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mCherry is a monomeric red fluorescent protein derived from Discosoma sp. DsRed. FPbase lists it as excited at 587 nm and emitting at 610 nm, a fast-maturing monomer of 26.7 kDa, which is why it is widely used as a genetic fusion tag in the red channel.
Short answer
mCherry is a genetically encoded red fluorophore: ex 587 nm, em 610 nm, extinction coefficient 72,000 M-1cm-1, quantum yield 0.22, maturation half-time about 15 minutes, monomeric. It is dimmer than tdTomato or mScarlet but matures faster than either and, being a true monomer, is the usual choice when a fusion partner must not be forced to dimerise.
Definition and scope: what is mCherry and what is red fluorescent protein?
A red fluorescent protein (RFP) is a genetically encoded protein that fluoresces in the red part of the spectrum, so it can be expressed in cells or organisms without adding a dye. Wild-type yellow-to-red fluorescent proteins are obligate tetramers and are often disruptive or toxic when fused to a protein of interest; this was the motivation for engineering monomeric variants (Shaner et al. 2004, Nature Biotechnology 22:1567-1572). mCherry came from that work. FPbase records it as derived from mRFP1.5, with mutations numbered against DsRed.
How mCherry is used at the bench
Because it is a monomer, mCherry is commonly fused to a protein of interest to follow its location in cells, or expressed alone as a transfection or transduction marker. Related workflows on this site include lentiviral transduction, Cre-lox reporter and driver lines and bimolecular fluorescence complementation, all of which depend on choosing a fluorescent protein whose spectrum and oligomeric state suit the experiment.
mCherry excitation, emission and wavelength
FPbase gives excitation maximum 587 nm and emission maximum 610 nm. Those are peak values; actual signal depends on the excitation source and emission filter in your instrument, so match the red channel of your microscope or cytometer against the spectrum rather than assuming a specific filter set.
mCherry sequence, structure, plasmids and size
Sequence and structure are best taken from curated records rather than copied from a web page: the FPbase protein page, the UniProt/UniParc entry, the crystal structure RCSB PDB 6YLM, and Addgene plasmid records such as plasmid #176016. Protein mass is 26.7 kDa per FPbase. Always confirm the exact sequence of your own construct, including linker and any codon optimisation, from its plasmid map.
mCherry vs tdTomato vs mScarlet
All values are the FPbase entries read on 2026-11-07. Photostability figures are deliberately left out of the table because the underlying measurements used different conditions and are not comparable across rows.
| Property | mCherry | tdTomato | mScarlet |
|---|---|---|---|
| Excitation / emission (nm) | 587 / 610 | 554 / 581 | 569 / 594 |
| Extinction coefficient (M-1cm-1) | 72,000 | 138,000 | 100,000 |
| Quantum yield | 0.22 | 0.69 | 0.70 |
| Brightness (EC x QY / 1000) | 15.84 | 95.22 | 70.0 |
| Maturation half-time | 15 min | 60 min | 174 min |
| pKa | 4.5 | 4.7 | 5.3 |
| Oligomeric state | Monomer | Tandem dimer | Monomer |
| Mass | 26.7 kDa | 54.2 kDa | 26.4 kDa |
The tdTomato extinction coefficient and mass describe the tandem dimer, which carries two chromophores in one 54.2 kDa polypeptide; that is why its brightness figure is high and also why it is about twice the size of the other two as a fusion tag. mScarlet is described in Bindels et al. 2016, Nature Methods 14(1):53-56.
What fluorophore is tdTomato?
tdTomato is an orange-red fluorescent protein, derived from dTomato, that is a tandem dimer: two copies in one polypeptide. FPbase lists it at ex 554 / em 581 nm.
What is the difference between mCherry and mScarlet?
Per the FPbase values above, mScarlet is roughly four times brighter by the EC x QY measure (70.0 vs 15.84) and has a higher pKa (5.3 vs 4.5), but it matures much more slowly (174 vs 15 minutes). Both are monomers of about 26 kDa. FPbase records mScarlet as derived from mRed7Q1S1BM with F84Y, V176A and E199K substitutions.
A choice checklist tied to the numbers
- Is the tag fused to a protein that must not oligomerise? Prefer a monomer (mCherry or mScarlet); tdTomato is a tandem dimer of 54.2 kDa.
- Do you need a signal soon after expression starts? Maturation half-time is 15 min for mCherry, 60 min for tdTomato and 174 min for mScarlet, so a fast-maturing tag reports earlier.
- Is the compartment acidic? A lower pKa (mCherry 4.5) means fluorescence holds to a lower pH.
- Is the target weakly expressed? Brightness (EC x QY) favours tdTomato and mScarlet over mCherry.
- Which spectrum fits your detector? Compare emission maxima (581, 594 and 610 nm) against your filters and any other fluorophores in the experiment.
What is the fluorescence half-life of mCherry?
It depends on which half-life is meant. The maturation half-time, how long the chromophore takes to become fluorescent after the protein folds, is 15 minutes for mCherry (FPbase). The photobleaching half-time listed on FPbase is 68 seconds, measured under arc-lamp illumination (Shu et al. 2006). Photobleaching times depend on illumination intensity, optics and sample, so a number from one paper cannot be transferred to another microscope.
Common misunderstandings
- “mCherry and RFP are the same thing.” RFP is a class of proteins; mCherry is one specific engineered monomer within it.
- “Brighter always means better.” The tandem-dimer size of tdTomato and the slow maturation of mScarlet are real costs for some fusion experiments.
- “A published photostability number applies to my microscope.” It applies only to the conditions of that measurement.
- “The excitation peak is the wavelength to use.” The peak is a property of the protein; the usable range depends on the light source and filters.
Frequently asked questions
What is the fluorescence half-life of mCherry?
Maturation half-time 15 minutes; photobleaching half-time 68 seconds under the arc-lamp conditions FPbase cites.
What fluorophore is tdTomato?
A tandem-dimer orange-red fluorescent protein derived from dTomato (ex 554 / em 581 nm, 54.2 kDa).
What is red fluorescent protein?
A genetically encoded protein that fluoresces in the red part of the spectrum; mCherry, tdTomato and mScarlet are examples.
What is the difference between mCherry and mScarlet?
mScarlet is brighter and matures far more slowly; mCherry matures fast and is dimmer. Both are monomers.
Sources
- FPbase, mCherry, tdTomato and mScarlet protein pages (fpbase.org/protein/mcherry/, /tdtomato/, /mscarlet/), read 2026-11-07.
- Shaner NC et al. (2004). Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22(12):1567-1572. doi:10.1038/nbt1037.
- Bindels DS et al. (2016). mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat Methods 14(1):53-56. doi:10.1038/nmeth.4074.
- RCSB PDB entry 6YLM; Addgene plasmid #176016; UniProt/UniParc record UPI000046F63B.
