Neocles B. Leontis, Advisor Advances in rapid prototyping technology (RP) and supporting software provide capabilities for generating different kinds of physical three-dimensional (3D) models of biological macromolecules (DNA, RNA, carbohydrates, and proteins) for a variety of research and pedagogical applications. The suitability of two RP techniques, PowderBinder Printing (PBD) and Fused Deposition Modeling (FDM), were evaluated for building models in support of RNA nanotechnology and of RNA structural bioinformatics. It was determined that the PBD technology is most suitable for constructing space-filling models of modular motifs that can be assembled in Lego-like fashion in support of modular design of complex architectures for RNA nanotechnology applications. Therefore, a variety of powders and binders were evaluated for constructing these modules so as to optimize their strength, resilience and feature resolution. Furthermore, a method was developed for joining modular RNA units in the correct 5’ to 3’ orientations at reproducible helical interfaces using appropriately positioned and oriented neodymium magnets embedded in the exterior basepair faces. For models intended to represent the complex relationships between structural elements in folded RNA molecules for RNA structural bioinformatics applications, the crucial criteria are strength, flexibility and visibility of the underlying covalent and hydrogen-bonding networks. For these applications, FDM was found to be more suitable as it allowed to build strong but open models in which the primary unit of representation is the covalent bonds and hydrogen-bonds joining individual atoms. It was found that complex stick

James R Zubricky

Papers

Physical Models of Biochemicallly Important Molecules Using Rapid Prototyping Techniques