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2’- O -methylation alters the RNA secondary structural ensemble

https://doi.org/10.1101/2020.05.28.121996
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Hydrophobic Groups Stabilize the Hydration Shell of 2′-O-Methylated RNA Duplexes
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SAM‐II Riboswitch Samples at least Two Conformations in Solution in the Absence of Ligand: Implications for Recognition
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Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy
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Nuclear magnetic resonance study of the impact of ribose 2′‐O‐methylation on the aqueous solution conformation of cytidylyl‐(3′ → 5′)‐cytidine
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Chemical Shifts in Nucleic Acids Studied by Density Functional Theory Calculations and Comparison with Experiment
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Defects in tRNA Anticodon Loop 2′-O-Methylation Are Implicated in Nonsyndromic X-Linked Intellectual Disability due to Mutations inFTSJ1
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NMRPipe: A multidimensional spectral processing system based on UNIX pipes
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The folding of an enzyme
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Conformations of nucleosides and nucleotides
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Sequences containing methylated nucleotides at the 5′ termini of messenger RNAs: Possible implications for processing
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Alterations in Nucleolar Structure and Gene Expression Programs in Prostatic Neoplasia Are Driven by the MYC Oncogene
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scaRNAs regulate splicing and vertebrate heart development
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RNA ribose methylation (2′-O-methylation): Occurrence, biosynthesis and biological functions
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Synthesis and solution conformation studies of the modified nucleoside N4,2′-O-dimethylcytidine (m4Cm) and its analogues
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p53 Acts as a Safeguard of Translational Control by Regulating Fibrillarin and rRNA Methylation in Cancer
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Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
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Probing RNA Conformational Equilibria within the Functional Cellular Context
inferredcites →https://doi.org/10.1016/j.jmb.2019.12.009openalex-snapshot
Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States
inferredcites →https://doi.org/10.1016/j.jmr.2019.106589openalex-snapshot
Direct evidence for (G)O6···H2-N4(C)+ hydrogen bonding in transient G(syn)-C+ and G(syn)-m5C+ Hoogsteen base pairs in duplex DNA from cytosine amino nitrogen off-resonance R1ρ relaxation dispersion measurements
inferredcites →https://doi.org/10.1016/j.molcel.2020.01.001openalex-snapshot
The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness
inferredcites →https://doi.org/10.1016/j.molcel.2020.01.002openalex-snapshot
LARP7-Mediated U6 snRNA Modification Ensures Splicing Fidelity and Spermatogenesis in Mice
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Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion
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Advances in RNA structure analysis by chemical probing
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Characterizing excited conformational states of RNA by NMR spectroscopy
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Exploration of the Transition State for Tertiary Structure Formation between an RNA Helix and a Large Structured RNA
inferredcites →https://doi.org/10.1016/s0092-8674(00)81308-2openalex-snapshot
Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs
inferredcites →https://doi.org/10.1017/s003358351600007xopenalex-snapshot
Bridging the gap betweenin vitroandin vivoRNA folding
inferredcites →https://doi.org/10.1021/acs.biochem.6b00285openalex-snapshot
Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales
inferredcites →https://doi.org/10.1021/acs.joc.8b01329openalex-snapshot
Adjusting the Structure of 2′-Modified Nucleosides and Oligonucleotides via C4′-α-F or C4′-α-OMe Substitution: Synthesis and Conformational Analysis
inferredcites →https://doi.org/10.1021/ar200137dopenalex-snapshot
Mapping the Landscape of RNA Dynamics with NMR Spectroscopy
inferredcites →https://doi.org/10.1021/bi00119a012openalex-snapshot
Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group
inferredcites →https://doi.org/10.1021/bi401677dopenalex-snapshot
Understanding the Effect of Locked Nucleic Acid and 2′-O-Methyl Modification on the Hybridization Thermodynamics of a miRNA–mRNA Pair in the Presence and Absence of AfPiwi Protein
inferredcites →https://doi.org/10.1021/cr9603791openalex-snapshot
Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides
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Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations
