Denaturation was examined for the first time in a ternary mixed solution of water/hydrophilic/ hydrophobic organic solvent using λ-DNA and a plasmid as models. The absorbance of λ-DNA and the plasmid at 260 nm gradually increased for several days up to 1.68 and 1.38 times the initial values, respectively, in a water/acetonitrile/ethyl acetate (15:3:2, volume ratio) mixed solution, whereas there was little change in a water/acetonitrile (15:3, volume ratio) mixed solution. The plasmid treated with the ternary mixed solution was also examined with agarose gel electrophoresis. These experimental data indicated that λ-DNA changed from a double helix structure to a single helix structure and that the plasmid partially transformed to generate a denaturation bubble in the structure. The new idea of using the ternary mixed solution first enabled the interaction of the hydrophobic organic solvent (e.g., ethyl acetate) molecule with the double helical structure of DNA, leading to specific slow-proceeding denaturation.
Wang, X., Lim, H.J. and Son, A. (2014) Characterization of Denaturation and Renaturation of DNA for DNA Hybridization. Environmental Health and Toxicology, 29, e2014007. https://doi.org/10.5620/eht.2014.29.e2014007
Bonner, G. and Klibanov, A.M. (2000) Structural Stability of DNA in Nonaqueous Solvents. Biotechnology and Bioengineering, 68, 339-344.
Sicard, F., Destainville, N. and Manghi, M. (2015) DNA Denaturation Bubbles: Free-Energy Landscape and Nucleation/Closure Rates. Journal of Chemical Physics, 142, 034903/1-034903/9. https://doi.org/10.1063/1.4905668
Nogami, T., Fujinaga, S., Jinno, N., Hashimoto, M. and Tsukagoshi, K. (2012) Elution Behavior of Lambda-DNA with Ternary Mixed Carrier Solvents in an Open-Tubular Capillary under Laminar Flow Conditions. Analytical Sciences, 28, 617-620. https://doi.org/10.2116/analsci.28.617
Brahms, J., Michelson, A.M. and Van Holde, K.E. (1966) Adenylate Oligomers in Single- and Double-Strand Conformation. Journal of Molecular Biology, 15, 467-488. https://doi.org/10.1016/S0022-2836(66)80122-5
Blake, B.D. and Fresco, J.R. (1973) Polynucleotides. XI. Thermodynamics of (A)N.2(U)00 from the Dependence of TmN (Helix-Coil Transition Temperature) on Oligomer Length. Biopolymers, 12, 775-789.