NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

Abstract

The NMR solution structure is reported of a duplex, 59GUGAAGCCCGU/39UCACAGGAGGC, containing a 4 @ 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 59GAA/39AGG, 59GAG/39AGG, 59GAA/39AAG, and 59AAG/39AGG. The structural information is compared with predictions made with the MC-Sym program.

RNA families in Epstein–Barr virus

“…For example, 265-7 nt and 313-5 nt in Figure 4 are modeled to form a symmetric three-by-three nt internal loop (where three unpaired nt are arranged across from three unpaired nt). Comprised entirely of purines, this loop can form a stable and helical "3RRs" motif 68 where opposing purines in the loop form sheared base pairs.…”

RNA Structures as Mediators of Neurological Diseases and as Drug Targets

“…Nucleobases involved in Watson-Crick base pairing or G-quadruplexes are colored aquamarine and green; other bases are colored magenta. PDB IDs for 3D structures: stem-loop – 4TV0 (Zhang et al, 2014), internal loop – 2L8F (Lerman et al, 2011), bulge – 1AJL (Luebke et al, 1997), pseudo-knot – 2A43 (Pallan et al, 2005), G-quadruplex – 2KBP (Martadinata and Phan, 2009). B) Model of eukaryotic translation initiation complex.…”

Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson–Crick Pairs and Comparison to Three-Dimensional Predictions

“…Noncanonical pairs, 20 especially GA 21–26 and AC 27, 28 (Figure 1), have conformations that are very sensitive to sequence and structural environment. GA pairs can be involved in a two hydrogen bond imino pair (cis Watson-Crick/Watson-Crick), two hydrogen bond sheared pair (trans Hoogsteen/sugar edge), and base triples.…”

“…29, 30 They can create larger, multi-pair conserved motifs such as the Loop E motif, 31 the sarcin-ricin loop, 32, 33 kink-turn, 34 and the 3RRs motif. 27 The 3RRs motif consists of three consecutive sheared purine-purine pairs, including three GA pairs or a combination of GA, GG, and AA pairs and is known to be thermodynamically stabilizing. 27, 35 …”

“…27 The 3RRs motif consists of three consecutive sheared purine-purine pairs, including three GA pairs or a combination of GA, GG, and AA pairs and is known to be thermodynamically stabilizing. 27, 35 …”