What Are YL578 YueLu Dyes?
YL578 (YueLu dyes) is a class of asymmetric rhodamine fluorescent probes engineered for high brightness, high photostability, and a large Stokes shift in super-resolution and confocal microscopy. Developed by the Zhang Xiaobing–Yuan Lin research group at Hunan University and published in Nature Communications (2022, 13, 2264), the YL578 scaffold introduces a 2-(2,2,2-trifluoroethyl)octahydropyrrolo[1,2-a]pyrazine motif to the rhodamine core. This modification simultaneously inhibits twisted intramolecular charge transfer (TICT) — which suppresses nonradiative decay and photobleaching — and generates vibronic structure in the excited state, enlarging the Stokes shift to 56 nm. The result: a quantum yield of 0.74 (vs 0.31 for Rhodamine B) and a brightness (ε × Φ) of 66,400 M⁻¹cm⁻¹, double that of Rhodamine B. An independent 2026 review in Chemical & Biomedical Imaging (ACS) selected YL578 as a landmark fluorinated dye alongside Stefan Hell's silicon rhodamines. J&K Scientific is the authorized supplier, offering seven derivatives for protein labeling, STED nanoscopy and biosensor development.
Why Are Conventional Rhodamine Probes Insufficient for STED?
Rhodamine B photobleaches within minutes under continuous 560 nm irradiation, and its 27 nm Stokes shift forces tight filter settings that cause spectral crosstalk in multicolor experiments. Under the high-powered 775 nm depletion laser required for STED, even state-of-the-art carbopyronine probes — 580CP-Halo, CPY-Halo, JF608-Halo — deliver only 2–3 usable frames before dropping below 50% of their initial brightness. This is far too few for 3D STED reconstruction, which requires sequential xzy-scanning across many frames. The core trade-off in rhodamine design is that the structural features producing high quantum yields (rigid, planar scaffolds) also limit Stokes shifts and concentrate excitation and emission in a narrow spectral window. YL578 breaks this trade-off through the trifluoroethyl-pyrrolo-piperazine substitution, which decouples brightness from spectral crowding by introducing vibronic fine structure without sacrificing quantum yield.
How Does YL578 Compare to 580CP, CPY and JF608 in STED?
YL578-Halo delivers 9 STED frames at above 50% initial intensity — 3× more than the current benchmarks — with a FWHM resolution of 57 ± 5 nm under standard conditions and 37 ± 4 nm when optimized. This was measured on vimentin-HaloTag in live U-2 OS cells using a 775 nm depletion laser, the same protocol used for all four probes.
| Probe | Frames >50% initial intensity | FWHM resolution |
|---|---|---|
| YL578-Halo | 9 | 57 ± 5 nm (std) / 37 ± 4 nm (opt) |
| 580CP-Halo | 2–3 | 116 ± 6 nm |
| CPY-Halo | 2–3 | 86 ± 9 nm |
| JF608-Halo | 2–3 | 83 ± 10 nm |
The 3× frame advantage is what makes 3D STED feasible. Sequential z-stack acquisition demands frame counts that conventional probes cannot provide without catastrophic photobleaching.
What Is the Stokes Shift Advantage of YL578?
YL578 has a Stokes shift of 56 nm (λex 578 nm → λem 634 nm), compared to 27 nm for Rhodamine B and 20–35 nm for most rhodamine-family STED probes. This large spectral separation reduces crosstalk between excitation and emission channels, simplifies filter design, and — critically for STED — allows YL578 to be paired with conventional short-Stokes-shift probes on a single 775 nm depletion laser. Three-color STED has been demonstrated by combining YL578-Halo with MaP555-actin, SiR-DNA, and GeR-tubulin, all sharing the same depletion laser. For multicolor STED users, this eliminates the need for multiple depletion lines and the alignment headaches that come with them.
How Bright Is YL578 Compared to Rhodamine B?
YL578 is 2× brighter than Rhodamine B by the standard ε × Φ metric, and 2.4× higher in quantum yield.
| Property | YL578 | Rhodamine B | Fold change |
|---|---|---|---|
| λex / λem | 578 / 634 nm | 554 / 576 nm | — |
| Stokes shift | 56 nm | 27 nm | 2.1× |
| Quantum yield (Φ) | 0.74 | 0.31 | 2.4× |
| Brightness (ε × Φ) | 66,400 M⁻¹cm⁻¹ | 32,500 M⁻¹cm⁻¹ | 2.0× |
| Photostability (confocal, 560 nm) | Negligible loss over 10 min | Bleached within 10 min | — |
The brightness advantage comes from the trifluoroethyl substitution inhibiting TICT-mediated nonradiative decay. Under confocal illumination at 560 nm, YL578 shows negligible signal loss over 10 minutes of continuous imaging — a duration that completely photobleaches Rhodamine B.
