer + N₃ balances hydrophilicity and accessibility; used to build more “flexible” click conjugates with reduced steric effects.
Conjugation intermediate | Short PEG spacer (PEG6-NHS)	—	C595620	Cy5-PEG6-NHS ester	≥96%	Cy5 + PEG6 + NHS provides a longer, flexible linker to facilitate mild aqueous amine coupling and reduce functional perturbation of the target; commonly used for gentle antibody/protein labeling.
Oligonucleotide synthesis reagent | Phosphoramidite	—	C664276	Cyanine 3 Phosphoramidite	≥97%	For solid-phase oligonucleotide (DNA/RNA) synthesis to introduce Cy3 at ends/sites; suitable for probes, primers, FISH probes, and molecular diagnostic probe preparation.
Pre-labeled protein | Affinity system (Streptavidin)	—	S293782	Cy5-labeled Streptavidin	Ex: 647 nm, Em: 665 nm	Ready-to-use product for detection/imaging of biotinylated antibodies/nucleic acids/proteins; compatible with immunofluorescence, ELISA/microarrays, flow cytometry, and affinity-capture visualization.
Pre-labeled protein | General carrier/standard (BSA)	—	B1455234	Cy5.5-labeled Bovine Serum Albumin	≥98%	Often used as a fluorescent tracer protein, negative background control, or methodological standard; for permeability/distribution studies, nonspecific adsorption evaluation, and imaging validation.
Labeled peptide probe | Disease-related model (Aβ42)	—	C1444883	Cy5-β-Amyloid (42–1), human	≥98%	Fluorescent Aβ42 peptide for Alzheimer’s-related aggregation/binding assays, imaging, and inhibitor screening; ready-made improves reproducibility.
Labeled oligonucleotide / control | Negative control	—	C1454369	Cy5-Zorevunensen negative control	≥99%	Labeled oligonucleotide negative control to assess nonspecific uptake/background; suitable for controls in cellular delivery and imaging/quantification workflows.
Reactive small-molecule dye | Thiol conjugation (Maleimide)	—	C596046	Cy7 Maleimide	≥96%	NIR Cy7-Mal for direct thiol labeling of proteins/peptides (Cys-directed) to build NIR imaging probes; reacts without requiring prior PEG attachment.
Building module | Bifunctional “re-activatable” (diacid)	—	C596010	Cy5.5 Diacid	≥98%	Two carboxyl sites enable diverse coupling after EDC/NHS activation (linker installation, dual-end conjugation, etc.); suitable for custom synthesis and materials modification.
Reactive dye | Aldehyde/glycan labeling (Hydrazide)	—	C595980	Cy7.5 Hydrazide	≥95%	Hydrazide reacts with aldehydes (e.g., oxidized glycans, aldehyde-functionalized surfaces) to form hydrazones / via reductive amination routes; used for glycoprotein/glycan labeling, surface chemistry, and imaging probe construction.
Small-molecule reactive dye | Amine conjugation (NHS)	—	C595956	Cy5 Succinimidyl Ester	≥96%	Classic Cy5-NHS amine-labeling dye; for rapid protein/antibody labeling, suitable for immunofluorescence, flow cytometry, and imaging.

Table 6 | Cyanine Dye Application-Ready Products & System Tools (PEG Conjugation | Oligo Synthesis/Enzymatic Incorporation | Delivery Lipids | Protein/Microsphere Products | Drug Conjugates | Functional Probes)

