The development of a computationally based, molecular model for the interaction of charged ligand (such as small ions, oligoelectrolytes, proteins and drugs) with nucleic acids is the long-term goal of the proposed research. Such a model must include the electrostatic interactions in an accurate yet tractable manner and must predict experimentally accessible properties of nucleic acids solutions. The Monte Carlo computational method will be used to simulate the solute (and solvent) distribution near model poly-and oligonucleotides.
The specific aims of this project ar to: 1) Develop an accurate model of an oligonucleotide and surrounding solution that can be used to examine the effect of base sequence and geometry on the univalent ion concentrations near the surface of the oligonucleotide. 2) Extend the model to examine the interaction of higher valent counterions (such as cobalt (III) hexamine) and counterions with structural flexibility (such as polyamines) with oligonucleotides and 3) Develop a model that can be used to predict experimentally accessible parameters and thus can be used to test the veracity of various models. The MBRS student will participate in any or all aspects of this proposed research depending upon his or her interests.
