How reliable are the native PAGE ladders

Native PAGE (Polyacrylamide Gel Electrophoresis) ladders are often used as molecular weight standards to estimate the sizes of proteins or nucleic acids being analyzed in the gel. The reliability of native PAGE ladders depends on several factors:

1. Purity and Composition:

   • The reliability of native PAGE ladders depends on the purity and composition of the molecular weight markers used. Commercially available markers are typically well-characterized and provide reliable size estimates for proteins or nucleic acids.

2. Accuracy of Molecular Weight Determination:

   • The accuracy of the molecular weights assigned to the ladder bands is crucial. These values are typically determined through various methods such as mass spectrometry or gel filtration chromatography.
   • If the molecular weights assigned to the ladder bands are accurate, then the ladder can reliably estimate the sizes of unknown samples based on their migration distances relative to the ladder bands.

3. Consistency and Reproducibility:

   • The consistency and reproducibility of the ladder bands are essential for reliable size estimation. Commercially available native PAGE ladders are usually well-characterized and provide consistent results from batch to batch.
   • However, variations in gel preparation, electrophoresis conditions, and handling can impact the migration distances of the ladder bands and should be minimized to ensure reliability.

4. Range and Resolution:

   • The range and resolution of the ladder bands should match the sizes of the samples being analyzed. Some ladders may have a limited range or resolution, which could affect the accuracy of size estimation for larger or smaller proteins or nucleic acids.

5. Cross-Contamination:

   • Care should be taken to prevent cross-contamination between ladder bands during gel loading. Cross-contamination could lead to inaccurate size estimation if bands from neighboring lanes merge during electrophoresis.

In summary, native PAGE ladders are generally reliable for estimating the sizes of proteins or nucleic acids being analyzed, provided that they are well-characterized, accurately assigned with molecular weights, consistent, and handled carefully to minimize artifacts. However, it is essential to validate the reliability of ladder bands through appropriate controls and validation experiments, especially when using homemade ladders or when analyzing samples with unusual properties.