Structural characterization of naturally occurring RNA single mismatches

Abstract

RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence-structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.

Figure 1.

Single mismatch graph (top) and MC-Search input descriptor (bottom). The nucleotides are numbered A1 to A3 and B1 to B3 in the 5′ to 3′ direction. The ‘A’ and ‘B’ letter designations specify opposing RNA strands. The letter ‘N’ represents any nucleotide. The input descriptor identifies the canonical nearest neighbors by limiting the allowed pairing interactions to the canonical pairs defined by the Roman (85–87) and Arabic (88,89) numerals. Not all possible numerals for A–U, U–A, G–C, C–G, G–U and U–G pairs are shown here due to space limitations. The input descriptor identifies the mismatched nucleotides by allowing an interaction defined by no hydrogen bonds, while also prohibiting the canonical pairing interactions defined by the Roman and Arabic numerals.

Figure 2.

Representation of an A·G mismatch in the ^5′(A)H/^3′(G)S pairing, antiparallel, trans orientation with XI hydrogen bonding pattern (PDB ID 1C04), which is the most common orientation and interaction determined for the most frequently occurring A·G mismatch-nearest neighbor combinations (84) that were also represented in the PDB.

Figure 3.

Representation of a U·U mismatch in the ^5′(U)W/^3′(U)W pairing, antiparallel, cis orientation with XVI hydrogen bonding pattern (PDB ID 1FJG), which is the most common orientation and interaction determined for the most frequently occurring U·U mismatch-nearest neighbor combinations (84) that were also represented in the PDB.

Figure 4.

Representation of in the hydrogen bonded, stacked orientation (PDB ID 1O9M) (a) and in the non-hydrogen bonded, unstacked orientation (PDB ID 1O9M) (b).

Figure 5.

Representation of an A·C mismatch in the ^5′(A)H/^3′(C)W pairing, antiparallel, trans orientation with XXV hydrogen bonding pattern (PDB ID 1FJG)), which is the most common orientation and interaction determined for the A·C mismatch-nearest neighbor combination of . This mismatch-nearest neighbor sequence combination is found in the 30 most frequently occurring single mismatches (84) and accounts for 80% of the total A·C mismatches found in this study.

Figure 6.

Representation of a C·U mismatch in the ^5′(C)W/^3′(U)W pairing, antiparallel, cis orientation with one_hbond hydrogen bonding pattern (PDB ID 1FJG), which is the most common orientation and interaction determined for the most frequently occurring C·U mismatch-nearest neighbor combinations (84) that were also represented in the PDB.

Figure 7.

Representation of a G·G mismatch annotated as having no interaction (PDB ID 2QAM), which is the most common orientation and interaction determined for the most frequently occurring G·G mismatch-nearest neighbor combination, (84) that was also represented in the PDB.