The toeprinting assay, also known as the primer extension inhibition assay,[1] is a method used in molecular biology that allows one to examine the interactions between messenger RNA and ribosomes or RNA-binding proteins.
[2] It is different from the more commonly used DNA footprinting assay.
The toeprinting assay has been utilized to examine the formation of the translation initiation complex.
[3] To do a toeprint assay, one needs the mRNA of interest, ribosomes, a DNA primer, free nucleotides, and reverse transcriptase (RT), among other reagents.
[4] The assay involves letting the RT generate cDNA until it gets blocked by any bound ribosomes, resulting in shorter fragments called toeprints when the results are observed on a sequencing gel.