Written and maintained by CASRAI Editorial Board
Last updated
Short answer: Takara Bio’s protein ladders for SDS-PAGE and western blotting are the CLEARLY Protein Ladder family: an unstained ladder (Code No. 3453A, 10 to 250 kDa) intended as a precise size standard, and a pre-stained ladder (Code No. 3454A, 10 to 210 kDa) intended for monitoring migration and transfer, not for exact molecular-weight calculation. Both are research-use-only products (Takara datasheets v201901, read 2026-11-08).
This page is for researchers and lab staff deciding which ladder lane belongs on a gel. It is general product information and not a protocol or advice for any individual experiment.
Definition and scope
A protein ladder (also called a protein marker or molecular-weight marker) is a mixture of proteins of known size that is run in a lane beside the samples, so that bands in the sample lanes can be compared with it. The general concept is explained in our protein marker guide and the gel technique in SDS-PAGE protein gel electrophoresis.
The datasheets describe each Takara ladder as a mixture of 11 recombinant, highly purified proteins. The unstained ladder is resolved into identifiable bands from 10 to 250 kDa when run by SDS-PAGE and stained with Coomassie Brilliant Blue R-250 (see Coomassie blue). The stained ladder is resolved into visible bands from 10 to 210 kDa without a staining step.
How the ladders are used in practice
Both datasheets give the same handling pattern. Each ladder is pre-mixed with loading buffer and ready to load; pre-heating is not required, and the vial is thawed at room temperature and checked to be completely dissolved. The standard loading volume is 5 µl per minigel lane for the unstained ladder and 10 µl per lane for the stained ladder. A 500 µl vial is therefore sufficient for 100 lanes (unstained) or 50 lanes (stained).
For the unstained ladder, the datasheet’s application example follows electrophoresis with Coomassie Brilliant Blue R-250 staining. For the stained ladder, the datasheet states it is useful for monitoring protein migration during SDS-PAGE and for verifying transfer efficiency at western blotting; the general workflow is described in western blot protocol basics.
Reference bands
In each ladder, two bands carry four times the mass of the other bands and serve as reference indicators: 30 and 80 kDa in the unstained ladder, and 30 and 70 kDa in the stained ladder. This lets a reader orient on the gel without counting every band.
Gel percentage
Both datasheets recommend a 5 to 20% gradient SDS-polyacrylamide gel. They caution that if the gel concentration is too low, low-molecular-weight bands migrate faster than the bromophenol blue (BPB) tracking dye, and if it is too high, high-molecular-weight bands may separate poorly or fail to migrate.
Stained versus unstained: a datasheet cross-walk
Every value below is taken from the two Takara datasheets (3453A and 3454A, both v201901, 500 µl).
| Feature | CLEARLY Protein Ladder (Unstained), 3453A | CLEARLY Stained Protein Ladder, 3454A |
|---|---|---|
| Composition | 11 recombinant, highly purified proteins | 11 pre-stained recombinant, highly purified proteins |
| Band range | 10 to 250 kDa (after Coomassie R-250 staining) | 10 to 210 kDa (visible without staining) |
| Reference (four-fold mass) bands | 30 and 80 kDa | 30 and 70 kDa |
| Stated purpose | Precise size standard to calculate the molecular weight of a protein of interest | Monitoring migration in SDS-PAGE and verifying transfer efficiency at western blotting |
| Use as a precise size standard | Yes, as intended | Not recommended |
| Loading per minigel lane | 5 µl | 10 µl |
| Lanes per 500 µl | 100 | 50 |
| Pre-heating | Not required | Not required |
| Recommended gel | 5 to 20% gradient | 5 to 20% gradient |
Where it matters for labs
The practical consequence of the table is that the two ladders answer different questions. If a figure or report needs an estimated molecular weight for a band, the datasheet points to the unstained ladder. If the question is whether the run progressed and whether proteins moved onto the membrane, the datasheet points to the stained ladder. Because the stained ladder’s size-standard role is explicitly disclaimed, a lab that wants both migration monitoring and a calibrated size estimate has to read the two datasheets as describing two separate jobs.
Storage and handling are the same for both. The datasheets give storage at -20 °C, stability for 6 months when kept at 4 °C, and stability after 50 freeze-thaw cycles. They also state that the products are for research use only and are not intended for therapeutic or diagnostic procedures in humans or animals, and that Takara products may not be resold or transferred or used to manufacture commercial products without written approval from Takara Bio Inc.
Common misunderstandings
“A pre-stained ladder can be used for exact molecular weights.”
Takara’s datasheet says otherwise. It explains that covalent coupling of the dye to the proteins affects their electrophoretic behavior relative to unstained proteins, so the stained ladder is not recommended as a precise size standard.
“The ladder range is the same as the gel range.”
The ladders span 10 to 250 kDa and 10 to 210 kDa respectively, but the datasheets note that the gel percentage still determines how well the bands separate; a gel that is too high in percentage may keep high-molecular-weight bands from migrating.
“Every ladder behaves like the Bio-Rad Precision Plus or Kaleidoscope ladders.”
Each manufacturer defines its own band set, reference bands and intended use in its own datasheet. For the Bio-Rad ladder, see our separate Precision Plus protein ladder guide rather than assuming equivalence.
Frequently asked questions
Which Takara protein ladder is for western blot transfer checks?
The CLEARLY Stained Protein Ladder (3454A). Its datasheet states it is useful for monitoring protein migration during SDS-PAGE and verifying transfer efficiency at western blotting.
Which Takara ladder should be used to calculate molecular weight?
The CLEARLY Protein Ladder (Unstained, 3453A), which the datasheet describes as intended as a precise size standard for calculating the molecular weight of a protein of interest.
Is it a western blot ladder or an SDS-PAGE ladder?
Both terms describe the same kind of reagent, run in an SDS-PAGE lane. Takara’s unstained ladder is documented for SDS-PAGE with Coomassie staining, and the stained ladder for SDS-PAGE and western blotting.
Does the ladder need heating before loading?
No. Both datasheets say the ladder is pre-mixed with loading buffer, ready to load, and that pre-heating is not required.
Can it be used for diagnostic work?
No. Both datasheets state the products are for research use only and not intended for therapeutic or diagnostic procedures for humans or animals.
Sources
- Takara Bio Inc. datasheet, CLEARLY Protein Ladder (Unstained), Code No. 3453A, v201901; read 2026-11-08.
- Takara Bio Inc. datasheet, CLEARLY Stained Protein Ladder, Code No. 3454A, v201901; read 2026-11-08.
- Takara Bio, Protein molecular weight markers product category; read 2026-11-08.
