(174d) Investigating Self-Assembly and Kinetics of the DNA-Peptide Complex Formation

The phenomenon of counterion-mediated DNA-condensation is fundamental to most DNA related activity in the cell, from chromosome packaging to control over translational mechanisms. Developing synthetic systems to manipulate DNA-condensation is essential for the development of biotechnologies for gene encapsulation and DNA-separation. We investigate the dynamics of the DNA-condensation by using our model peptide where the interaction between DNA and peptide is non-specific. We have designed a peptide that shows switchable surface activity, where the folded form of the peptide is amphiphilic and the unfolded form is not amphiphilic. The peptide is α-helical, containing 23 amino acids with variation in the number and distribution of hydrophobic and charged amino acids. The designs incorporate hydrophobic residues on one side (leucines and alanines) and hydrophilic residues on the opposite side so that helix is surface active. The secondary structure has been characterized by using circular dichroism spectropolarimetry, and we show that the peptide has a transient secondary structure as a function of monovalent salt concentration. The behavior of the peptide at air-water interface is characterized by pendant drop/bubble method and modeled accordingly. Our hypothesis is that the unfolded peptide is in equilibrium with the folded peptide in the bulk solution but in presence of DNA, the unfolded peptide folds and then binds to DNA. Critical Aggregate concentration of the peptide for DNA condensation is determined by using multi angle light scattering, which is also used to calculate the radius of gyration and molecular weight of these condensates. We investigate the kinetics of the condensation process by using Circular dichroism in Stop-flow mode and also by isothermal titration calorimetry.