Physical Models of Biochemically Important Molecules Using Rapid Prototyping Techniques

The application of rapid prototyping (RP) to the field of molecular modeling is growing due to the availability of computer programs and RP machines at major research institutions. Two RP techniques that are applicable to the study are powder-binder printing and Fused Deposition Modeling (FDM). Both of these technologies are available at BGSU and can be used in order to study the basepair interactions in many different types of RNA motifs. I have determined that the powder-binder technique is preferred when the tertiary structure of RNA is desired; conversely, FDM is better when the primary and secondary structures of RNA motifs are desired. By using FDM modeling, you can see the orientation of non-canonical basepairs, hydrogen bonds between atoms, the phosphate- sugar backbone, as well as structural motifs in RNA. I then applied our knowledge of RP technology by creating physical models of the C-loop motif, RNase P RNA, the kink-turn, the sarcin-ricin loop, and the SARS virus genome. Advisors/Committee Members: Leontis, Neocles B.