Electronic Theses and Dissertations





Document Type


Degree Name

Doctor of Philosophy




Physical Chemistry

Committee Chair

Yongmei Wang

Committee Member

Abby L. Parrill-Baker

Committee Member

Donald Bashford

Committee Member

Mohamed Laradji


In this dissertation, ion interactions with nucleic acids were studied using two theoretical methods: atomistic molecular dynamics simulations and a Poisson-Boltzmann approach. Ion interactions, specifically cation interactions, with nucleic acids are essential for proper nucleic acid folding and function. Cations enable proper folding and function by partially compensating for the build-up of repulsive electrostatic potentials caused by the close approach of negatively charged phosphate groups. Cations can bind at specific sites, forming long-term interactions, or through diffuse interactions that create a dynamic "ion atmosphere." Theoretical investigations are useful because current experimental techniques often cannot provide a complete, detailed understanding of cation binding. Molecular dynamics simulations were used to study the effect of initial ion coordinates on monovalent (Na+) and divalent (Mg2+) ion interactions. For monovalent ions, there was no significant dependence on the initial position of the ion. However, Mg2+ binding demonstrated strong dependence on both the initial position and solvation structure of the cation. Based on these results and experimental observations, it was concluded that Mg2+ should be fully solvated in molecular dynamics simulations. Ion distributions from molecular dynamics simulations were also compared to distributions obtained from a Poisson-Boltzmann approach. Monovalent ion distributions agreed quite well between the methods, particularly the integrated properties of the distributions. Agreement for divalent ions was poor in comparison, with only fair agreement observed under specific conditions. The effect of ion interactions on the structure of a nucleic acid dimer was also examined. The structure of the nucleic acid demonstrated sensitivity to Mg2+ binding to the dimer interface, resulting in conformations not observed in Na+ only systems. This sensitivity provides an explanation for the differences observed in experimental titrations performed in monovalent or divalent salt solutions.


Data is provided by the student.

Library Comment

Dissertation or thesis originally submitted to the local University of Memphis Electronic Theses & dissertation (ETD) Repository.