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Title
Alternate RNA Structures
Authors
Keywords
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Journal
Cold Spring Harbor Perspectives in Biology
Volume 12, Issue 1, Pages a032425
Publisher
Cold Spring Harbor Laboratory
Online
2020-01-03
DOI
10.1101/cshperspect.a032425
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- (2018) Sumit Mukherjee et al. Scientific Reports
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- (2018) Yongfeng Jin et al. Wiley Interdisciplinary Reviews-RNA
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- (2017) Joseph E. Wedekind et al. JOURNAL OF BIOLOGICAL CHEMISTRY
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- (2017) Sha Gong et al. MOLECULES
- An excited state underlies gene regulation of a transcriptional riboswitch
- (2017) Bo Zhao et al. Nature Chemical Biology
- RNA modifications and structures cooperate to guide RNA–protein interactions
- (2017) Cole J.T. Lewis et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch
- (2017) Heesoo Uhm et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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- Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes
- (2017) Sanjaya C. Abeysirigunawardena et al. Nature Communications
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- (2017) Adrien Chauvier et al. Nature Communications
- A Stably Protonated Adenine Nucleotide with a Highly Shifted pK a Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer
- (2016) Antje C. Wolter et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses
- (2016) Anna V. Sherwood et al. Annual Review of Microbiology
- RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure
- (2016) Zhipeng Lu et al. CELL
- N 6 -Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding
- (2016) Katherine I. Zhou et al. JOURNAL OF MOLECULAR BIOLOGY
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs
- (2016) Lorena G. Parlea et al. METHODS
- The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
- (2016) Dan Dominissini et al. NATURE
- DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo
- (2016) Meghan Zubradt et al. NATURE METHODS
- Cotranscriptional folding of a riboswitch at nucleotide resolution
- (2016) Kyle E Watters et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Transcriptional start site heterogeneity modulates the structure and function of the HIV-1 genome
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- (2016) Kyle E Watters et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial Group II Intron
- (2015) Maria Pechlaner et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- Translating the Genome in Time and Space: Specialized Ribosomes, RNA Regulons, and RNA-Binding Proteins
- (2015) Zhen Shi et al. Annual Review of Cell and Developmental Biology
- Kinetic regulation mechanism of pbuE riboswitch
- (2015) Sha Gong et al. JOURNAL OF CHEMICAL PHYSICS
- A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning
- (2015) Christopher Wostenberg et al. JOURNAL OF MOLECULAR BIOLOGY
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- (2015) Caroline Roost et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Mn 2+ -Sensing Mechanisms of yybP-ykoY Orphan Riboswitches
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- Bacterial Riboswitches Cooperatively Bind Ni 2+ or Co 2+ Ions and Control Expression of Heavy Metal Transporters
- (2015) Kazuhiro Furukawa et al. MOLECULAR CELL
- An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies
- (2015) Mohit Chawla et al. NUCLEIC ACIDS RESEARCH
- Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark
- (2015) Meredith Corley et al. NUCLEIC ACIDS RESEARCH
- The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication
- (2015) Chringma Sherpa et al. NUCLEIC ACIDS RESEARCH
- An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding
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- In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state
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- Role of lysine binding residues in the global folding of thelysCriboswitch
- (2015) Erich Smith-Peter et al. RNA Biology
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- (2015) Katrina M. Kutchko et al. RNA
- Long-range RNA pairings contribute to mutually exclusive splicing
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- Hierarchy of RNA Functional Dynamics
- (2014) Anthony M. Mustoe et al. Annual Review of Biochemistry
- Temperature-driven differential gene expression by RNA thermosensors
- (2014) Stefanie Sandra Krajewski et al. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms
- Structure and function of preQ 1 riboswitches
- (2014) Catherine D. Eichhorn et al. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms
- The purine riboswitch as a model system for exploring RNA biology and chemistry
