Vikas P. Jain and Raymond S. Tu. Department of Chemical Engineering, The City College of New York, The School of Engineering, T305 Steinman hall, 140th street and Convent avenue, New York, NY 10031
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. The main purpose of this study is to elucidate the cooperative process of DNA-condensation with a set of self-assembling peptide building blocks, particularly studying the effect of charge distribution. The peptides that have been rationally designed are α-helical containing 23 amino acids with variation in the number and distribution of positive charge. The approach used in designing the peptide applies a sequence algorithm that is based on combining intrinsic folding propensities and helical periodicity. These designs incorporate hydrophobic residues on one side (leucines and alanines) and hydrophilic residues on the opposite side so that peptides have amphiphilic nature. These peptides designed with a periodicity (two turns for every seven amino acids) such that they strongly nucleate the secondary structure at air-water interface. The secondary structure is characterized by using circular dichroism spectropolarimetry and behavior at the air-water interface is investigated by using pendant drop/bubble method. The peptide behavior is characterized as a function of its concentration in presence of salt (electrolyte) and DNA (polyelectrolyte). Additionally, we investigate the dynamics of the condensation process, where the peptide transitions from a random coil secondary structure to an α-helix as a function of binding. Variations in the design of the peptide show that both charge number and distribution affect the DNA condensation process