Bead Modeling of Transport Properties of Macromolecules in Free Solution and in a Gel

• Main Author: Pei, Hongxia
• Format: Others
• Published: Digital Archive @ GSU 2010
• Subjects: Agarose gel; Bead model; Complex formation; DNA; Effective medium; Hydrodynamic interaction; NMR; Peptide; Relaxation; Salt dependence; Chemistry
• Online Access: http://digitalarchive.gsu.edu/chemistry_diss/49; http://digitalarchive.gsu.edu/cgi/viewcontent.cgi?article=1047&context=chemistry_diss

On the bead modeling methodology, or BMM, a macromolecule is modeled as a rigid, non-overlapping bead array with arbitrary radii. The BMM approach was pioneered by Kirkwood and coworkers (Kirkwood, J.G., Macromolecules, E.P. Auer (Ed.), Gordon and Breach, New York, 1967; Kirkwood, J.G., Riseman, J., J. Chem. Phys., 1948, 16, 565) and applied to such transport properties as diffusion, sedimentation, and viscosity. With the availability of computers, a number of investigators extended the work to account for the detailed shape of biomolecules in the 1970s. A principle objective of my research has been to apply the BMM approach to more complex transport phenomena such as transport in a gel, electrophoresis (free solution and in a gel), and also transport in more complex media (such as the viscosity of alkanes and benzene). Variables considered by the BMM include the number of beads (N), the radii of the beads, net charge and charge distribution, conformations, salt type, and salt concentration. The BMM has been extended to: (1) account for the existence of a gel; (2) characterize the charge and secondary structure of macromolecules; (3) account more accurately for hydrodynamic interaction (remove the orientationnal preaveraging approximation of hydrodynamic interaction); (4) study the effect of ion relaxation for particles in arbitrary size, shape, and charge; (5) consider the salt dependence of electrokinetic properties; (6) account for the formation of possible complex between guest ions and BGE ions. We also did diffusion constant measurement by NMR for amino acids and short peptides in 10%D2O-90% H2O at room temperature and applied to our modeling study by BMM.