NMR Spectroscopy of RNA

Fürtig, Boris; Richter, Christian; Wöhnert, Jens; Schwalbe, Harald

doi:10.1002/cbic.200300700

Cited by 462 publications

(445 citation statements)

References 148 publications

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“…By one-dimensional NMR spectroscopy, we found that Lin28-binding RNAs contain imino resonances from 10 to 12.2 ppm, indicative of non-canonical hydrogen bonds (48,51,60). The imino resonance pattern is characteristic of the G:G:G:G hydrogen-bonding networks found in G4s (48,51,61).…”

Section: Discussionmentioning

confidence: 88%

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

O’Day

Imai

et al. 2015

Journal of Biological Chemistry

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Background: Lin28 is an evolutionary conserved RNA-binding protein that regulates miRNAs and mRNAs; Lin28 overexpression is linked to poor prognosis in cancer. Results: Lin28 binds to guanine-rich miRNAs and mRNAs that contain G-quartet structural features and remodels these structures. Conclusion: Lin28 recognition of G-quartets is a unifying feature of Lin28-regulated RNAs. Significance: Small molecules that bind to G-quartets might be useful inhibitors of Lin28 function.

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Section: Discussionmentioning

confidence: 88%

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

O’Day

Imai

et al. 2015

Journal of Biological Chemistry

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“…Nonexchangeable and exchangeable resonance assignments (BMRB deposition 6509) were obtained by using standard methodologies (see Supporting Methods, which is published as supporting information on the PNAS web site) (30) at 25°C and 10°C, respectively. NMR experiments were acquired on Varian Inova 500 MHz (Texas A&M University), Varian Inova 600 MHz (Texas A&M University͞Scripps Research Institute), or Bruker 900 MHz (Scripps Research Institute) spectrometers.…”

Section: Methodsmentioning

confidence: 99%

A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated –1 ribosomal frameshifting

Cornish

Hennig

Giedroc

2005

Proc. Natl. Acad. Sci. U.S.A.

170

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The molecular determinants of stimulation of ؊1 programmed ribosomal frameshifting (؊1 PRF) by RNA pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA pseudoknot that promotes ؊1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3 nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2 -OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1-2 -OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2-S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV͞BWYV chimeric pseudoknots reveal that the ScYLV RNA stimulates a higher level of ؊1 PRF (15 ؎ 2%) relative to the BWYV pseudoknot (6 ؎ 1%), a difference traced largely to the identity of the 3 nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by Ϸ1.5 kcal⅐mol ؊1 (pH 7.0, 37°C) with respect to the wild-type pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs.base triple ͉ RNA pseudoknot ͉ translational recoding

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“…The GSR apt -RNA comprises 73 nucleotides and is at the upper size limit for NMR analysis (32). To obtain site-resolved information by one-dimensional real-time NMR methods, selective isotope labeling of the RNA in combination with NMR filter experiments (33) was used.…”

Section: Two-mentioning

confidence: 99%

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Buck

Fürtig²,

Noeske³

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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131

140

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spectroscopy ͉ riboswitches ͉ dynamics ͉ purine ͉ caged compound S tructural transitions of proteins and RNA constitute an important aspect of cellular function and information transfer. In proteins, the kinetics of these structural transitions, mainly from an unfolded ensemble to a single unique folded state, can be investigated by hydrogen exchange experiments monitored by NMR spectroscopy (1). Such studies have profoundly influenced our understanding of protein-folding pathways. In hydrogen exchange experiments, labile hydrogen atoms become protected against exchange with the bulk solvent during folding. This acquired exchange protection indicates formation of a persistent structure at atomic resolution. Incorporation of structural information derived from exchange experiments into molecular dynamics (MD) simulations (2), including data from methods exhibiting time and atomic resolution together with -value analysis (3) derived from mutational work, has provided detailed structural information of intermediates populated during folding.RNA molecules can adopt a variety of secondary and tertiary conformations (4, 5). In general, the energetic difference between alternate RNA conformations is very small, and the equilibrium distribution is strongly affected through the binding of proteins (6), ions (7), or small metabolites (8-10), or by structural modifications (11). Alternate RNA structures are stabilized by different Watson-Crick base-pairing interactions (12). To date, RNA folding has been investigated by using x-ray footprinting (13), oligonucleotide hybridization, and classical biochemical methods in conjunction with mutational data (14). Although hydrogen exchange rates can be used as reporters of RNA ground-state dynamics and stability (15-17), RNA hydrogen exchange experiments conducted in a pulse-chase manner fail in most cases because of the high intrinsic exchange rates observed even in folded RNA structures.Here, we report on ligand-induced conformational changes of an RNA at atomic resolution by using real-time NMR methods. We investigated the hypoxanthine-induced folding of the guanine-sensing riboswitch aptamer domain (GSR apt ) of the Bacillus subtilis xpt-pbuX operon (18). Riboswitch RNAs have emerged as an important example of macromolecular structural transitions that lead to transcriptional or translational regulation of protein expression induced through the specific binding of a metabolite (reviewed in refs. 19 and 20). Riboswitches are located in the 5Ј-untranslated region (5Ј-UTR) of bacterial mRNA and consist of a highly specific metabolite receptor region (aptamer domain) coupled to a 3Ј-downstream sequence (expression platform). Gene expression is thought to be modulated in response to conformational differences between the ligand-bound and ligand-free conformations of the aptamer domain (21). Crystal structures of the ligand-bound aptamer domains belonging to the class of purine riboswitches (guanineand adenine-sensing riboswitches) have revealed the presence of complex tertiary stru...

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NMR Spectroscopy of RNA

Cited by 462 publications

References 148 publications

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates

A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated –1 ribosomal frameshifting

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

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