The study of RNA as a regulatory molecule is a rapidly expanding field. Biological RNA appears to be modular: it has structural motifs connected by double-stranded helices that combine to establish its form and function. The sarcin-ricin domain (SRD) is one of these motifs in RNA. By understanding what a section of RNA such as the SRD does when functioning correctly, we can modify the structure to test many kinds of hypotheses regarding its function. An open issue regarding motifs in RNA is understanding the importance of the bases at the transition from one domain to another, such as the transition from SRD RNA to A-form double-helical RNA. Systems such as molecular dynamics help us gain more insight on how RNA functions. The trajectories of structures obtained from MD can be analyzed quickly using tools such as communication propensity and RMSD of 4. Other aspects of RNA base pair interactions, such as slide and roll, can be obtained using programs like DSSR (dissecting the spatial structure of RNA) and analyzed with Origin and Excel. The molecular dynamics package AMBER allows us to modify the RNA and run tests in a variety of conditions.<br/>The SRD is characterized by an S-turn strand, which has one base pair with a backbone that is locally parallel, and a more regular helical strand. We have investigated the capping base pairs of the SRD - the first canonical Watson-Crick pairs on each side of the domain. These pairs were varied so that each possible Watson-Crick base pair was tried at the transition, making seven different models. The CG-GC cap, which has a C S-strand, G helical strand just above the base triplet and G S-strand C- helical strand, has been identified as the model with the most varied from the other 6 based on communication propensity and RMSD for adjacent base pairs. We will continue therefore to study this model more closely.

Molecular dynamics study of the sarcin-ricin domain

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.