What is the purpose of a “ladder” in molecular biology?

Answer: A “ladder” serves as both a control and a tool with which to measure the weight of macromolecules like DNA in gel electrophoresis.

DNA ladder gel electrophoresis

One tool that is frequently used in molecular biology is called gel electrophoresis. Using gel electrophoresis, large molecules such as DNA, RNA, or proteins can be separated out from one another by running on an agarose gel, driven by electrical current. Generally, it is used for DNA. Ladders are sometimes called also called “molecular weight size markers.”

Normally, a small sample of the genetic material is loaded into a well, a small indentation built into the top of the gel. It is important to load either a ladder or a marker into one of the wells.

A ladder is a solution that contains a series of well-defined DNA fragments of particular lengths. Some ladders may contain DNA fragments of sizes such as 100 base pairs all the way up to 10,000 base pairs (10 kbp). The appropriate ladder to use depends on the molecular weight of the target you are interested in studying. You can use a ladder to identify the approximate number of base pairs in the band that you are interested in.

Besides measuring base pair length, ladders serve another purpose. If the gels were not poured correctly, there may be differences in the thickness of the gel across the width of the gel. This may happen in larger gels. If this is the case, the DNA may not electrophorese at the same rates. Running a ladder on both ends of the gels ensure that a good comparison can be made across the entire width of the gel.