Toeprint

Toeprint is a term used in molecular biology to describe a reverse-transcription based assay that reveals the position of ribosomes on messenger RNA during translation. In a toeprinting experiment, a labeled primer anneals to a defined region of the mRNA and reverse transcriptase extends the cDNA. When a ribosome is bound to the mRNA, the enzyme stalls, producing a truncated cDNA fragment—the toeprint. By comparing the length of the toeprint to sequencing ladders, researchers infer the ribosome’s position on the transcript.

Applications of toeprinting include mapping translation initiation sites, studying start codon selection and ribosome scanning, and analyzing pausing or stalling induced by sequence elements, secondary structures, regulatory proteins, or small molecules. The method is commonly used to validate how specific changes in mRNA or factors influence translation.

Procedure overview typically involves an in vitro or extract-based translation system, a defined mRNA region, a labeled primer, and a reverse transcriptase. After cDNA synthesis, the products are resolved by denaturing gel electrophoresis or capillary methods, revealing discrete bands that correspond to ribosome positions. Appropriate controls ensure that observed bands reflect ribosome-dependent stops rather than nonspecific RT pausing.

History and terminology indicate that toeprinting emerged in the 1980s as a practical approach to study translation initiation. The term derives from the appearance of the cDNA termination point, likened to a toe imprint. Outside biology, toeprint also refers to a physical footprint left by a toe on a surface, but in scientific contexts it denotes this mapping technique.

See also: footprinting, ribosome profiling.