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Background   Mariner- like elements ( MLEs ) are widespread DNA transposons in animal genomes. Although  in vitro  transposition reactions require only the transposase, various factors depending on the host, the physico-chemical environment and the transposon sequence can interfere with the  MLEs  transposition  in vivo .    Results  The transposition of  Mos1 , first isolated from  drosophila mauritiana , depends of both the nucleic acid sequence of the DNA stuffer (in terms of GC content), and its length. We provide the first  in vitro  experimental demonstration that MITEs of  MLE  origin, as small as 80 to 120-bp, are able to transpose. Excessive temperature down-regulates  Mos1  transposition, yielding excision products unable to re-integrate. Finally, the super-helicity of the DNA transposon donor has a dramatic impact on the transposition efficiency.    Conclusion  The study highlights how experimental conditions can bias interpretation of  mariner  excision frequency and quality.  In vitro , the auto-integration pathway markedly limits transposition efficiency to new target sites, and this phenomenon may also limit events in the natural host. We propose a model for small transposons transposition that bypasses DNA bending constraints.

Factors acting on Mos1 transposition efficiency