Characterization of DNA duplex structure, stability and formation kinetics in a eutectic solvent and its aqueous mixtures
Laughlin, Brandon Patrick
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In this work, properties and behavior of DNA oligonucleotides in a non-aqueous eutectic comprised of glycerol and choline chloride mixed at varying ratios, as well as aqueous mixtures of the eutectic are explored. Physical parameters of buffer-containing eutectics such as density and viscosity at 293 K are determined. The effects the eutectic have upon the stability of the duplex formation of an oligonucleotide through melting and reannealing relative to that in a buffer are determined, and thermodynamic parameters also derived. It is found that the oligonucleotides explored form stable duplex structures in all investigated conditions. Structural studies by circular dichroism spectroscopy of the oligonucleotides have also been done, and show the subtle effects on DNA secondary structure alterations of the eutectic composition can have, with all conditions maintaining a B-form structure. Finally, the rate constants of the annealing reaction of the two complementary strands are determined through monitoring recovery of duplex structure after heating and rapid cooling.