Synthetic Polymer Origami

Abstract

The extraordinary function of proteins is derived from their ability to fold into precise structures. They are widely used in therapeutics, catalysis, and energy. However, they are difficult to design, expensive to manufacture, and are prone to degradation. As a result, scientists are looking to develop synthetic polymers that can serve as a simple, robust, and inexpensive alternative to natural proteins. Peptide nucleic acids (PNAs) are a synthetic polymer alternative explored in this paper using MD simulation. PNAs are DNA analogues that share the hybridization and melting behavior of DNA but are more flexible, show stronger binding, and are less prone to degradation. PNAs are theoretically an ideal thermally-controlled folding motif. Using a coarse-grained model, the melting behavior of PNA duplexes, formation of hairpin loops, and the controlled folding of PNA strands through the tuning of temperature and primary sequence was demonstrated. This thesis demonstrates the feasibility of using PNAs to design temperature-controlled synthetic polymers.