Formation of intramolecular tetraplex structures by the thrombin-binding DNA aptamer (TBA) in the presence of K(+), Pb(2+), Ba(2+), Sr(2+) and Mn(2+) has been studied by vibrational spectroscopy. All tetraplex structures contain G-G Hoogsteen type base pairing, both C2'endo/anti and C2'endo/syn deoxyguanosine glycosidic conformations and local B like form DNA phosphate geometries. Addition of Pb(2+) ions modifies the structure by interacting at the level of the guanine carbonyl groups. The very important downshift of the guanine C6=O6 carbonyl vibration mode in the TBA spectrum induced by the addition of one Pb(2+) ion per TBA molecule is in agreement with a localization of the metal ion between both guanine quartets. FTIR melting experiments show an important stabilization of the tetraplex structure upon addition of Pb(2+) ions (DeltaT = 15 degrees C). This strong interaction of lead cations may be correlated with a change in the geometry of the cage formed by the two guanine quartets. A similar but weaker effect is observed for barium and strontium cations.
We investigate the behavior of a model methane clathrate cage under high hydrostatic pressures. The methane clathrate cage consists of 20 water molecules forming 12 pentagonal faces, with a methane molecule positioned at the cage center. The clathrate compound is located inside a fullerene-type arrangement of 180 He atoms to simulate an isotropic pressure. Different pressures are simulated by decreasing the radius of the He array. The minimal energy of the total system for each configuration is calculated by using density functional theory. The variation of the energy with the volume of the imprisoned clathrate cage leads to the proposal of a (cold) equation of state in the pressure range [0,60] GPa. The elastic parameters of the state equation are found in agreement with equivalent quantities measured on clathrates in their sI conformation. Special attention is given to the distribution of the confined atoms and the eventual symmetry lost from the clathrate cage with the pressure, as the clathrate cage constitutes a basic structural unit of the crystal. Finally, the strengths and limitations of the model are discussed.
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