SiR Dye 1: Properties, Applications & FAQs

SiR dye 1 is a silicon-rhodamine–based far-red fluorescent dye designed for live-cell labeling and super-resolution fluorescence microscopy applications.

Product Name

SiR Dye 1

SKU / Catalog Number

S1451912

Dye Class

Silicon-rhodamine (SiR) far-red fluorescent dye

Primary Application

Live-cell fluorescence and super-resolution microscopy (e.g., STED, SIM, STORM)

Key Advantage

Cell-permeant, low background due to environment-sensitive fluorogenicity

Reference / Cross-Reference

MCE-TJY: HY-D1103

What Is SiR Dye 1?

SiR Dye 1 (catalog number S1451912) is a member of the silicon-rhodamine (SiR) family of fluorescent dyes. Silicon-rhodamine dyes are derived from the classic rhodamine scaffold by replacing the oxygen bridging atom with silicon, which red-shifts excitation and emission into the far-red spectral region (typically ~650 nm excitation / ~670 nm emission). This far-red profile minimizes autofluorescence from biological samples, reduces phototoxicity, and is compatible with standard far-red laser lines (e.g., 647 nm or 660 nm) available on most confocal and STED microscope systems.

A hallmark property of SiR dyes is their cell permeability and fluorogenicity: the dye exists in equilibrium between a non-fluorescent, cell-permeable spirocyclic (closed) form and a fluorescent, open zwitterionic form. Binding to a protein target or a hydrophobic environment shifts the equilibrium toward the fluorescent open form, enabling low-background, wash-free or minimal-wash labeling in live cells.

Key Properties and Spectral Characteristics

Silicon-rhodamine dyes, including SiR Dye 1, generally exhibit the following physicochemical and photophysical properties relevant to research use:

• Excitation maximum: approximately 645–652 nm (far-red region; compatible with 647 nm laser lines)
• Emission maximum: approximately 661–674 nm
• Cell permeability: high; the spirocyclic closed form passively diffuses across cell membranes
• Photostability: SiR dyes are noted for high photostability relative to many green or yellow fluorescent probes, making them suitable for time-lapse and STED imaging
• Fluorogenicity: significant fluorescence enhancement upon target engagement, enabling reduced background without extensive washing steps
• Biocompatibility: suitable for live-cell experiments at appropriate working concentrations

Note: Specific molar extinction coefficients, quantum yields, and precise spectral maxima for SiR Dye 1 (S1451912) should be confirmed in the product datasheet. Values cited above are representative of the SiR dye class.

Applications in Biological Research

SiR Dye 1 is used across a range of fluorescence microscopy and cell biology applications, leveraging its far-red spectral window, cell permeability, and fluorogenicity:

• Super-resolution microscopy: SiR dyes are well-established probes for STED (stimulated emission depletion) microscopy, enabling nanoscale visualization of cellular structures in living cells. They are also compatible with structured illumination microscopy (SIM) and single-molecule localization methods (e.g., STORM/PALM).
• Live-cell labeling of specific organelles or proteins: When conjugated to appropriate targeting ligands (e.g., HaloTag ligands, SNAP-tag substrates, or organelle-targeting moieties), SiR dyes allow specific, low-background imaging of targets such as actin, tubulin, lysosomes, or DNA in living cells.
• Multicolor imaging: The far-red emission of SiR Dye 1 is spectrally distinct from common green (e.g., GFP, Alexa Fluor 488) and red (e.g., Cy3, Alexa Fluor 555) fluorophores, enabling multicolor co-labeling experiments with minimal spectral crosstalk.
• Time-lapse and dynamic studies: High photostability and live-cell compatibility make SiR Dye 1 suitable for extended imaging sessions tracking dynamic cellular processes.

Handling, Storage, and Safety Guidelines

Proper handling and storage of SiR Dye 1 (S1451912) are essential to maintain reagent integrity and ensure reproducible experimental results:

• Storage: Store the compound as indicated on the product datasheet and certificate of analysis (typically at −20 °C, protected from light and moisture). Aliquot stock solutions to avoid repeated freeze-thaw cycles.
• Solvent: SiR dyes are commonly dissolved in anhydrous DMSO to prepare stock solutions. Confirm the recommended solvent and stock concentration in the product datasheet.
• Light sensitivity: All fluorescent dyes should be protected from prolonged exposure to light during preparation and storage to prevent photobleaching of the stock.
• Working concentrations: Optimal working concentrations for live-cell imaging should be determined empirically for each cell type and application. Excessive dye concentrations may increase background or cytotoxicity.
• Safety: Handle in accordance with standard laboratory safety practices. Consult the Safety Data Sheet (SDS) for SiR Dye 1 (S1451912) available from Aladdin Scientific for specific hazard information.

