Repetitive Extragenic Palindrome (REP) elements represent relatively well characterized types of noncoding repetitive DNA in bacteria. The REPs play a variety of roles in the cell and can be cleaved and transfered to the target site by the associated REP-associated tyrosine transposase (RAYT, Nunvar et al. 2010). The ability of RAYT to catalyze cleavage and recombination of REP sequences was experimentally confirmed for E. coli (Messing et al. 2012) and newly determined for Haemophilus parasuis (Nečasová et al., 2014, to be published). Recognition between single-stranded REP DNA and RAYT is necessary for nucleoprotein complex formation and subsequent DNA strand cleavage and transfer (Messing et al. 2012).
In this work, we studied solution conformations of several REP-related oligonucleotides from H. parasuis by circular dichroism spectroscopy. Our results indicate that REP oligonucleotides from H. parasuis form predominantly a monomolecular hairpin conformation in solution which may be important for RAYT recognition. Interactions between the fluorescently labeled oligonucleotide with sequence of H. parasuis REP and the associated RAYT were determined by microscale thermophoresis technique. Data show that the RAYT protein interacts with REP DNA from H. parasuis with high affinity, dissociation constant of binding RAYT to REP DNA was determined as 5 ± 0.8 nM.
This work is supported by grant CZ.1.07/2.3.00/30.0020 from the Ministry of Education of the Czech Republic (MSMT), and by grant P305/12/1801 from Czech Science Foundation.