What is a Molecular Weight Marker?

A molecular weight marker is a molecule used to provide an estimate of the size of molecules subjected to gel electrophoresis. This is a technique in which DNA, RNA, or proteins are separated by size, using an electrical current on a gel. This term should not be confused with molecular markers in genetics — areas in which an organism’s DNA differs from the rest of the population and can be identified with a DNA probe.

Protein molecular weight markers are commonly used when proteins are separated by gel electrophoresis. The molecular weight marker is a group of proteins of known molecular weight, which are generally provided by biotechnology companies in a particular size range. One chooses the size range based on the samples being studied. The molecular weight markers are loaded together and separate out during the run. By measuring the distance traveled by the markers and the protein of interest, one can determine the size of the experimental protein.

Different types of markers can be visualized in different manners. Some of the molecular markers are unlabeled and are stained in the gel with the rest of the proteins. They are not visible until the whole gel is stained. Other types of protein molecular markers come pre-stained with colors, and each type of protein is a different color. The separation is visible as the gel is running.

One advantage of a pre-stained molecular weight marker is for Western blots. This is a technique in which the proteins are transferred to a membrane and then stained with antibodies to detect a particular protein. Having colored markers helps determine if the transfer of the proteins is complete before one proceeds with the rest of the procedure.

Molecular weight markers are commonly used for analyzing DNA on gels. Frequently, DNA molecular markers are made from the bacterial virus lambda. Restriction enzymes are made by bacteria to digest the DNA of invading organisms, and the restriction enzyme HindIII is often used to degrade the lambda DNA. It produces a series of differently-sized, reproducible fragments known as a DNA ladder. By comparing the distance run by the standards on a logarithmic scale, one can determine the size of the DNA fragments being analyzed.

This DNA molecular weight marker can be used to analyze the size of DNA produced during the isolation of genes, and in genetic engineering experiments. It can also be used during the polymerase chain reaction(PCR), in which small amounts of DNA or RNA are amplified to produce large amounts of product. PCR techniques are commonly associated with paternity testing and forensic science, but they are also very common in medical and basic biological research. Special molecular weight markers are available for smaller products generated from some types of PCR or small RNA molecules.