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Self-consistent molecular-orbital methods. 22. Small split-valence basis sets for second-row elements
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Self-consistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements
inferredcites →https://doi.org/10.1021/ja3001419openalex-snapshot
Studying “Invisible” Excited Protein States in Slow Exchange with a Major State Conformation
inferredcites →https://doi.org/10.1021/ja302148gopenalex-snapshot
Synthesis of (6-13C)Pyrimidine Nucleotides as Spin-Labels for RNA Dynamics
inferredcites →https://doi.org/10.1021/ja409835yopenalex-snapshot
Characterizing Slow Chemical Exchange in Nucleic Acids by Carbon CEST and Low Spin-Lock Field R1ρ NMR Spectroscopy
inferredcites →https://doi.org/10.1021/ja513080vopenalex-snapshot
Structure and Thermodynamics of N 6 -Methyladenosine in RNA: A Spring-Loaded Base Modification
inferredcites →https://doi.org/10.1021/ja909052hopenalex-snapshot
ϕ-Value Analysis for Ultrafast Folding Proteins by NMR Relaxation Dispersion
inferredcites →https://doi.org/10.1021/jacs.9b10939openalex-snapshot
NMR Chemical Exchange Measurements Reveal That N 6 -Methyladenosine Slows RNA Annealing
inferredcites →https://doi.org/10.1021/jm049167jopenalex-snapshot
Fully 2‘-Modified Oligonucleotide Duplexes with Improved in Vitro Potency and Stability Compared to Unmodified Small Interfering RNA
inferredcites →https://doi.org/10.1021/jp506703gopenalex-snapshot
Interplay of LNA and 2′- O -Methyl RNA in the Structure and Thermodynamics of RNA Hybrid Systems: A Molecular Dynamics Study Using the Revised AMBER Force Field and Comparison with Experimental Results
inferredcites →https://doi.org/10.1038/383732a0openalex-snapshot
Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides
inferredcites →https://doi.org/10.1038/cr.2017.15openalex-snapshot
YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA
inferredcites →https://doi.org/10.1038/gt.2011.100openalex-snapshot
Chemical modification and design of anti-miRNA oligonucleotides
inferredcites →https://doi.org/10.1038/nature11112openalex-snapshot
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
inferredcites →https://doi.org/10.1038/nature11498openalex-snapshot
Visualizing transient low-populated structures of RNA
inferredcites →https://doi.org/10.1038/nature14227openalex-snapshot
Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes
inferredcites →https://doi.org/10.1038/nbt.3765openalex-snapshot
The chemical evolution of oligonucleotide therapies of clinical utility
inferredcites →https://doi.org/10.1038/nchembio.2427openalex-snapshot
An excited state underlies gene regulation of a transcriptional riboswitch
inferredcites →https://doi.org/10.1038/ncomms4786openalex-snapshot
Observation of a three-dimensional topological Dirac semimetal phase in high-mobility Cd3As2
inferredcites →https://doi.org/10.1038/ncomms5786openalex-snapshot
Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics
inferredcites →https://doi.org/10.1038/nmeth.4294openalex-snapshot
Nm-seq maps 2′-O-methylation sites in human mRNA with base precision
inferredcites →https://doi.org/10.1038/nrd1955openalex-snapshot
Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease
inferredcites →https://doi.org/10.1038/nrm3742openalex-snapshot
A day in the life of the spliceosome
inferredcites →https://doi.org/10.1038/nsb1101-932openalex-snapshot
Studying excited states of proteins by NMR spectroscopy.
inferredcites →https://doi.org/10.1038/nsmb.2832openalex-snapshot
Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution
inferredcites →https://doi.org/10.1038/nsmb.2992openalex-snapshot
Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly
inferredcites →https://doi.org/10.1038/s41467-018-05243-zopenalex-snapshot
A potentially abundant junctional RNA motif stabilized by m6A and Mg2+
inferredcites →https://doi.org/10.1038/s41467-019-11375-7openalex-snapshot
Modification of messenger RNA by 2′-O-methylation regulates gene expression in vivo
inferredcites →https://doi.org/10.1038/s41580-018-0078-yopenalex-snapshot
Ribosome assembly coming into focus
inferredcites →https://doi.org/10.1038/s41580-019-0136-0openalex-snapshot
The roles of structural dynamics in the cellular functions of RNAs
inferredcites →https://doi.org/10.1038/s41594-018-0030-zopenalex-snapshot
2′-O-methylation in mRNA disrupts tRNA decoding during translation elongation
inferredcites →https://doi.org/10.1039/c7ob02317kopenalex-snapshot
Substoichiometric ribose methylations in spliceosomal snRNAs
inferredcites →https://doi.org/10.1056/nejmp1614154openalex-snapshot
Oligonucleotide Therapeutics — A New Class of Cholesterol-Lowering Drugs
inferredcites →https://doi.org/10.1063/1.438955openalex-snapshot
Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions
inferredcites →https://doi.org/10.1073/pnas.0705097104openalex-snapshot
Φ-Value analysis of a three-state protein folding pathway by NMR relaxation dispersion spectroscopy
inferredcites →https://doi.org/10.1073/pnas.1305688110openalex-snapshot
NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers
inferredcites →https://doi.org/10.1073/pnas.1407969111openalex-snapshot
Invisible RNA state dynamically couples distant motifs
inferredcites →https://doi.org/10.1073/pnas.1707674114openalex-snapshot
Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes
inferredcites →https://doi.org/10.1073/pnas.1905491116openalex-snapshot
RNA base-pairing complexity in living cells visualized by correlated chemical probing
inferredcites →https://doi.org/10.1073/pnas.71.10.3971openalex-snapshot
Identification of Methylated Nucleosides in Messenger RNA from Novikoff Hepatoma Cells
inferredcites →https://doi.org/10.1073/pnas.95.17.9819openalex-snapshot
A 1.3-Å resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation
inferredcites →https://doi.org/10.1093/nar/gkg680openalex-snapshot
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
inferredcites →https://doi.org/10.1093/nar/gkm855openalex-snapshot
The 3D rRNA modification maps database: with interactive tools for ribosome analysis
inferredcites →https://doi.org/10.1093/nar/gkw810openalex-snapshot
High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues
inferredcites →https://doi.org/10.1093/nar/gkx1239openalex-snapshot
Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs
inferredcites →https://doi.org/10.1093/nar/gkx525openalex-snapshot
Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics
inferredcites →https://doi.org/10.1093/nar/gky811openalex-snapshot
Landscape of the complete RNA chemical modifications in the human 80S ribosome
inferredcites →https://doi.org/10.1093/nar/gkz498openalex-snapshot
Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site
inferredcites →https://doi.org/10.1103/physrevb.37.785openalex-snapshot
Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
inferredcites →https://doi.org/10.1126/science.1621097openalex-snapshot
Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy
inferredcites →https://doi.org/10.1139/v78-457openalex-snapshot
The synthesis of oligoribonucleotides. II. The use of silyl protecting groups in nucleoside and nucleotide chemistry. VII
inferredcites →https://doi.org/10.1146/annurev-cellbio-100616-060758openalex-snapshot
Rethinking m6A Readers, Writers, and Erasers
inferredcites →https://doi.org/10.1161/circgenetics.111.961474openalex-snapshot
Noncoding RNA Expression in Myocardium From Infants With Tetralogy of Fallot
inferredcites →https://doi.org/10.1261/rna.041806.113openalex-snapshot
Post-transcriptional modifications modulate conformational dynamics in human U2–U6 snRNA complex
inferredcites →https://doi.org/10.1261/rna.044321.114openalex-snapshot
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states
inferredcites →https://doi.org/10.1261/rna.044503.114openalex-snapshot
Characterization of two homologous 2′-O-methyltransferases showing different specificities for their tRNA substrates
inferredcites →https://doi.org/10.1261/rna.065136.117openalex-snapshot
The life of U6 small nuclear RNA, from cradle to grave
inferredcites →https://doi.org/10.1261/rna.066258.118openalex-snapshot
Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics
inferredcites →https://doi.org/10.1261/rna.1582609openalex-snapshot
Evidence that U2/U6 helix I promotes both catalytic steps of pre-mRNA splicing and rearranges in between these steps
inferredcites →https://doi.org/10.1261/rna.2060210openalex-snapshot
Regulation of pre-mRNA splicing inXenopusoocytes by targeted 2′-O-methylation
inferredcites →https://doi.org/10.1261/rna.30706openalex-snapshot
Position-specific chemical modification of siRNAs reduces “off-target” transcript silencing
inferredcites →https://doi.org/10.1261/rna.7186504openalex-snapshot
Modified nucleotides at the 5′ end of human U2 snRNA are required for spliceosomal E-complex formation
inferredcites →https://doi.org/10.1371/journal.pone.0224850openalex-snapshot
m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB
inferredcites →https://doi.org/10.1385/0-89603-281-7:81openalex-snapshot
Oligoribonucleotide Synthesis: The Silyl-Phosphoramidite Method
inferredcites →https://doi.org/10.1515/hsz-2018-0205openalex-snapshot
Modifications in small nuclear RNAs and their roles in spliceosome assembly and function
inferredcites →https://doi.org/10.3390/biom7010013openalex-snapshot
Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation
inferredcites →https://doi.org/10.3390/biom8040106openalex-snapshot
2′-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation?
inferredcites →https://doi.org/10.3390/genes10020117openalex-snapshot
RNA 2′-O-Methylation (Nm) Modification in Human Diseases
inferredcites →https://doi.org/10.3390/jcdd5020026openalex-snapshot
The Role of scaRNAs in Adjusting Alternative mRNA Splicing in Heart Development
inferredcites →https://doi.org/10.7554/elife.31311openalex-snapshot
YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Recent advances in functional annotation and prediction of the epitranscriptome
inferred← citeshttps://doi.org/10.3390/ncrna7030051openalex-snapshot
The Importance of the Epi-Transcriptome in Translation Fidelity
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