DNA transposon

A DNA transposon is a transposable element whose mobilization proceeds through a DNA intermediate rather than through an RNA intermediate. This distinguishes it from a retrotransposon. It does not by itself specify whether a particular event removes the original copy, creates an additional copy or requires machinery supplied by another element.^[ref]

An original copy-location model separates the questions. Start with one copy at a donor site and none at a recipient site. A cut-and-paste model ends with zero at the donor and one at the recipient; a replicative model ends with one at each. The totals are one and two, respectively. Both are DNA-level bookkeeping models. Establishing a real mechanism requires evidence about the molecular intermediate and the fate of the donor, rather than only observing a changed total gene copy number.

The P element supplies a concrete experimental system. A P-element vector can retain mobile recognition sequences around inserted cargo while P-element transposase is supplied separately. The carrier's recognition sequences and the enzyme's coding sequence are therefore distinct functional components.^[ref] Not every DNA transposon must encode its own active enzyme, and the detailed P-element arrangement should not be imposed on every other family.

Tn5 is a bacterial DNA transposon used as a model for how mobile DNA ends are recognized, processed and inserted into another DNA molecule. The element is a DNA sequence; Tn5 transposase is the protein that supplies its catalytic machinery. The assembled enzyme–DNA complex is a transpososome.

A 2000 structure determined Tn5 transposase bound to transposon-end DNA at $2.3\text{A˚}$ resolution. Two protein subunits contacted each end and positioned the ends in the active sites. The geometry explained how recognition by one subunit and cleavage by the other could coordinate the reaction.^[ref]

This machinery became useful beyond studying a naturally mobile element. The 2013 ATAC-seq study used transposition to introduce sequencing adaptors into native chromatin, generating fragments informative about chromatin accessibility and molecular organization.^[ref]

The distinction between element and enzyme clarifies the tool. A DNA fragment processed by a prepared Tn5 transposase complex need not itself contain the gene encoding the enzyme. Observing a tagged fragment therefore establishes an enzyme-mediated event, rather than showing that every product has acquired autonomous transposition machinery. The sequence, catalyst and experimental readout describe different parts of the system.