Identification and Characterization of New RNA Tetraloop Sequence Families

Abstract

There is an abundance of RNA sequence information available due to the efforts of sequencing projects. However, current techniques implemented to solve the tertiary structures of RNA, such as NMR and X-ray crystallography, are difficult and time-consuming. Therefore, biophysical techniques are not able to keep pace with the abundance of sequence information available. 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. RNA tetraloops are one of the most common naturally occurring secondary structure motifs. Here, we use RNA Characterization of Secondary Structure Motifs (CoSSMos), Dissecting the Spatial Structure of RNA (DSSR), and a bioinformatic approach to search for and characterize tertiary structure patterns among tetraloops. Not surprising, we identified the well-known GNRA and UNCG tetraloops, as well as the previously identified RNYA tetraloop. However, some previously identified characteristics of these families were not observed in this data set, and some new characteristics were identified. In addition, we also identified and characterized three new tetraloop sequence families: YGAR, UGGU, and RMSA. This new structural information sheds light on the tertiary structure of tetraloops and contributes to the efforts of RNA tertiary structure prediction from sequence.

Figure 1.

Secondary structure of a tetraloop with residues numbered. Figure was generated with XRNA.

Figure 2.

UPGMA cluster analysis of the tetraloops. The tetraloops included in the clusters are colored according to the legend. Each tetraloop is named by the PDB ID of the structure in which it appears followed by the tetraloop sequence (including closing base pairs), the chain ID, and the residue ID of the first nucleotide in the loop (after the 5’ closing nucleotide). Each tetraloop sequence occurs only once due to the selection of sequence-representative structures for each unique sequence. The distance scale at the bottom left of the tree is in Å. The tree was generated with Archaeopteryx 0.9901 beta.

Figure 3.

Cluster representative structures for each of the six clusters (A-F). The sugar conformations, base pairing, and stacking interactions found in ≥ 75% of sequence representative structures (and those shown in blue text in Tables 5–7) are drawn. Base pairing and stacking interactions are represented with dashed lines and arrows, respectively. Cartoon representations were created using DSSR-Jmol. Cluster-representative structures are named with the PDB ID, sequence, and the first residue involved in the loop. Clusters are named with the degenerate sequence shown in bold font.