DNA compaction determined by energy dissipation measurements on a quartz-crystal oscillator

摘要

A quartz-crystal oscillator has been used as a mass measuring device whose resonance frequency decreases linearly on increase of the mass on the oscillator plate. Here, hydration amounts and viscoelastic properties of DNA strands in aqueous solutions were studied by a DNA-immobilized quartz-crystal oscillator connected with a network analyzer for admittance analysis, in which not only resonance frequency changes (a dagger F (water)) but also energy dissipation changes (a dagger D (water)) could be obtained simultaneously in aqueous solutions. Single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) exist as a flexible string structure and vibrate with hydrodynamic water around them under the low ionic condition, indicating a large a dagger F (water) in comparison with their mass (a dagger F (air) as dry mass) on the oscillator. Both DNA strands also showed high energy dissipation (a dagger D (water)) due to their flexible (viscotic) structures in aqueous solutions. When cations such as Na+, spermidine [NH2(CH2)(3)NH(CH2)(4)NH2], and Co(NH3) (6) (3+) were added, the a dagger F (water) increased and a dagger D (water) decreased with increase in cation concentrations, indicating that the DNA was dehydrated and entangled (became elastic) with cations. These effects were in the order of Co(NH3) (6) (3+) > spermidine a parts per thousand Na+. ssDNA was found to form more compact (more dehydrated and more elastic) structures than dsDNA on addition of these cations. The [(-a dagger F (water))/(-a dagger F (air)) - 1] and [a dagger D (water)/(-a dagger F (air))] values, which reflect the bound water ratio per unit mass and the energy dissipation parameters per unit mass respectively, could be used to characterize conformational changes of the DNA strands.