Molecular Weight Markers

Molecular weight markers, or ladders, are a set of standards that are used for determining the approximate size of a protein or a nucleic acid fragment run on an electrophoresis gel. These standards contain pre-determined fragment (or protein) sizes and concentrations. When the markers are loaded in adjacent lanes to samples, sample fragment or protein size and concentration estimations are easily determined.

DNA ladders contain DNA fragments of varying sizes. These ladders are sometimes made from restriction enzyme digestion of plasmid DNA with a known sequence. Often, DNA molecular weight markers and ladders come in two formats: pre-mixed with loading dye, or with the loading dye separate.

DNA Step Ladders contain DNA bands of defined sizes and equal intensity with fragment lengths at defined increments. For example, step ladder DNA fragments could be in increments of 100bp from 100bp all the way up to 4000bp. Step Ladders are not intended for concentration estimations. They are great when more specific fragment length verification is desired than can be inferred from a typical ladder with larger, or less consistent increments.

Similarly to DNA ladders, RNA ladders contain RNA fragments of varying sizes. To determine fragment sizes, RNA is typically run in a denaturing electrophoresis gel. Because RNA migrates faster than DNA through electrophoresis gels, the appropriate nucleic acid ladder (RNA vs DNA) should be used.

Protein molecular weight markers consist of proteins whose weight is measured in kDa. They are most commonly used in SDS-PAGE and western blotting. Protein molecular weight markers are sometimes used as a control when verifying protein migration and observing transfer efficiency.