Interpretation of Effects of Hydroxylated Solutes on DNA Hairpin Stability

Abstract

The identification and quantification of the interactions between hydroxylated solutes and biological macromolecules will aid in the development of solutes, as tools, in a number of biochemical contexts including protein stabilization and crystallization. Little information is known regarding these noncovalent interactions, thus, this study used solubility analysis to quantify the interactions between the surfaces on hydroxylated solutes and purine/pyrimidine derivatives. Subsequently, we utilized DNA melting studies to quantify the effects of the solutes on the overall stability of DNA hairpins. Interpretation of this data using the solute partitioning model allowed for the identification of these specific interactions and the development of the ability to predict the effect of any hydroxylated solute on DNA stability. Glycerol was found to have a favorable preferential interaction with the sp2N, sp3N, and sp3C of DNA bases/analogs and an unfavorable preferential interaction with sp20 (other solutes exhibited similar trends). The effect of these hydroxylated solutes on 12nt and l6nt DNA hairpin stability has also been quantified, and the data demonstrates a positive correlation between solute surface area and the destabilization of DNA.