Category	CAS No.	Aladdin Cat. No.	Product Name	Specs / Purity	Key Features & Applications
Long-PEG conjugated dye | Cy5.5-PEG-Mal (thiol conjugation)	—	C1452373	CY5.5-PEG5000-Mal	—	PEG5000 long spacer + maleimide for selective coupling to thiols (Cys) on proteins/peptides/antibodies; improves water solubility and reduces nonspecific adsorption—suited for stable fluorescent conjugates (PEG2000 is also common in the same series).
Solid-phase oligo support | CPG (1000 Å)	—	C1492054	Cy3 CPG (1000 Å)	—	Solid support for oligonucleotide synthesis to produce 3′ Cy3-labeled oligos/probes; suitable for primers, FISH probes, and molecular diagnostic probes.
Oligonucleotide synthesis monomer | Phosphoramidite	—	C1492082	Cy5 Phosphoramidite	—	Introduces Cy5 labels during solid-phase synthesis (commonly 5′-end or site-specific); suitable for custom oligo probes, qPCR/imaging probes, and FRET system construction.
Enzymatic incorporation nucleic-acid labeling | Dye-dUTP	—	S598307	Sulfo-Cy3-E-dUTP (sulfonated Cy3–ethyl–dUTP)	—	Water-soluble sulfonated Cy3-dUTP for PCR/primer extension/nick translation and other enzymatic incorporations to label DNA fluorescently; suitable for highly aqueous systems and reduced nonspecific adsorption.
Delivery/lipid systems | Peptide-targeting lipid conjugate	—	C1439555	Cy3 iRGD-PEG-DSPE	—	DSPE lipid anchor + PEG spacer + iRGD peptide enables insertion into liposomes/LNPs/membrane systems and supports targeting/penetration studies; used for delivery-system tracing and cellular uptake evaluation.
Oligonucleotide/miRNA negative control (ready-to-use)	—	C1456642	Cy3 MicroRNA Antagomir Negative Control	—	Cy3-labeled miRNA antagomir negative control for transfection/delivery experiments to evaluate background signal, nonspecific uptake, and workflow QC.
Aldehyde/glycan labeling | Hydrazide	—	C171343	Cy3 Hydrazide	—	Hydrazide reacts with aldehydes (e.g., oxidized glycans/aldehyde-functionalized surfaces) to form hydrazones / via reductive amination routes; used for glycoprotein/glycan labeling and surface-chemistry conjugation.
Pre-labeled protein conjugate | Transferrin (Cy3-Transferrin)	—	C1425079	Cy3-labeled Transferrin	—	Common tracer protein for receptor-mediated endocytosis studies; used for cellular uptake, targeted delivery evaluation, co-localization imaging, and method validation.
Nano standard / carrier | PS microspheres (100 nm)	—	C1449720	Cy5-Polystyrene microsphere (100 nm)	—	100 nm fluorescent beads for flow/microscopy/nanoparticle method development (alignment, sensitivity/drift evaluation, particle tracing); also used as model nanocarriers.
Dye–drug conjugate | Paclitaxel	—	C1426240	Cy7–Paclitaxel	—	Tracks paclitaxel-related behavior via an NIR channel; used for drug uptake, distribution, carrier loading/release, and tissue imaging studies.
Dye–metal-drug conjugate | Cisplatin	—	C1450249	Cy3–Ccisplatin	—	Model for cisplatin tracing/delivery studies; used for uptake/distribution and validating carrier-conjugation strategies (fluorescent readout as a proxy for hard-to-measure steps).
Water-soluble active ester | Sulfo-bis-SE (bis-succinimidyl ester)	—	S598185	Sulfo-Cy5 bis-SE (Sulfo-Cy5 bis-succinimidyl ester)	—	Sulfonation improves water solubility + dual active esters for amine coupling to construct Cy5-labeled products (multi-point linking/bridging); suited for aqueous reactions and reduced hydrophobic aggregation.
Water-soluble precursor | Sulfo-free acid	—	S598153	Sulfo-Cy3-3 free acid	—	Sulfonated free-acid precursor: can be further activated for amine coupling to synthesize more complex water-soluble Cy3 derivatives/linker probes.
Functional probe | Membrane potential (carbocyanine/cyanine-type)	—	D598333	DiOC5(3) membrane potential fluorescent probe	—	Cyanine/carbocyanine-type membrane-potential probe for monitoring plasma-membrane potential changes (commonly in flow cytometry/imaging); suitable for pharmacological stimulation, ion-channel studies, and cellular state assessment.

Note: The above are representative Aladdin products. For additional specifications and options, refer to the product list at the end of the article or search on the Aladdin website by product name/CAS number.

Aladdin: https://www.aladdinsci.com/