A'-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC)

Abstract

Here we demonstrate the presence of the A'-RNA conformation using the single crystal structure of a tridecamer: r(UGAGCUUCGGCUC). The average A'-RNA conformation deduced from X-ray fiber diffraction data had only been available previously, but now the presence of the A'-RNA conformation has been found in a single crystal structure for the first time. Statistical analysis showed that the A'-RNA conformation is distinguishable from the A-RNA conformation in a plot of the major groove width against the base pair inclination angle. The major groove of the A'-RNA conformation is wide enough to accommodate a protein or peptide while that of the A-RNA conformation is too narrow to do so. The presence of the A'-RNA conformation is significant for protein-RNA interaction.

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

“…Among RNA double-helices, two major right-handed conformations: the 11-fold helix of A-RNA and 12-fold helix of A'-RNA have been identified experimentally in crystal structures [11][12][13][14][15][16] . The major A-RNA conformation is apparent in natural RNA polynucleotides, or when crystallized from solutions of low ionic strength, while A'-RNA is formed from higher ionic strength solutions.…”

“…In general, unlike the regular conformation of DNA, such as A-, B-or Z-DNA, RNA structures are strikingly diverse, from linear duplex RNA, hairpin molecules to loop structures [6][7][8][9][10] . Among RNA double-helices, two major right-handed conformations: the 11-fold helix of A-RNA and 12-fold helix of A'-RNA have been identified experimentally in crystal structures [11][12][13][14][15][16] .…”

“…[11][12][13] For example, from Protein Database Bank (PDB) and Nucleic Acid Database (NDB) survey data, the following three RNA molecules have been found to adopt the structural features of A'-RNA: the tridecamer r(UGAGCUUCGGCUC), the RNA dodecamer duplex (r-GGACUUCGGUCC) 2 and helix IV of 5S rRNA. 16,18,19 For later reference the helical parameters, groove widths and torsion angles of these structures are provided in Table 1, computed utilizing two common structural analysis programs 3DNA 20 and CURVES. 21,22 Understanding both the structure and dynamics of RNA molecules on the atomistic level is critical to gaining a clearer picture of their role and function as therapeutic agents in gene silencing.…”

Imperfect CAG Repeats Form Diverse Structures in SCA1 Transcripts

“…Which of the postulated two geometries of the U-C pairs occurs in the RNAs: the U-Cϩ (with the neighboring carbonyl and imino groups involved in the formation of hydrogen bonds) or the neutral U-C pair (with N3-imino proton of U forming a watermediated hydrogen bond to the N3 of C)? Some answers to these questions come from the crystal structures of RNA duplexes containing the U-C pairs (43)(44)(45). It appears that the RNA duplex containing two tandem U-C mismatches in its central positions is very unstable compared with a similar duplex with the U-U mismatches (43).…”

Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

“…[43] To explore the conformational transition of RNA, the clustering analysis was applied to acquire the representative RNA structures. Figure 5 shows the structure of RNA at 300, 350, and 375 K and that in X-ray, and the conformation of RNA were found to be transitioned.…”