A molecular weight size marker is used to identify the approximate size of a molecule run on a gel, using the principle that molecular weight is inversely proportional to migration rate through a gel matrix. Therefore when used in gel electrophoresis, markers effectively provide a logarithmic scale by which to estimate the size of the other fragments (providing the fragment sizes of the marker are known). These markers can be composed either of different proteins of known size, or nucleic acids of different sizes. Markers are loaded in lanes adjacent to samples lanes before the commencement of the run.
Protein or DNA markers with pre-determined fragment sizes and concentrations are commercially available. These can be run in either agarose or polyacrylamide gels.
A commonly used DNA molecular weight marker is the genome of the Lambda phage following digestion using the restriction enzyme HindIII. This produces an array of fragments ranging from 125 to 23,125 base pairs. (Actual fragment sizes are: 23130, 9416, 6557, 4361, 2322, 2027, 564, and 125 bp.)
Commercial DNA markers are usually supplied with the loading dye included in a mix, due to the difficulty of visualizing DNA during electrophoresis. Commonly used are the dye pairs xylene cyanol and bromophenol blue; these migrate at approximately the same rate as DNA fragments 4000 and 500 base pairs in length respectively in a 1% agarose gel. Cresol red and orange G can also be used for this purpose; they migrate at approximately the same rate as DNA fragments 125 and 50 base pairs respectively under the same conditions. These dyes often exhibit different colours depending on the pH of the buffer used during the run.
Protein markers can be prestained or unstained prior to loading. Commercially available prestained markers are useful since they are clearly visible as the run progresses. These are made by conjugating the proteins to colored dyes. Unstained dyes are stained during the normal visualization process of the gel, commonly through the use of coomassie blue or Flamingo.