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A Small Molecule Microarray Platform To Select RNA Internal Loop−Ligand Interactions

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What this work says

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

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Tertiary Motifs in RNA Structure and Folding

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Click Chemistry: Diverse Chemical Function from a Few Good Reactions

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Monitoring Molecular Recognition of the Ribosomal Decoding Site

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Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems

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Chemical Microarrays to Identify Ligands that Bind Pathogenic Cells

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Using Selection to Identify and Chemical Microarray to Study the RNA Internal Loops Recognized by 6′‐N‐Acylated Kanamycin A

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Aminoglycoside Microarrays To Explore Interactions of Antibiotics with RNAs and Proteins

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Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

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All you wanted to know about SELEX

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Screening chemical libraries for nucleic-acid-binding drugs by in vitro selection: A test case with lividomycin

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[5] Synthesis of small RNAs using T7 RNA polymerase

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Synthesis and evaluation of novel bacterial rRNA-binding benzimidazoles by mass spectrometry

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In vitro evolution of nucleic acids

inferredcites →https://doi.org/10.1016/s0968-0896(01)00262-0openalex-snapshot

Molecular recognition of DNA by small molecules

inferredcites →https://doi.org/10.1016/s0968-0896(99)00170-4openalex-snapshot

tRNA Phe binds aminoglycoside antibiotics

inferredcites →https://doi.org/10.1016/s0969-2126(02)00934-6openalex-snapshot

Comparison of X-Ray Crystal Structure of the 30S Subunit-Antibiotic Complex with NMR Structure of Decoding Site Oligonucleotide-Paromomycin Complex

inferredcites →https://doi.org/10.1016/s1074-5521(02)00125-4openalex-snapshot

Aminoglycosides Modified by Resistance Enzymes Display Diminished Binding to the Bacterial Ribosomal Aminoacyl-tRNA Site

inferredcites →https://doi.org/10.1016/s1074-5521(03)00147-9openalex-snapshot

Preferred RNA Binding Sites for a Threading Intercalator Revealed by In Vitro Evolution

inferredcites →https://doi.org/10.1016/s1359-6446(03)02933-7openalex-snapshot

The growing impact of click chemistry on drug discovery

inferredcites →https://doi.org/10.1021/ar000118kopenalex-snapshot

Targeting RNA with Small-Molecule Drugs: Therapeutic Promise and Chemical Challenges

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Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics

inferredcites →https://doi.org/10.1021/bi0121609openalex-snapshot

Sequence-Specific Recognition of the Major Groove of RNA by Deoxystreptamine

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The Relationship between Aminoglycosides' RNA Binding Proclivity and Their Antiplasmid Effect on an IncB Plasmid

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Biochemical and Thermodynamic Characterization of Compounds That Bind to RNA Hairpin Loops: Toward an Understanding of Selectivity

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An Aminoglycoside Microarray Platform for Directly Monitoring and Studying Antibiotic Resistance

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Solution Structure of (rGCGGACGC)2 by Two-Dimensional NMR and the Iterative Relaxation Matrix Approach

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Solution Structure of (rGGCAGGCC)2 by Two-Dimensional NMR and the Iterative Relaxation Matrix Approach,

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Thermodynamic Analysis of an RNA Combinatorial Library Contained in a Short Hairpin

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Targeting a Pneumocystis carinii Group I Intron with Methylphosphonate Oligonucleotides: Backbone Charge Is Not Required for Binding or Reactivity

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Fluorescence-Based Approach for Detecting and Characterizing Antibiotic-Induced Conformational Changes in Ribosomal RNA: Comparing Aminoglycoside Binding to Prokaryotic and Eukaryotic Ribosomal RNA Sequences

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Application of NMR SHAPES Screening to an RNA Target

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In Vitro Evolution of Functional DNA Using Capillary Electrophoresis

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Combating Drug-Resistant Bacteria: Small Molecule Mimics of Plasmid Incompatibility as Antiplasmid Compounds

inferredcites →https://doi.org/10.1021/ja051685bopenalex-snapshot

Size-Specific Ligands for RNA Hairpin Loops

inferredcites →https://doi.org/10.1021/ja056159zopenalex-snapshot

Aminoglycoside-Induced Reduction in Nucleotide Mobility at the Ribosomal RNA A-Site as a Potentially Key Determinant of Antibacterial Activity

inferredcites →https://doi.org/10.1021/ja991083qopenalex-snapshot

Printing Small Molecules as Microarrays and Detecting Protein−Ligand Interactions en Masse

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SAR by MS: A Ligand Based Technique for Drug Lead Discovery Against Structured RNA Targets

inferredcites →https://doi.org/10.1021/jm050815oopenalex-snapshot

SAR by MS: Discovery of a New Class of RNA-Binding Small Molecules for the Hepatitis C Virus: Internal Ribosome Entry Site IIA Subdomain

inferredcites →https://doi.org/10.1021/ol0493094openalex-snapshot

Polytriazoles as Copper(I)-Stabilizing Ligands in Catalysis

inferredcites →https://doi.org/10.1038/35030019openalex-snapshot

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics

inferredcites →https://doi.org/10.1038/80729openalex-snapshot

Structural genomics of RNA.

