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Class one transposons, called retrotransposons, require transcription into an RNA intermediate before insertion into target DNA. Class two transposons, or DNA-only transposons, remain in DNA form throughout transposition. Both types can move within genomes, but DNA-only transposons use a cut-and-paste mechanism involving the enzyme transposase.

Terminal inverted repeats are short DNA sequences flanking the transposase gene, typically 9 to 40 base pairs long and reverse complements of each other. Transposase monomers bind to these repeats, and when they dimerize, they bring the inverted repeats together to form a stable DNA-protein complex called a transpososome, enabling transposon mobilization.

During insertion, transposase makes staggered cuts in target DNA, creating single-stranded overhangs. The transposon's 3' OH end joins the target DNA's 5' terminal, leaving gaps. DNA polymerase fills these gaps using the 3' end as a primer, and DNA ligase seals the newly synthesized DNA to the transposon, completing target site duplication.

Transposon insertion can alter gene expression by introducing novel promoters or insulators that turn genes on or off. Additionally, if a transposon contains new splice sites, it can disrupt normal exon splicing during mRNA generation, creating aberrant mRNA transcripts and changing the resulting protein structure or function.

Exon shuffling occurs when imperfect excision of transposable elements carries genomic sequences along with the transposon. When inserted at a new location, this positions unrelated exons adjacent to each other, creating new gene structures. This process allows transposition to reorganize non-mobile genetic elements and generate genetic diversity.

DNA-only transposons are autonomous because they encode transposase, the multifunctional enzyme required for their own transposition mechanism. This self-sufficiency allows them to move independently within the genome without requiring proteins from other sources, making them powerful tools in genome editing and transgenesis applications.

The Sleeping Beauty transposon is a synthetic DNA transposon widely used in transgenesis as a gene vehicle to introduce foreign DNA into host organisms. Researchers use it across diverse species ranging from protozoa to small vertebrates like fishes, frogs, and mice to study foreign DNA effects, introduce new traits, or discover novel genes.