The folding of the specific DNA recognition subdomain of the sleeping beauty transposase is temperature-dependent and is required for its binding to the transposon DNA.

The reaction of DNA transposition begins when the transposase enzyme binds to the transposon DNA. Sleeping Beauty is a member of the mariner family of DNA transposons. Although it is an important tool in genetic applications and has been adapted for human gene therapy, its molecular mechanism remains obscure. Here, we show that only the folded conformation of the specific DNA recognition subdomain of the Sleeping Beauty transposase, the PAI subdomain, binds to the transposon DNA. Furthermore, we show that the PAI subdomain is well folded at low temperatures, but the presence of unfolded conformation gradually increases at temperatures above 15°C, suggesting that the choice of temperature may be important for the optimal transposase activity. Overall, the results provide a molecular-level insight into the DNA recognition by the Sleeping Beauty transposase

2D [¹H,¹⁵N]-HSQC spectra of the PAI subdomain.

<p>The spectra were collected in 25 mM aqueous sodium phosphate buffer at pH 5.0 (top panel) and 7.0 (bottom panel) in the range of temperatures from 5 to 45°C with a 5°C increment.</p

Self-diffusion coefficients.

<p>The PAI self-diffusion coefficient at pH 5.0 (squares) and 7.0 (circles) are plotted vs. temperature over the range from 5 to 35°C. Protein samples were prepared in 25 mM sodium phosphate buffer using 100% D₂O. The temperature dependence of the self-diffusion coefficient of BPTI (stars) is shown for comparison. Solid lines represent fits of Arrhenius dependence of the self-diffusion coefficient to experimental data.</p

DNA-binding of folded and unfolded conformations of the PAI subdomain.

<p>(A) 2D [¹H,¹⁵N]-HSQC spectrum of the PAI subdomain collected at the temperature of 5°C in 25 mM aqueous sodium phosphate buffer at pH 5.0 in the presence of 250 mM NaCl. The folded and unfolded conformations exist in slow exchange on the NMR time scale. Thus, two resonances are observed for each residue. Non-overlapping resonances originating from the same residue in both the folded and unfolded conformations are labeled. (B) Cartoon representation of the PAI subdomain (PDB code 2m8e <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112114#pone.0112114-Carpentier1" target="_blank">[7]</a>). The DNA-binding site is colored blue. Side chains of the residues that were used for the analysis of the DNA-binding are labeled and shown as red sticks. (C) Relative intensities of resonances corresponding to the folded and unfolded conformations are plotted as a function of PAI:DNA molar ratio. Relative intensities were calculated by dividing the resonance intensity at a given PAI:DNA molar ratio by the intensity of this resonance in the absence of DNA.</p

Intrinsic tyrosine fluorescence.

<p>(Left panel) The location of Y46 on the cartoon representation of the PAI subdomain (PDB code 2m8e <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112114#pone.0112114-Carpentier1" target="_blank">[7]</a>) is shown. (Right panel) The integral fluorescence of Y46 at pH 5.0 (squares) and pH 7.0 (circles) is plotted vs. temperature. Shown data is the average of three independent experiments. Error bars in many cases do not exceed the size of the symbol. Solid lines represent best fits of experimental data.</p