Over the past decade our understanding of RNA’s biological role has greatly expanded. As much as 80% of the DNA in the human genome is transcribed, but only 2% of this is translated. The conservation of numerous nontranslated sequences across mammals and even distantly related eukaryotes indicates these structures have specific functions. Understanding these RNAs will require efficient deciphering of their two- and three-dimensional structures as well as the dynamics of these structures, a daunting task. Luckily, RNA tertiary structure is guided by motifs. These are specific structures that occur frequently in RNA often with the same or related functions. Therefore, understanding the dynamics of various RNA motifs will be pivotal to decoding complex RNAs.<br/>Our work focuses on the sarcin/ricin domain (SRD), an RNA motif that ranges from multiple occurrences in the ribosome where it has structural and protein binding roles to a replication control region in the potato spindle tuber viroid (PSTVd). This work seeks to use adaptively biased molecular dynamics (MD) to learn the full dynamic range of the conformations of the SRD. We are also modeling how this conformational range is modulated by base changes. These changes range from subtle alterations in the quality of base stacking to rearrangements to related motifs. Once cataloged, we intend to measure these conformations in the laboratory, which may require additional analytical tools.

Molecular dynamics investigation of the stability of sarcin/ricin domains: Towards using adaptively biased MD to find the full dynamic range of RNA

252nd National Meeting (2016)

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