Name: Cy3.5 BCN
Brand: AAT Bioquest
SKU: 70541
Price: 115 USD
Availability: InStock

Cy3.5 BCN

Cy3.5 BCN is a bright orange-red fluorescent dye used for site-specific labeling of peptides, oligonucleotides, and other biomolecules via copper-free click chemistry.

Bioorthogonality: The reaction is selective for azido or tetrazine.
High reaction rate: BCN reacts faster than most other click reactions.
Catalyst-free: The reaction does not require a toxic metal catalyst like copper.
High biocompatibility: The reaction occurs under physiological pH and room temperature.
Versatility: It can be used for site-specific modification of a wide range of macromolecules.

Datasheet

SDS

COA

Catalog	Size	Price	Quantity
70541	1 mg	Price

Overview

Cy3.5 BCN is a bioorthogonally clickable derivative of Cy3.5, a widely used orange-red fluorescent dye for labeling biomolecules such as peptides and oligonucleotides. Cy3.5 is characterized by strong fluorescence intensity, high photostability, and pH-independent emission across a broad range (pH 4–10).To improve conjugation performance, Cy3.5-BCN incorporates a PEG spacer, which reduces steric hindrance and minimizes potential interference with target binding sites. This design maximizes conjugation efficiency while preserving the biological activity of the resulting conjugate. The bicyclononyne (BCN) moiety enables strain-promoted azide–alkyne cycloaddition (SPAAC) with azido groups, forming stable triazole linkages under catalyst-free conditions. In addition, unlike dibenzocyclooctyne (DBCO), BCN also reacts efficiently with tetrazines through an inverse electron-demand Diels–Alder (IEDDA) reaction. This reaction is rapid, selective, and bioorthogonal, allowing labeling of biomolecules under physiological conditions without the need for metal catalysts or disruption of native biological processes.

Calculators

Common stock solution preparation

Table 1. Volume of DMSO needed to reconstitute specific mass of Cy3.5 BCN to given concentration. Note that volume is only for preparing stock solution. Refer to sample experimental protocol for appropriate experimental/physiological buffers.

	0.1 mg	0.5 mg	1 mg	5 mg	10 mg
1 mM	62.982 µL	314.909 µL	629.818 µL	3.149 mL	6.298 mL
5 mM	12.596 µL	62.982 µL	125.964 µL	629.818 µL	1.26 mL
10 mM	6.298 µL	31.491 µL	62.982 µL	314.909 µL	629.818 µL

Molarity calculator

Enter any two values (mass, volume, concentration) to calculate the third.

Mass (Calculate)		Molecular weight		Volume (Calculate)		Concentration (Calculate)		Moles
mg	÷	1587.76 g/mol	=	mL	x	mM	=	mmol

References

View all 29 references: Citation Explorer

Hybridization on DNA-Coated Ultrasmall Gold Nanoparticles (2 nm).

Authors:

Sager, Jonas and Loza, Kateryna and Prymak, Oleg and Heggen, Marc and Huber, Alexander and Voskuhl, Jens and Oliveira, Cristiano L P and Epple, Matthias

Journal:

Chemistry (Weinheim an der Bergstrasse, Germany) (2025): e02421

Gradient Functionalization of Poly(lactic acid)-Based Materials with Polylysine for Spatially Controlled Cell Adhesion.

Authors:

Korzhikov-Vlakh, Viktor and Mikhailova, Aleksandra and Sinitsyna, Ekaterina and Korzhikova-Vlakh, Evgenia and Tennikova, Tatiana

Journal:

Polymers (2024)

Membrane staining and phospholipid tracking in Pseudomonas aeruginosa PAO1 using the phosphatidylcholine mimic propargyl-choline.

Authors:

Graham, Chris L B and Bryant, Jack and Roper, David I and Banzhaf, Manuel

Journal:

Access microbiology (2024)

Tag-free protein modification by lipoate ligase A: exploring substrate tolerance.

Authors:

Yamazaki, Shunsuke and Takahashi, Kazutoshi and Matsuda, Yutaka

Journal:

Analytical sciences : the international journal of the Japan Society for Analytical Chemistry (2024): 1111-1119

Cell-resistant wavelength-shifting molecular beacons made of L-DNA and a clickable L-configured uridine.

Authors:

Lang, Fabian and Rönicke, Franziska and Wagenknecht, Hans-Achim

Journal:

Organic & biomolecular chemistry (2024): 4568-4573

Physical properties

Molecular weight	1587.76
Solvent	DMSO

Spectral properties

Correction factor (260 nm)	0.08
Correction factor (280 nm)	0.178
Extinction coefficient (cm ^-1 M ^-1)	150000
Excitation (nm)	579
Emission (nm)	591
Quantum yield	0.15

Usage and storage

Intended use	Research Use Only (RUO)
Storage	Freeze (< -15 °C); Minimize light exposure

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Page updated on July 15, 2026