EdvoTech Tips: How to choose the correct DNA ladder

Gel electrophoresis is a powerful technique to separate biomolecules for further analysis. We’ve discussed agarose gel electrophoresis, for analyzing DNA or RNA, and polyacrylamide gel electrophoresis (PAGE), for analyzing proteins, previously on this blog. However, we often get questions about how to select the correct standard markers to run alongside our experimental samples. Today, we will discuss the different DNA and protein markers available and how to choose the perfect pairing for your experiment.

Edvotek’s DNA Standard Marker and the sizes of the seven DNA bands.

Standard markers, or “ladders”, are fundamental components of most electrophoresis experiments. Occasionally, gel results can be analyzed directly by comparing the sizes of bands across different lanes containing different samples. This works well for optimized experiments – if we already know what to expect then it can be easy to tell if the correct bands are present or missing. However, in cases where we need to determine the precise length of the fragments, we will use a standard marker. Each standard marker contains a mixture of DNA or protein fragments of precisely a determined size. Markers can contain anywhere from 4 or 5 fragments, in a simple mixture, to complex ladders containing 40 or more fragments!

Importantly, different standard markers are designed to be most useful across a pre-selected range of fragment sizes. Our most commonly used DNA marker, the Edvotek DNA Standard Marker, has seven different DNA fragments between 630 bp and 6751 bp. Therefore, it can help give a reasonable estimate of DNA sizes between those extremes. However, if your band is smaller than 630 bp, or larger than 6751 bp, this marker will provide far less accurate estimates.

Fortunately, Edvotek also provides additional standard markers. Our 100 bp ladder includes 40 DNA fragments from 100 bp – 4000 bp in 10 bp fragments. This marker is incredibly useful if you need to measure small DNA bands and is incredibly accurate. However, many of the bands start to become difficult to distinguish at the higher end of the ladder, making it a poor choice for larger fragments. The EdvoQuick™ DNA Ladder is designed to work with many of our PCR experiments, providing a convenient range between 200 bp – 2640 bp. This range gives excellent separation between the bands and makes creating a standard curve quick and easy for students.

Edvotek’s 100 bp Ladder and EdvoQuick™ DNA Ladders.

Protein markers are designed to identify the relative size of denatured proteins in an SDS-PAGE gel. In this way, they behave similarly to the DNA markers previously discussed. Edvotek’s Prestained Lyophilized Protein Gel Markers include six protein bands between 14,000 Da and 94,000 Da. Additionally, these proteins are prestained blue, making them easy to identify while the gel is running!

One final note regarding DNA and Protein markers – almost all Edvotek experiments include a standard marker that is designed to work with that specific experiment. In these cases, we always recommend using the provided marker, rather than selecting something different! Finally, it’s important to note that standard markers are most useful for determining the exact size of your unknown fragments once you have created a standard curve to compare fragment size and distance traveled in the gel. Our blog post on Sizing DNA Fragments contains a wealth of information on how to create a standard curve and use it to precisely measure your DNA or protein bands.

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