Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex

“…First, the number of paired loop residues can vary from two up to seven (22,23,35). In addition, some of the kissing complexes possess nonpaired bases (22,24,25,(47)(48)(49). For example, the crystal structures of the HIV-1 MAL and LAI kissing complexes (49), the anticodon-anticodon interaction in tRNA Asp (47), and a loop-loop interaction in 23S rRNA (48) show coaxial alignment of the two opposite stems due to flanking residues on the 5Ј side.…”

“…In addition, some of the kissing complexes possess nonpaired bases (22,24,25,(47)(48)(49). For example, the crystal structures of the HIV-1 MAL and LAI kissing complexes (49), the anticodon-anticodon interaction in tRNA Asp (47), and a loop-loop interaction in 23S rRNA (48) show coaxial alignment of the two opposite stems due to flanking residues on the 5Ј side. The stabilization observed in the UV-melting data for this type of 5Ј configuration is likely to be caused by coaxial stacking (36).…”

Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon–codon hydrogen bonds as a major determinant of tRNA compositional variations

“…Out of 13 medial bp in four stems only bp 11-24 (in Archaea and Eukarya) displays the covariation patterns similar to the end residues. Interestingly, the refined crystallographic analysis revealed bases 11 and 24 as highly mobile in the yeast tRNA Asp (U11-A24), but not in the yeast tRNA Phe (C11-G24) (Westhof et al 1988).…”

“…There is some evidence suggesting that tRNAs with a 3-nt-long, i.e., minimized, Da region (adjacent to the invariable G18G19 forming a tertiary link with the T-loop in the corner of the tRNA tertiary fold) may possess a more labile tertiary structure in comparison to tRNAs with Da-4 (Westhof et al 1988;Amano and Kawakami 1992). If this is the case, the distribution of the eukaryotic DL size variations lies in line with the variations of D-stems (weak anticodon 0 strong DS and vice versa) in both Archaea and Eukarya.…”

RNA Junction Motifs as Scaffolds for Construction of Multifunctional RNA Nanoparticles

“…Each of these RNAs has a complex 3D fold, involving more than simple intrahelix interactions. Prior to publication of the high-resolution structures (Cate et al, 1996;Costantino et al, 2008;Martick and Scott, 2006;Westhof et al, 1988), significant biochemical or bioinformatic data describing tertiary interactions were available for each RNA. The secondary structure was also known to high accuracy in each case.…”