There is an abundance of RNA sequence information available due to the efforts of recent sequencing projects. However, current techniques implemented to solve the tertiary structures of these sequences, NMR and X-ray crystallography, are difficult and time consuming. These techniques, therefore, are not able to keep up with the abundance of available sequences. Because of this, there is a need to develop quick and efficient ways to predict RNA tertiary structure from sequence. One promising approach is to identify structural patterns within previously solved 3D structures and apply these patterns to new sequences. Here, we present an automated protocol that uses RNA CoSSMos and other existing programs and algorithms to search for and characterize tertiary structure patterns. This protocol has been implemented and has successfully identified and characterized the well-known GNRA tetraloop from the entire database of tetraloops found in the Protein Data Bank. This protocol can be utilized to identify other sequence families which adopt similar structures and may be used as part of a larger protocol to predict RNA 3D structure.

Searching RNA 3D structures for tertiary structural patterns

254th National Meeting (2017)

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