DNA ladder. Molecular size marker. Standard DNA fragments. You may have heard these terms before, but been confused as to what they are. The great thing is that these terms all refer to the same reagent, which makes it easy to explain what they do and why they are essential in the biotechnology laboratory.
DNA ladders are used in agarose gel electrophoresis. This is a biotechnology technique that uses electricity and a porous gel matrix to separate mixtures of DNA molecules into discrete zones, or bands, based on its size. As the length of a DNA molecule increases, the distance it can travel decreases. So we find larger molecules at the top of the gel, and smaller molecules at the bottom. (For a more in-depth discussion of electrophoresis, see our previous blog post here.)
But how do you know the size of your DNA fragments after electrophoresis? You use the DNA ladder! The DNA ladder allows us to determine the size of our experimental DNA fragments after they are separated by electrophoresis. A DNA ladder contains a series of DNA fragments of known molecular weight that we compare to our experimental samples. They are run on the same gel as our experimental bands so that a direct comparison can be made. (We cover this in detail in our previous blog post, Biotech Basics: Sizing DNA Fragments.)
We get a lot of questions on the DNA ladder and how to use it, so we decided to create a short video as an explainer! In this video, we will discuss the DNA ladder — why we use them, how we use them, and how not to use them!
We can use the DNA ladder to create a standard curve to more accurately calculate the molecular weight of the fragments. If you want to make the measurements and plot the results using technology, we have a quick guide to walk you through the process:
We have also designed our dye electrophoresis to have “molecular weight markers” so that students can analyze these experiments the same way they would analyze DNA electrophoresis experiments. The first lane is a “molecular weight standard,” which is a series of samples of “known weight” which can be used to estimate the size of our unknowns. The other lanes are our experimental samples which will be analyzed by the students. They each represent “DNA fragments” of different molecular weights. They’re not necessarily supposed to match up with the standard; rather, they are to be compared to the standard for molecular weight determination.
Like with DNA, we would refer back to the standard ladder (lane 1) to determine the size of each of the bands in our experimental samples (lanes 2-6). For reference, we chose dyes that we could plot to create a standard curve, much like with DNA fragments. So, with these simple dye experiments, you can experience everything a DNA ladder can do!