Faculty Sponsor's Department(s):
The storage of DNA in a cell is highly dynamic, as packed strands are constantly unpacked, manipulated, and returned to storage during various cellular processes. Our understanding of dynamic DNA packaging is complicated by DNA’s high charge, which requires the cell to tightly manage the electrostatic conditions, to allow for the controlled packaging and release of DNA. Here, we undertake experiments to clarify the electrostatic interactions between DNA molecules. We created a procedure to determine the frictional force between two double stranded DNA molecules [dsDNA] as they move past each other, and to determine the electrostatic basis of that friction by performing the measurement in various concentrations of monovalent and divalent salts. Briefly, our measurement involves: braiding together two dsDNAs in various salt solutions, cutting one of the dsDNA and measuring the relaxation of the bead and its deviation from the relaxation predicted by hydrodynamic drag alone. Preliminary results have demonstrated the success of this procedure in producing the desired relaxation events in 30mM NaCl solutions. Further work must be done to measure the relaxation in other salt solutions. Continuation of this work will provide further insights into the mechanisms of DNA interactions in biopolymer dynamics, leading to a greater understanding of a diverse range of phenomena which involve relative motion of two biopolymers such as protein folding, injection of dsDNA by eukaryotic viruses, and the diffusion of biopolymers through pores.