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Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/anie.199410841openalex-snapshot

Isolation of RNA Aptamers for Biological Cofactors by In Vitro Selection

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Highly Modular Structure and Ligand Binding by Conformational Capture in a Minimalistic Riboswitch

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Rapid Identification of Noncanonical RNA Structure Elements by Direct Detection of OH⋅⋅⋅OP, NH⋅⋅⋅OP, and NH2⋅⋅⋅OP Hydrogen Bonds in Solution NMR Spectroscopy

inferredcites →https://doi.org/10.1002/anie.201304391openalex-snapshot

Efficient Detection of Hydrogen Bonds in Dynamic Regions of RNA by Sensitivity‐Optimized NMR Pulse Sequences

inferredcites →https://doi.org/10.1002/anie.201507365openalex-snapshot

What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin‐Sensing Riboswitch

inferredcites →https://doi.org/10.1002/anie.201609184openalex-snapshot

A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP‐Binding RNA Aptamer

inferredcites →https://doi.org/10.1002/pro.3632openalex-snapshot

From fluorescent proteins to fluorogenic RNAs: Tools for imaging cellular macromolecules

inferredcites →https://doi.org/10.1002/wrna.1383openalex-snapshot

Fluorophore‐binding RNA aptamers and their applications

inferredcites →https://doi.org/10.1002/wrna.1482openalex-snapshot

Guanidine‐sensing riboswitches: How do they work and what do they regulate?

inferredcites →https://doi.org/10.1006/jmbi.1996.0263openalex-snapshot

Molecular Recognition in the FMN – RNA Aptamer Complex

inferredcites →https://doi.org/10.1006/jmbi.1996.0690openalex-snapshot

A Network of Heterogeneous Hydrogen Bonds in GNRA Tetraloops

inferredcites →https://doi.org/10.1006/jmbi.2000.3951openalex-snapshot

2.8 Å crystal structure of the malachite green aptamer 1 1Edited by J. A. Doudna

inferredcites →https://doi.org/10.1006/jmre.2001.2350openalex-snapshot

Calculation of 13C Chemical Shifts in RNA Nucleosides: Structure-13C Chemical Shift Relationships

inferredcites →https://doi.org/10.1007/s10858-017-0140-7openalex-snapshot

NMR experiments for the rapid identification of P=O···H–X type hydrogen bonds in nucleic acids

inferredcites →https://doi.org/10.1007/s12104-016-9715-6openalex-snapshot

NMR resonance assignments for the tetramethylrhodamine binding RNA aptamer 3 in complex with the ligand 5-carboxy-tetramethylrhodamine

inferredcites →https://doi.org/10.1016/1074-5521(95)90188-4openalex-snapshot

A novel RNA motif for neomycin recognition

inferredcites →https://doi.org/10.1016/j.bpj.2012.03.074openalex-snapshot

Individual Basepair Stability of DNA and RNA Studied by NMR-Detected Solvent Exchange

inferredcites →https://doi.org/10.1016/j.cbpa.2013.05.014openalex-snapshot

New approaches for sensing metabolites and proteins in live cells using RNA

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Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes

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The Structure of the Stemloop D Subdomain of Coxsackievirus B3 Cloverleaf RNA and Its Interaction with the Proteinase 3C

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Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer–ligand complex

inferredcites →https://doi.org/10.1017/s1355838201002515openalex-snapshot

Geometric nomenclature and classification of RNA base pairs

inferredcites →https://doi.org/10.1021/cb500499xopenalex-snapshot

RNA Mango Aptamer-Fluorophore: A Bright, High-Affinity Complex for RNA Labeling and Tracking

inferredcites →https://doi.org/10.1021/ja00084a010openalex-snapshot

Molecular Recognition of Amino Acids by RNA-Aptamers: An L-Citrulline Binding RNA Motif and Its Evolution into an L-Arginine Binder