Note: Specific storage conditions, recommended solvents, and concentration ranges for S1451912 should be verified against the current product datasheet.

Ordering Information

SiR Dye 1 is available from Aladdin Scientific under catalog number S1451912. For current pricing, available pack sizes, and stock availability, please visit the Aladdin Scientific website or contact your local Aladdin Scientific sales representative. Bulk quantities and custom packaging may be available upon request.

Cross-reference: This product is also referenced as HY-D1103 in the MCE-TJY catalog, which may assist researchers sourcing the compound from multiple suppliers or cross-referencing literature protocols.

Frequently asked questions

What is SiR Dye 1 and how does it differ from classical rhodamine dyes?

SiR Dye 1 is a silicon-rhodamine fluorescent dye in which the oxygen atom of the xanthene core is replaced by silicon, red-shifting the excitation and emission spectra into the far-red region (~650/670 nm). Unlike classical rhodamine dyes that emit in the green or yellow-green range and can suffer from high cellular autofluorescence, SiR Dye 1 operates in a spectral window with minimal biological background. Additionally, SiR dyes are fluorogenic—they exist in a non-fluorescent spirocyclic form that opens and becomes highly fluorescent upon target binding, enabling low-background imaging without extensive washing.

Is SiR Dye 1 suitable for STED super-resolution microscopy?

Yes. Silicon-rhodamine dyes, including SiR Dye 1, are among the most widely used probes for STED microscopy in living cells, owing to their far-red excitation and emission that aligns with standard STED depletion lasers (typically 775 nm), high photostability, and live-cell compatibility. Their fluorogenic character also helps keep background low, which is important for achieving high contrast at nanoscale resolution. SiR Dye 1 may also be compatible with other super-resolution modalities such as SIM and single-molecule localization microscopy.

What solvents and storage conditions are recommended for SiR Dye 1 (S1451912)?

SiR dyes are typically dissolved in anhydrous DMSO to prepare stock solutions, as they may have limited aqueous solubility in the absence of a carrier solvent. Stock solutions and dry material are generally stored at −20 °C, protected from light and moisture. To maintain stock solution integrity, it is advisable to prepare single-use aliquots to minimize freeze-thaw cycles. Please refer to the official product datasheet and certificate of analysis for S1451912 available from Aladdin Scientific for confirmed storage conditions and solubility data specific to this product.

Can SiR Dye 1 be used for multicolor fluorescence imaging alongside GFP or other common fluorophores?

Yes. The far-red emission of SiR Dye 1 (approximately 670 nm) is well-separated from the emission of common fluorophores such as GFP (~510 nm), YFP (~530 nm), Alexa Fluor 488, mCherry (~610 nm), and Cy3 (~570 nm), making it an excellent choice for multicolor co-labeling experiments with minimal spectral crosstalk. Researchers should verify filter set compatibility on their specific microscope system and confirm spectral overlap calculations when combining with very red-shifted dyes such as Cy5 or Alexa Fluor 647.

How do I determine the optimal working concentration of SiR Dye 1 for live-cell imaging?

The optimal working concentration of SiR Dye 1 must be determined empirically, as it depends on the specific cell type, target abundance, labeling strategy (e.g., HaloTag, SNAP-tag, or direct conjugate), and imaging modality. A typical starting range for SiR-class dyes in live-cell experiments is in the sub-micromolar range (e.g., 100 nM to 1 µM), but concentrations should be titrated to balance specific signal, background, and cytotoxicity. Always include appropriate negative controls (unlabeled cells or cells lacking the target protein) to assess background fluorescence at the chosen concentration.

References

1. Lukinavicius G, et al. A near-infrared fluorophore for live-cell super-resolution microscopy of cellular proteins. Nature Chemistry, 2013.
2. Aladdin Scientific product datasheet: SiR Dye 1, catalog number S1451912.
3. MCE-TJY product reference: HY-D1103 (SiR Dye 1 cross-reference).

Products are supplied for research and development use only. Not for use in humans, animals, diagnosis, or therapy.