Cy5.5 Fluor Dye, NIR Emission
Cy5.5 Fluor Dye NHS Ester is a reactive near-infrared cyanine dye that selectively labels primary amines through its N-hydroxysuccinimide (NHS) ester group. Following conjugation to amino-modified DNA, RNA, PNA, aptamers, antisense oligonucleotides, siRNA, or molecular probes, the resulting fluorescent oligonucleotide exhibits bright near-infrared emission with excellent sensitivity and low background fluorescence.
Compared with Cy5, Cy5.5 emits at longer wavelengths, reducing interference from biological autofluorescence while providing deeper optical penetration in biological samples. These properties make Cy5.5 a popular fluorophore for in vivo imaging, fluorescence-guided studies, multiplex assays, and high-sensitivity analytical applications.
Bio-Synthesis offers custom Cy5.5-labeled oligonucleotides prepared by reacting Cy5.5 NHS ester with amino-modified oligonucleotides. Labeling can be performed at the 5′ end, 3′ end, or internal amino-modified positions, depending on the experimental design.
Typical applications include:
- Near-infrared fluorescence imaging
- In vivo imaging
- Flow cytometry
- Fluorescence microscopy
- Confocal microscopy
- FRET acceptor labeling
- Hybridization probes
- Molecular beacons
- Biosensor development
- DNA nanotechnology
- Multiplex fluorescence assays
Typical Specifications
| Property |
Specification |
| Modification |
Cy5.5 Fluor Dye |
| Modification Type |
Near-infrared fluorescent dye |
| Synthesis Chemistry |
NHS ester (post-synthetic conjugation to amino-modified oligonucleotides) |
| Dye Family |
Cyanine (Cy) dye |
| Reactive Group |
N-Hydroxysuccinimide (NHS) ester |
| Reaction Partner |
Primary amines (Amino C6, Amino-TEG, internal amino modifiers) |
| Excitation Maximum |
Approximately 675 nm |
| Excitation Color |
Red |
| Emission Maximum |
Approximately 694 nm |
| Emission Color |
Near-Infrared (NIR) |
| Recommended Laser |
633 nm or 640 nm |
| Typical Placement |
5′ end, 3′ end, or internal amino-modified positions |
| Compatible Oligonucleotides |
DNA, RNA, PNA, LNA/BNA, siRNA, ASOs, aptamers, molecular probes |
| Typical Applications |
Near-infrared imaging, in vivo imaging, fluorescence microscopy, flow cytometry, FRET, hybridization assays, biosensors, multiplex fluorescence |
| Comparable Dyes |
Alexa Fluor® 680, ATTO® 680, DY-680, CF® 680, IRDye® 680 (approximate spectral equivalents) |
Product Information
Cy5.5 Fluor Dye, NIR Emission
Near infrared fluorescent dye
Extinction Coefficient, ε(λ):
209,000
-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at -20°C) in a nuclease-free environment should be stable for years.
References/Citations:
- Mujumdar RB, Ernst LA, Mujumdar SR, Lewis CJ, Waggoner AS. Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. Bioconjugate Chemistry. 1993;4(2):105-111.
- Lakowicz JR. Principles of Fluorescence Spectroscopy. 3rd Edition. Springer; 2006.
- Hermanson GT. Bioconjugate Techniques. 3rd Edition. Academic Press; 2013.
- Waggoner A. Fluorescent labels for proteomics and genomics. Current Opinion in Chemical Biology. 2006;10:62-66.
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