inferredcites →https://doi.org/10.1021/ja00150a001openalex-snapshot

Improved RNA Structure Determination by Detection of NOE Contacts to Exchange-Broadened Amino Protons

inferredcites →https://doi.org/10.1021/ja031504aopenalex-snapshot

Informational Complexity and Functional Activity of RNA Structures

inferredcites →https://doi.org/10.1021/ja037994oopenalex-snapshot

Aptamers Switch on Fluorescence of Triphenylmethane Dyes

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Aptamers Selected for Higher-Affinity Binding Are Not More Specific for the Target Ligand

inferredcites →https://doi.org/10.1038/346818a0openalex-snapshot

In vitro selection of RNA molecules that bind specific ligands

inferredcites →https://doi.org/10.1038/364550a0openalex-snapshot

An RNA motif that binds ATP

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Structural basis of RNA folding and recognition in an AMP–RNA aptamer complex

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Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA

inferredcites →https://doi.org/10.1038/nsmb710openalex-snapshot

Adenine riboswitches and gene activation by disruption of a transcription terminator

inferredcites →https://doi.org/10.1073/pnas.0705884104openalex-snapshot

Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine

inferredcites →https://doi.org/10.1073/pnas.1720406115openalex-snapshot

Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems

inferredcites →https://doi.org/10.1073/pnas.182095699openalex-snapshot

Isolation of high-affinity GTP aptamers from partially structured RNA libraries

inferredcites →https://doi.org/10.1073/pnas.242720799openalex-snapshot

Mutations linked to dyskeratosis congenita cause changes in the structural equilibrium in telomerase RNA

inferredcites →https://doi.org/10.1073/pnas.96.11.6131openalex-snapshot

Laser-mediated, site-specific inactivation of RNA transcripts

inferredcites →https://doi.org/10.1093/nar/24.5.977openalex-snapshot

Use of Cis- and Trans-Ribozymes to Remove 5' and 3' Heterogeneities From Milligrams of In Vitro Transcribed RNA

inferredcites →https://doi.org/10.1093/nar/gkh321openalex-snapshot

A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo

inferredcites →https://doi.org/10.1093/nar/gkm565openalex-snapshot

Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain

inferredcites →https://doi.org/10.1093/nar/gkp956openalex-snapshot

High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA

inferredcites →https://doi.org/10.1093/nar/gkq082openalex-snapshot

Selecting RNA aptamers for synthetic biology: investigating magnesium dependence and predicting binding affinity

inferredcites →https://doi.org/10.1107/s0021889800008372openalex-snapshot

Solving the generalized indirect Fourier transformation (GIFT) by Boltzmann simplex simulated annealing (BSSA)

inferredcites →https://doi.org/10.1107/s0021889809000338openalex-snapshot

DAMMIF , a program for rapid ab-initio shape determination in small-angle scattering

inferredcites →https://doi.org/10.1107/s0021889892001663openalex-snapshot

Determination of the regularization parameter in indirect-transform methods using perceptual criteria

inferredcites →https://doi.org/10.1126/science.1207339openalex-snapshot

RNA Mimics of Green Fluorescent Protein

inferredcites →https://doi.org/10.1126/science.2200121openalex-snapshot

Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase

inferredcites →https://doi.org/10.1126/science.272.5266.1343openalex-snapshot

Structural Basis of Ligand Discrimination by Two Related RNA Aptamers Resolved by NMR Spectroscopy

inferredcites →https://doi.org/10.1126/science.282.5387.296openalex-snapshot

Controlling Gene Expression in Living Cells Through Small Molecule-RNA Interactions

inferredcites →https://doi.org/10.1126/science.287.5454.820openalex-snapshot

Adaptive Recognition by Nucleic Acid Aptamers

inferredcites →https://doi.org/10.1126/science.7510417openalex-snapshot

High-Resolution Molecular Discrimination by RNA

inferredcites →https://doi.org/10.1139/o08-008openalex-snapshot

Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteineThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process.

inferredcites →https://doi.org/10.1146/annurev.biochem.78.070507.135656openalex-snapshot

