We plan to elucidate the molecular mechanism of recognition between novel tyrosine transposases from the IS200/IS605 family, RAYT, and single stranded DNA, ssDNA. RAYTs from Escherichia coli and Xanthomonas campestris are predicted to bind and cut specific DNA sequences (REPs) physically associated with RAYT encoding genes. The mobility of REPs is an important feature of plasticity of prokaryotic genomes. To advance understanding of the complex process of protein/DNA recognition in this system, we willcombine thermodynamic and kinetic study by surface plasmon resonance and crystallographic structural analysis. Complementary energetic and structural views of the interaction will reveal the role of variability and dynamics of residues at the interface.Comprehensive biophysical characterization of non/binding ssDNA sequences is expected to elucidate the role of energetically marginally stable but kinetically trapped states in the process of recognition. The knowledge generated by the project will enable us to draw biologically significant parallels between the ssDNA and RNA behavior.
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