Remarkable morphological variability of a common RNA folding motif: the GNRATetraloop-receptor interaction

Abramovitz, Dana L; Pyle, Anna Marie

doi:10.1006/jmbi.1996.0810

Cited by 104 publications

(90 citation statements)

References 46 publications

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“…However, both interactions help organize helical packing and stabilize the tertiary structure. Although similar GNRA loop-loop receptor interactions have been reported (Abramovitz and Pyle 1997;Geary et al 2008), these interactions show a diversity beyond GNRA loop interactions.…”

Section: Tetraloop-tetraloop Receptor and Other Loop-loop Receptor Momentioning

confidence: 52%

Annotation of tertiary interactions in RNA structures reveals variations and correlations

Xin

Laing

Leontis

et al. 2008

RNA

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RNA tertiary motifs play an important role in RNA folding and biochemical functions. To help interpret the complex organization of RNA tertiary interactions, we comprehensively analyze a data set of 54 high-resolution RNA crystal structures for motif occurrence and correlations. Specifically, we search seven recognized categories of RNA tertiary motifs (coaxial helix, A-minor, ribose zipper, pseudoknot, kissing hairpin, tRNA D-loop/T-loop, and tetraloop-tetraloop receptor) by various computer programs. For the nonredundant RNA data set, we find 613 RNA tertiary interactions, most of which occur in the 16S and 23S rRNAs. An analysis of these motifs reveals the diversity and variety of A-minor motif interactions and the various possible loop-loop receptor interactions that expand upon the tetraloop-tetraloop receptor. Correlations between motifs, such as pseudoknot or coaxial helix with A-minor, reveal higher-order patterns. These findings may ultimately help define tertiary structure restraints for RNA tertiary structure prediction. A complete annotation of the RNA diagrams for our data set is available at http://www.biomath.nyu.edu/motifs/.

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Section: Tetraloop-tetraloop Receptor and Other Loop-loop Receptor Momentioning

confidence: 52%

Annotation of tertiary interactions in RNA structures reveals variations and correlations

Xin

Laing

Leontis

et al. 2008

RNA

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“…One example, which provided the rationale for the experiments in Figure 3, is how the two paralogs of the pre-miRNA processing protein Dicer distinguish between their closely related RNA substrates through the presence or absence of a loop (Lee et al 2004;Tsutsumi et al 2011). Similarly, the length and sequence of the GNRA tetraloop of the yeast mitochondrial ai5g group II intron are critical for forming tertiary sequence-specific interactions (Abramovitz and Pyle 1997;Costa and Michel 1997). Likewise, the conserved internal loop of archaeal box C/D sRNAs imposes, through a mechanism not yet understood, a dimeric assembly of the in vitro-assembled box C/D sRNP.…”

Section: Discussionmentioning

confidence: 99%

The box C/D sRNP dimeric architecture is conserved across domain Archaea

Bower-Phipps

Taylor²,

Wang³

et al. 2012

RNA

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Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze RNA-guided 29-O-ribose methylation in two of the three domains of life. Recent structural studies have led to a controversy over whether box C/D sRNPs functionally assemble as monomeric or dimeric macromolecules. The archaeal box C/D sRNP from Methanococcus jannaschii (Mj) has been shown by glycerol gradient sedimentation, gel filtration chromatography, native gel analysis, and single-particle electron microscopy (EM) to adopt a di-sRNP architecture, containing four copies of each box C/D core protein and two copies of the Mj sR8 sRNA. Subsequently, investigators used a two-stranded artificial guide sRNA, CD45, to assemble a box C/D sRNP from Sulfolobus solfataricus with a short RNA methylation substrate, yielding a crystal structure of a mono-sRNP. To more closely examine box C/D sRNP architecture, we investigate the role of the omnipresent sRNA loop as a structural determinant of sRNP assembly. We show through sRNA mutagenesis, native gel electrophoresis, and single-particle EM that a di-sRNP is the near exclusive architecture obtained when reconstituting box C/D sRNPs with natural or artificial sRNAs containing an internal loop. Our results span three distantly related archaeal species-Sulfolobus solfataricus, Pyrococcus abyssi, and Archaeoglobus fulgidus-indicating that the di-sRNP architecture is broadly conserved across the entire archaeal domain.

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“…The first is the GAGA tetraloop that adopts the classic GNRA-type fold (R ϭ purine, N ϭ G, C, A, or U) [79]. This structure is characterized by extensive base stacking, which reduces the flexibility of the unpaired bases and adds stability to the hairpin fold.…”

Section: Structural Determinants Of Aminoglycoside Bindingmentioning

confidence: 99%

Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry

Turner

Hagan

Kohlway

et al. 2006

J. Am. Soc. Mass Spectrom.

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The binding modes and structural determinants of the noncovalent complexes formed by aminoglycoside antibiotics with conserved domains of the HIV-1 packaging signal (⌿-RNA) were investigated using electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). The location of the aminoglycoside binding sites on the different stemloop structures was revealed by characteristic coverage gaps in the ion series obtained by sustained off-resonance irradiation collision induced dissociation (SORI-CID) of the antibiotic-RNA assemblies. The site positions were confirmed using mutants that eliminated salient structural features of the ⌿-RNA domains. The effects of the mutations on the binding properties of the different substrates served to validate the position of the aminoglycoside site on the wild-type structures. Additional information was provided by docking experiments performed on the different aminoglycoside-stemloop complexes. The results have shown that, in the absence of features disrupting the regular A-helix of the double-stranded stem, aminoglycosides tend to bind in an area situated between the upper stem and the loop regions, as demonstrated for stemloop SL3. The presence of a tandem wobbles motif in SL4 modifies the regular geometry of the upper stem, which does not affect the general site location, but greatly increases its solution binding affinity compared with SL3. The platform motif in SL2 locates the binding site in the stem midsection and confers upon this stemloop an intermediate affinity toward aminoglycosides. In SL3 and SL4, the extensive overlap of the antibiotic site with the region used to bind the nucleocapsid (NC) protein provides the basis for a competition mechanism that could explain the aminoglycoside inhibition of the NC·SL3 and NC·SL4 assemblies. In contrast, the minimal overlap between the aminoglycoside and the NC sites in SL2 accounts for the absence of inhibition of the NC·SL2 complex. . The relatively low mutation frequency of this ϳ120 nt stretch of genomic RNA makes the packaging signal a very promising target for the development of new therapeutic strategies to contend with the rapid emergence of drug resistant strains [7,8]. For this reason, steps have been made toward the identification of possible inhibitors that may bind specific ⌿-RNA structures and disrupt their normal functions [9 -11]. In a systematic investigation of classic nucleic acid ligands, we have recently shown that aminoglycosidic antibiotics are not only capable of binding individual domains of ⌿-RNA, but can also inhibit their interactions with NC in a structure-specific fashion [12]. Initial tests to locate the actual binding sites on the different RNA substrates, which is crucial to explain the mechanism of preferential inhibition, were based on the analysis of mutant-ligand complexes performed by electrospray ionization (ESI) [13,14] and Fourier transform mass spectrometry (FTMS) [15,16].The favorable energetics characteristic of ESI enable the analysis of relatively labile noncovalent complex...

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Remarkable morphological variability of a common RNA folding motif: the GNRATetraloop-receptor interaction

Cited by 104 publications

References 46 publications

Annotation of tertiary interactions in RNA structures reveals variations and correlations

Annotation of tertiary interactions in RNA structures reveals variations and correlations

The box C/D sRNP dimeric architecture is conserved across domain Archaea

Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry

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