Here we investigated the stability of an aptamer, which is formed by two RNA-strands and binds the antibiotic streptomycin. Molecular dynamics simulations in aqueous solution confirmed the geometry and the pattern of hydrogen bond interactions that was derived from the crystalstructure (1NTB). The result of umbrella sampling simulations indicated a favored streptomycinbinding with a free energy of ܩ∆ ୠ୧୬ୢ°= -101.7 kJ mol -1 . Experimentally, the increase in oligonucleotide stability upon binding of streptomycin was probed by single-molecule force spectroscopy. Rate dependent force spectroscopy measurements revealed a decrease in the natural off-rate (k off-COMPLEX = 0.22 ± 0.16 s -1 ) for the aptamer-streptomycin complex compared to the aptamer having an empty binding pocket (k off-APTAMER = 0.49 ± 0.11 s -1 ). This decrease in the natural off-rate corresponds to a decrease in the Gibbs free energy of ∆∆G ୱ୦ୣୣ୰ ≈ 3.4 kJ mol -1 .The simulated binding pattern and the experimental results led to the conclusion that hydrogen-bonds between both RNA strands mainly contribute to the decrease in natural-off rate and Gibbs free energy of the aptamer system studied.
It was recently suggested that the electrostatic double-layer force between colloidal particles might weaken at high hydrostatic pressure encountered, for example, in deep seas or during oil recovery. We have addressed this issue by means of a specially designed optical trapping setup that allowed us to explore the interaction of a micrometer-sized glass bead and a solid glass wall in water at hydrostatic pressures of up to 1 kbar. The setup allowed us to measure the distance between bead and wall with a subnanometer resolution. We have determined the Debye lengths in water for salt concentrations of 0.1 and 1 mM. We found that in the pressure range from 1 bar to 1 kbar the maximum variation of the Debye lengths was <1 nm for both salt concentrations. Furthermore, the magnitude of the zeta potentials of the glass surfaces in water showed no dependency on pressure.
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