[Structural and thermodynamic analysis of conformational states of self-complementary deoxyhexanucleotides...

The conformational states of the self-complementary deoxyhexanucleotides d(GCATGC) and d(GCTAGC) capable of forming hairpin structures in aqueous solution have been studied by one- and two-dimensional 1H NMR spectroscopy and molecular dynamics simulations. The equilibrium thermodynamic parameters of the formation of duplex and hairpin forms have been determined, and the spatial structures of the d(GCATGC) and d(GCTAGC) conformers have been calculated. A comparative analysis of the thermodynamic and conformational parameters of self-association has been made. The molecular dynamics of the hexamer forms in the nanosecond time scale has been studied, and the mobility of their structural constituents has been evaluated. Possible reasons for the observed distinction in the thermodynamic stability of duplex and hairpin forms of the deoxyhexanucleotide sequences are discussed.