Choosing the right DNA ladder

When performing gel electrophoresis, scientists include DNA ladders that contain DNA fragments of known sizes. The ladder enables scientists to estimate the size of the DNA bands in their experimental samples by comparing them to the closest fragment in the ladder. Using the correct ladder will help you estimate your DNA band sizes accurately and quickly. But there are so many different DNA ladders! How do you choose the best one for your experiment? 

Size range

The most important factor in choosing a DNA ladder is the expected size of the DNA bands in your experiment. You want to make sure that the range of the DNA ladder, from its smallest to its largest fragment, includes the expected size of the DNA fragments you are testing (Figure 1). For example, if you are expecting small DNA fragments of 50 base pairs (bp), then you need to make sure the DNA ladder you select contains bands at least that small. On the other hand, if one of your samples contains a large 3 kilobase (kb) DNA fragment, then you need to make sure the DNA ladder you select contains bands that large. 

Figure 1. It is essential that the range of your ladder encompasses your sample bands. In this example, the sample contains a large ~ 3000 bp band. To accurately estimate the size, you need to use a ladder whose upper range is large enough. Because the largest band in Ladder B shown above is 1200 bp, it is not an appropriate choice for this experiment.

Number of bands in a given size range 

The other major consideration is the number of bands in the ladder over a given size range. Using a ladder with more bands within a given range makes it easier to accurately estimate the size of the DNA fragments in your samples. However, the trade-off is that you need to run the gel longer to clearly interpret a ladder with more bands. If knowing the precise size of a band is important, choose a ladder with more bands and run your gel for a longer time. If time is limited, or a rough estimate of band size is sufficient, choose a ladder that doesn’t have as many bands. 

Figure 2. Ladders with more bands in a given size range offer greater accuracy but take longer to resolve. In this example, the experimental sample has two bands at ~450 bp and ~300 bp. Both the 20 bp Ladder and the Fast DNA Ladder 1 have appropriate ranges to be used with this sample. However, the 50 bp Ladder has more bands than the Fast DNA Ladder 1. The Fast DNA Ladder 1 is fully resolved after only 15 minutes (left), whereas the 50 bp Ladder is fully resolved after 15 minutes (right). Because the 50 bp Ladder has more bands, if the ladder is fully resolved it allows to you more accurately estimate the sizes of the sample bands. The tradeoff is that you need to run the gel longer.

So which ladder is right for your experiment?

In the end, scientists choose from a broad range of different ladders depending on the needs of each specific experiment. It also comes down to personal preference—it can help to experiment with a few different ladders and figure out which ones you like best.

Figure 3. DNA ladders available from miniPCR bio™

DNA Ladders available from miniPCR bio

DNA Ladder Size range No. of bands Load Ready™?
50 bp DNA Ladder 50 – 500 bp 8 Yes
100 bp DNA Ladder 100 – 1,000 bp 10 Yes
Fast DNA Ladder 1 100 – 1,200 bp 6 Yes
1 kb DNA Ladder 300 – 10,000 bp 13 Yes


– Contributed by miniPCR bio curriculum specialist Allison Nishitani, PhD

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