The Structural and Functional Diversity of Metabolite-Binding Riboswitches

inferredcites →https://doi.org/10.1146/annurev.biophys.37.032807.130000openalex-snapshot

Riboswitches: Emerging Themes in RNA Structure and Function

inferredcites →https://doi.org/10.1261/rna.058909.116openalex-snapshot

An intermolecular G-quadruplex as the basis for GTP recognition in the class V–GTP aptamer

inferredcites →https://doi.org/10.1261/rna.2162205openalex-snapshot

An artificial riboswitch for controlling pre-mRNA splicing

inferredcites →https://doi.org/10.1261/rna.2251306openalex-snapshot

Solution structure of an informationally complex high-affinity RNA aptamer to GTP

inferredcites →https://doi.org/10.1261/rna.5990203openalex-snapshot

Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer

inferredcites →https://doi.org/10.1261/rna.772408openalex-snapshot

Screening for engineered neomycin riboswitches that control translation initiation

What points at this work

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

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inferred← citeshttps://doi.org/10.1002/cbic.202300110openalex-snapshot

Advances, Applications, and Perspectives in Small‐Angle X‐ray Scattering of RNA

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Honeydew: A Fluorescent Aptamer for Low‐Cost Azo Food Dyes

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From fluorescent proteins to fluorogenic RNAs: Tools for imaging cellular macromolecules

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Analyzing aptamer structure and interactions: in silico modelling and instrumental methods

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Ligand specificity and affinity in the sulforhodamine B binding RNA aptamer

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Multifunctional rolling circle transcription-based nanomaterials for advanced drug delivery

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NMR of RNA - Structure and interactions

inferred← citeshttps://doi.org/10.1016/j.talanta.2023.125039openalex-snapshot

Highly-efficient selection of aptamers for detecting various HPV subtypes in clinical samples

inferred← citeshttps://doi.org/10.1016/j.tifs.2025.105196openalex-snapshot

Light-up fluorescent aptamer empowering smart bioanalysis

inferred← citeshttps://doi.org/10.1016/j.trac.2021.116311openalex-snapshot

Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c01330openalex-snapshot

RNA-Binding Small Molecules in Drug Discovery and Delivery: An Overview from Fundamentals

inferred← citeshttps://doi.org/10.1021/jacs.5c04576openalex-snapshot

Investigating the Conformational Diversity of the TMR-3 Aptamer

inferred← citeshttps://doi.org/10.1038/s41467-024-48478-9openalex-snapshot

Structural mechanisms for binding and activation of a contact-quenched fluorophore by RhoBAST

inferred← citeshttps://doi.org/10.1039/d5ay01084eopenalex-snapshot

Electrochemical aptasensing strategies for emerging organic pollutants in environmental analysis

inferred← citeshttps://doi.org/10.1073/pnas.2404060121openalex-snapshot

Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization

inferred← citeshttps://doi.org/10.1080/15476286.2023.2234732openalex-snapshot

Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer

inferred← citeshttps://doi.org/10.1093/nar/gkaf555openalex-snapshot

Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

inferred← citeshttps://doi.org/10.3389/fmolb.2022.1044126openalex-snapshot

An overview of structural approaches to study therapeutic RNAs

inferred← citeshttps://doi.org/10.3389/fmolb.2023.1157440openalex-snapshot

Editorial: RNAs at the crossroads between effectors and targets; discovery and development of new drugs

inferred← citeshttps://doi.org/10.3390/bios14050210openalex-snapshot

Recent Advances in Aptamer-Based Biosensors for Bacterial Detection

inferred← citeshttps://doi.org/10.3390/ijms21197394openalex-snapshot

Using Aptamers as a Novel Method for Determining GnRH/LH Pulsatility

inferred← citeshttps://doi.org/10.7150/thno.80579openalex-snapshot

Recent progress of emitting long-wavelength carbon dots and their merits for visualization tracking, target delivery and theranostics

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