- (2014) Ely B. Porter et al. Biochimica et Biophysica Acta-Gene Regulatory Mechanisms
- Themes and variations in riboswitch structure and function
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- Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins
- (2013) S. Li et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
- (2013) A. I. Petrov et al. RNA
- On the importance of cotranscriptional RNA structure formation
- (2013) D. Lai et al. RNA
- Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation
- (2013) Justin Ritz et al. PLoS Computational Biology
- snpTree - a web-server to identify and construct SNP trees from whole genome sequence data
- (2012) Pimlapas Leekitcharoenphon et al. BMC GENOMICS
- Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch
- (2012) Aiming Ren et al. NATURE
- Visualizing transient low-populated structures of RNA
- (2012) Elizabeth A. Dethoff et al. NATURE
- B12 cofactors directly stabilize an mRNA regulatory switch
- (2012) James E. Johnson Jr et al. NATURE
- Bacterial RNA thermometers: molecular zippers and switches
- (2012) Jens Kortmann et al. NATURE REVIEWS MICROBIOLOGY
- Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch
- (2012) Alla Peselis et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer
- (2012) P. C. Anthony et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structure and mechanism of purine-binding riboswitches
- (2012) Robert T. Batey QUARTERLY REVIEWS OF BIOPHYSICS
- Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches
- (2012) N. J. Baird et al. RNA
- Direct Observation of Cotranscriptional Folding in an Adenine Riboswitch
- (2012) K. L. Frieda et al. SCIENCE
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- Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch
- (2011) Ethan B. Butler et al. CHEMISTRY & BIOLOGY
- An equilibrium-dependent retroviral mRNA switch regulates translational recoding
- (2011) Brian Houck-Loomis et al. NATURE
- Conformational capture of the SAM-II riboswitch
- (2011) Andrea Haller et al. Nature Chemical Biology
- Viral subversion of the host protein synthesis machinery
- (2011) Derek Walsh et al. NATURE REVIEWS MICROBIOLOGY
- RNA secondary structure in mutually exclusive splicing
- (2011) Yun Yang et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch
- (2011) L. Huang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Role of HIV-1 nucleocapsid protein in HIV-1 reverse transcription
- (2011) Judith G Levin et al. RNA Biology
- New insights into RNA secondary structure in the alternative splicing of pre-mRNAs
- (2011) Yongfeng Jin et al. RNA Biology
- NMR Detection of Structures in the HIV-1 5'-Leader RNA That Regulate Genome Packaging
- (2011) K. Lu et al. SCIENCE
- Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride
- (2011) J. L. Baker et al. SCIENCE
- The Structure of a Tetrahydrofolate-Sensing Riboswitch Reveals Two Ligand Binding Sites in a Single Aptamer
- (2011) Jeremiah J. Trausch et al. STRUCTURE
- RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
- (2010) Mariusz Popenda et al. BMC BIOINFORMATICS
- A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate
- (2010) Tyler D. Ames et al. CHEMISTRY & BIOLOGY
- Structural Insights into Ligand Recognition by a Sensing Domain of the Cooperative Glycine Riboswitch
- (2010) Lili Huang et al. MOLECULAR CELL
- Riboswitch function: Flipping the switch or tuning the dimmer?
- (2010) Nathan J. Baird et al. RNA Biology
- Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster
- (2010) G. E. May et al. RNA
- Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
- (2010) N. J. Baird et al. RNA
- Identification of a tertiary interaction important for cooperative ligand binding by the glycine riboswitch
- (2010) T. V. Erion et al. RNA
- Riboswitches and the RNA World
- (2010) R. R. Breaker Cold Spring Harbor Perspectives in Biology
- Disease-Associated Mutations That Alter the RNA Structural Ensemble
- (2010) Matthew Halvorsen et al. PLoS Genetics
- Regulation of gene expression via the core promoter and the basal transcriptional machinery
- (2009) Tamar Juven-Gershon et al. DEVELOPMENTAL BIOLOGY
- A pH-responsive riboregulator
- (2009) Gal Nechooshtan et al. GENES & DEVELOPMENT
- Extending the Range of Microsecond-to-Millisecond Chemical Exchange Detected in Labeled and Unlabeled Nucleic Acids by Selective Carbon R1ρNMR Spectroscopy
- (2009) Alexandar L. Hansen et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element
- (2008) Andrew D. Garst et al. JOURNAL OF BIOLOGICAL CHEMISTRY
- Structural insights into amino acid binding and gene control by a lysine riboswitch
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- Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers
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- High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States
- (2008) Kevin A Wilkinson et al. PLOS BIOLOGY
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