Polymorphism and Flexibility of DNA in Alcohols

Molecular dynamics simulations are performed to investigate the polymorphism and flexibility of DNA in water, ethylene glycol (EG) and ethanol (EA) solutions. DNA in EG resembles the structure of DNA in water exhibiting B-DNA. In contrast, the DNA is an A-DNA state in the EA. We demonstrate that one important cause of these A\leftrightarrowB state changes is the competition between hydration and direct cation coupling to the phosphate groups on DNA backbones. To DNA structural polymorphism, it is caused by competition between hydration and cation coupling to the base pairs on grooves. Unlike flexible DNA in water and EA, DNA is immobilized around the canonical structure in EG solution, eliminating the potential biological effects of less common non-canonical DNA sub-states.