Structural and thermodynamic analysis of the conformational states of self-complementary hexanucleotides 5'-d(GCATGC) and 5'-d(GCTAGC) in aqueous solution

The conformational states of hexanucleotides 5'-d(GCATGC) and 5'-d(GCTAGC) capable of forming hairpins in aqueous solution were studied by 1D and 2D 1H NMR and molecular dynamics. The equilibrium thermodynamic parameters were determined for the formation of duplexes and hairpins, and the spatial structures were computed for the GCATGC and GCTAGC conformers. The mobility of the hexamer constituents was evaluated by nanosecond molecular dynamics simulation. The possible causes of the observed difference in the thermodynamic stability of the duplex and the hairpin are discussed. © 2007 Pleiades Publishing, Inc.