Molecular-weight size marker

Molecular-weight size markers, also known as DNA ladders, protein ladders, or molecular rulers, are essential tools used in molecular biology and biochemistry for estimating the size of DNA, RNA, or protein molecules during electrophoresis. These markers consist of a set of standards, where each component of the set is a molecule of known size. They are run alongside experimental samples on gel electrophoresis gels, allowing researchers to compare the migration distances of their samples with those of the markers and thus estimate their sizes.

Overview

Molecular-weight size markers are crucial for the analysis of nucleic acids and proteins in various applications, including DNA sequencing, PCR, restriction enzyme digestion, and Western blotting. They are commercially available in a range of sizes to accommodate different research needs, from small oligonucleotides to large genomic DNA fragments or small peptides to large proteins.

Types of Molecular-weight Size Markers

There are two main types of molecular-weight size markers:

DNA Ladders

DNA ladders are composed of linear DNA fragments of known lengths, typically generated by either restriction enzyme digestion of plasmids or by synthesizing specific lengths of DNA. They are used in gel electrophoresis for the sizing of DNA fragments. DNA ladders are available for a wide range of fragment sizes, from a few base pairs up to several kilobases.

Protein Ladders

Protein ladders consist of a mixture of proteins of known molecular weights, and they are used in SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) to estimate the molecular weight of protein samples. Protein ladders are typically denatured and treated with a tracking dye to ensure even migration through the gel.

Usage

To use a molecular-weight size marker, a researcher loads an aliquot of the marker into a well on the same gel as their samples. As the gel runs, the marker fragments migrate according to their size, creating a series of bands that serve as a reference for interpreting the experimental results.

Selection Criteria

When selecting a molecular-weight size marker, researchers should consider the following factors:

• The size range of the marker should encompass the expected size range of the samples.
• The resolution required for distinguishing between different sample sizes.
• The type of gel electrophoresis being used (e.g., agarose for DNA, SDS-PAGE for proteins).

Limitations

While molecular-weight size markers are invaluable tools, they have limitations. The migration of marker molecules can vary depending on the composition of the gel and the electrophoresis conditions. Therefore, markers should be used as approximate guides rather than absolute measures of molecular size.

See Also

• Gel electrophoresis
• Western blot
• Polyacrylamide gel electrophoresis
• Nucleic acid sequence