There are billions of RNA molecules that have been sequenced and made available. However, only thousands of these sequences have a solved 3D structure. This is due to the time and resources that go into solving an individual structure using current experimental techniques. To expedite this, computational methods have been developed to assist in RNA tertiary structure prediction. The approach of this study is to determine patterns observed in secondary motifs of solved structures and apply them to sequences with unknown structures. The knowledge gained from this will assist in solving tertiary structure. Single nucleotide bulges are a commonly occurring secondary structure in RNA, but few studies focus on their structural patterns. Bulges of one were collected from the RNA Characterization of Secondary Structure Motifs (CoSSMos) website, clustered with root-mean-square deviation (RMSD), and characterized with Dissecting Spatial Structure of RNA (DSSR). This method led to the classification of 11 clusters of bulges of one with unique observable traits. These include CKGCG, CSCGG, GAYGC, KDMKS, KMGCM, SWGCS, UKYRR, UMAUA, WAGCW, WWCGW, and YMBVR. The interactions associated with each of these clusters helps add to our current understanding of single bulge secondary structure. They also help with advancing efforts in RNA tertiary structure prediction.

Jonathan Bostic would like to thank his faculty sponsor Dr. Brent Znosko for his support of this project.