Can YL578 Be Used for Wash-Free Live-Cell Imaging?
Yes. YL578-Halo achieves a nuclei-to-cytosol fluorescence ratio (Fnuc/Fcyt) of 18 without any washing steps, meaning unbound dye contributes minimal background. The fluorogenic derivative YL578-CF3-Halo (10-Halo) goes further: it exhibits a 490-fold fluorescence turn-on upon HaloTag binding, with an Fnuc/Fcyt ratio of 106 — effectively background-free. This fluorogenic behavior arises from controlled spirocyclization equilibrium: in the unbound state, the dye adopts a nonfluorescent closed form; HaloTag binding shifts the equilibrium to the open, fluorescent form. For live-cell experiments where washing steps would perturb delicate dynamics, YL578-CF3-Halo provides protein-specific signal without washing, fixation, or genetic reporters beyond the HaloTag fusion.
What Applications Has YL578 Been Demonstrated In?
3D STED microscopy
YL578-Halo enabled 3D STED reconstruction of Tomm20 along entire mitochondria in U-2 OS cells. This experiment requires sufficient frame counts to survive z-stack acquisition — effectively impossible with conventional fluorophores.
Multicolor STED
Three-color STED was achieved using YL578-Halo (λex 561 nm, STED 775 nm) alongside MaP555-actin, SiR-DNA, and GeR-tubulin on a single depletion laser.
Organelle staining
YL578-Mito and YL578-Lyso provide fast, wash-free mitochondrial and lysosomal staining, confirmed by colocalization with MitoTracker Green and LysoTracker Green.
Two-photon microscopy
YL578 shows strong performance under two-photon excitation.
Single-molecule validation
A 2026 Chemical & Biomedical Imaging review independently placed YL578 among landmark fluorinated dyes for single-molecule brightness, in the same figure as the Hell group's silicon rhodamines (Yang et al., Chem. Biomed. Imaging 2026, 4, 510–526).
Which YL578 Derivative Should I Use?
J&K Scientific is the authorized supplier of YueLu Dyes, produced in collaboration with the Zhang Xiaobing–Yuan Lin group at Hunan University. The YL578 derivatives cover the major labeling strategies:
| Product | Purity | Cat. No. | Primary use |
|---|---|---|---|
| YL578 | 95% | 9332511 | Parent fluorophore; general labeling |
| YL578-NHS | 90% | 9332512 | NHS ester for amine-reactive protein conjugation |
| YL578-COOH | 90% | 9332513 | Carboxyl derivative; custom conjugation |
| YL578-CF3 | 90% | 9332514 | Trifluoromethyl variant; tuned spirocyclization |
| YL578-COOH-NHS | — | 9332515 | Dual-functional intermediate |
| YL578-Halo | — | 9332516 | HaloTag ligand for protein labeling (confocal / STED) |
| YL578-CF3-Halo | — | 9332517 | Fluorogenic HaloTag ligand; wash-free live-cell imaging |
Selection guide:
- Protein labeling for confocal: YL578-Halo (HaloTag targets) or YL578-NHS (direct amine conjugation).
- STED nanoscopy: YL578-Halo for maximum photostability and resolution. For wash-free live-cell STED, YL578-CF3-Halo (fluorogenic).
- Multicolor STED: Pair YL578-Halo (λex 561 nm, STED 775 nm) with SiR-DNA or GeR-tubulin on the same depletion laser.
- Biosensor development: YL578-COOH — the free carboxyl group accepts custom conjugation while preserving the YL scaffold's brightness and photostability.
How Is the YueLu Dye Platform Extensible Beyond Rhodamines?
The trifluoroethyl-pyrrolo-piperazine substitution that defines YL578 is not limited to rhodamines. The same motif has been demonstrated on rhodol, pyronin, coumarin, and Boranil scaffolds, producing brightness improvements of 2.5–8.1× and Stokes shifts up to 136 nm. This makes the YueLu design a general-purpose strategy for upgrading any dialkylamino-containing fluorophore. Researchers working with custom scaffolds can apply the same structural logic to their own dye families — and J&K offers custom synthesis to implement it.
References
- Jiang G, Ren TB, D'Este E, et al. A synergistic strategy to develop photostable and bright dyes with long Stokes shift for nanoscopy. Nat. Commun. 2022, 13, 2264. DOI: 10.1038/s41467-022-29547-3
- Yang L, Zheng Y, Ye Z, Xiao Y. Single-Molecule Fluorescence Defines a New Dye Chemistry. Chem. Biomed. Imaging 2026, 4, 510–526. DOI: 10.1021/cbmi.5c00148
Technical Support
Standard catalog quantities ship from J&K Scientific's global network. Bulk and custom synthesis are available for scale-up or bespoke derivatives. Certificates of Analysis (COA) are provided on request for each lot.
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