Mechanochemical study of NaDNA and NaDNA-netropsin fibers in ethanol-water and trifluoroethanol-water solutions

Abstract

Highly oriented calf-thymus NaDNA fibers, prepared by a wet-spinning method, were complexed with netropsin in ethanol-water and trifluoroethanol (TFE)-water solutions. The relative fiber length, L/L0, was measured at room temperature as a function of ethanol or TFE concentration to obtain information on the B-A conformational transition. The B-A transition point and transition cooperativity of the fibers were calculated. The binding of netropsin to NaDNA fibers was found to stabilize B form and to displace the B-A transition to higher ethanol concentration, as indicated by its elongational effect on the fiber bundles. An increased salt concentration was found to reduce netropsin binding. In netropsin-free ethanol solution, the dissociation of bound netropsin from the DNA fibers was observable. Pure B-NaDNA fibers were found to be more stable in TFE solution than in ethanol solution. This was interpreted as being due to a different steric factor and a larger polarity of TFE compared with ethanol, resulting in its smaller capacity to reduce the water activity and dielectric constant of the medium in the immediate vicinity of DNA fibers. Therefore, the effect of netropsin binding on the B-A transition of NaDNA fibers became less obvious in TFE solution. In another series of experiments, L/L0 was measured as a function of temperature to obtain information on the helix-coil transition, or melting, as well as the B-A transition of NaDNA and NaDNA-netropsin fibers. The melting temperature and helix-coil transition width were calculated from the melting curves. A phenomenological approach was used to describe the melting behavior of the fibers in and around the B-A transition region. The effect of netropsin on the melting of DNA fibers was attributed mainly to the stabilization of B-DNA and to a higher melting cooperativity in the B-DNA region.

Lysozyme Coated DNA and DNA/SWNT Fibers by Solution Spinning

“…Bragg‐spacing 0.4083 nm was observed in as‐received DNA, which corresponds to the spacing between the bases. This data confirmed the α‐form of DNA, which typically observed in Na‐DNA as well as dehydrated DNA fibers 30. In DNA/LSZ and DNA/SWNT–LSZ fibers, the Bragg‐spacing appeared at 0.4069 and 0.4077 nm, respectively.…”

Aggregated DNA in ethanol solution

“…This method was early modified for the preparation of a long fiber bundle of oriented DNA molecules from which a large number of reproducible samples could be taken for mechanochemical study [26]. Recently, a simple set-up was suggested for mechanochemical studies of conformational and helix-to-coil transitions in such DNA fiber samples [27,28,29,30]. A DNA fiber was held straight by a small weight in a measuring cylinder containing ethanol-water solution.…”