inferredcites →https://doi.org/10.1038/nature01145openalex-snapshot

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression

inferredcites →https://doi.org/10.1073/pnas.0401799101openalex-snapshot

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

inferredcites →https://doi.org/10.1073/pnas.94.8.3548openalex-snapshot

An inhibitor of the Tat/TAR RNA interaction that effectively suppresses HIV-1 replication

inferredcites →https://doi.org/10.1073/pnas.96.18.10129openalex-snapshot

Determinants of aminoglycoside-binding specificity for rRNA by using mass spectrometry

inferredcites →https://doi.org/10.1093/nar/28.10.2158openalex-snapshot

Specific binding of Hoechst 33258 to site 1 thymidylate synthase mRNA

inferredcites →https://doi.org/10.1093/nar/28.12.e66openalex-snapshot

Preparation of DNA and protein micro arrays on glass slides coated with an agarose film

inferredcites →https://doi.org/10.1093/nar/8.10.2275openalex-snapshot

Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence

inferredcites →https://doi.org/10.1126/science.1064921openalex-snapshot

Identification of Novel Genes Coding for Small Expressed RNAs

inferredcites →https://doi.org/10.1126/science.274.5291.1367openalex-snapshot

Structure of the A Site of Escherichia coli 16 S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic

inferredcites →https://doi.org/10.1126/science.3941911openalex-snapshot

The Intervening Sequence RNA of Tetrahymena Is an Enzyme

inferredcites →https://doi.org/10.1385/1-59259-676-2:177openalex-snapshot

Screening RNA-Binding Libraries Using a Bacterial Transcription Antitermination Assay

inferredcites →https://doi.org/10.2144/04372mt02openalex-snapshot

Characterization of an inexpensive, nontoxic, and highly sensitive microarray substrate

What points at this work

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

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Resistance to Aminoglycosides

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Structure–Activity Relationships through Sequencing (StARTS) Defines Optimal and Suboptimal RNA Motif Targets for Small Molecules

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Small‐Molecule‐Mediated Cleavage of RNA in Living Cells

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Structure–Activity Relationships through Sequencing (StARTS) Defines Optimal and Suboptimal RNA Motif Targets for Small Molecules

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Small‐Molecule‐Mediated Cleavage of RNA in Living Cells

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Covalent Small‐Molecule–RNA Complex Formation Enables Cellular Profiling of Small‐Molecule–RNA Interactions

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Investigating the Intramolecular Competition of Different RNA Binding Motifs for Neomycin B by Native Top‐Down Mass Spectrometry

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Computational Tools for Design of Selective Small Molecules Targeting RNA: From Small Molecule Microarrays to Chemical Similarity Searching

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The Expanding World of Small Molecule Microarrays

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A Microarray-Based Method to Perform Nucleic Acid Selections

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Chemical Tools to Target Noncoding RNAs

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Chemical Tools to Target Noncoding RNAs

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Enzymology of Bacterial Resistance

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Identifying and validating small molecules interacting with RNA (SMIRNAs)

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Defining RNA motif–aminoglycoside interactions via two-dimensional combinatorial screening and structure–activity relationships through sequencing

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A new small molecule DoNA binding to CAG repeat RNA

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Synthesis of hyaluronan-amikacin conjugate and its bactericidal activity against intracellular bacteria in vitro and in vivo

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Progress toward the development of the small molecule equivalent of small interfering RNA

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Methods for identifying and characterizing interactions involving RNA

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Microarray-based technologies for the discovery of selective, RNA-binding molecules

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Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence

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Using Genome Sequence to Enable the Design of Medicines and Chemical Probes

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Defining RNA–Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA

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Discovery of Inhibitors of MicroRNA-21 Processing Using Small Molecule Microarrays

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Structure-Specific Cleavage of an RNA Repeat Expansion with a Dimeric Small Molecule Is Advantageous over Sequence-Specific Recognition by an Oligonucleotide

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Massively Parallel Optimization of the Linker Domain in Small Molecule Dimers Targeting a Toxic r(CUG) Repeat Expansion

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High-Throughput Platform Assay Technology for the Discovery of pre-microRNA-Selective Small Molecule Probes

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Molecular Recognition of 6′-N-5-Hexynoate Kanamycin A and RNA 1x1 Internal Loops Containing CA Mismatches

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Secondary Structure of a Conserved Domain in an Intron of Influenza A M1 mRNA

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Two-Dimensional Combinatorial Screening Identifies Specific 6′-Acylated Kanamycin A− and 6′-Acylated Neamine−RNA Hairpin Interactions

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Two-Dimensional Combinatorial Screening Identifies Specific Aminoglycoside−RNA Internal Loop Partners

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RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning

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Two-dimensional combinatorial screening enables the bottom-up design of a microRNA-10b inhibitor

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New trends in the use of aminoglycosides

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Delivery of an active lysosomal enzyme using GNeosomes

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Probing the hras -1 Y i-motif with small molecules

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RNA-binding fluorogenic probes: G-clamp conjugated with a thiazole orange derivative for screening RNA-binding small molecules

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Devices and approaches for generating specific high-affinity nucleic acid aptamers

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Design of a small molecule against an oncogenic noncoding RNA

inferred← citeshttps://doi.org/10.1093/bioinformatics/btz375openalex-snapshot

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

inferred← citeshttps://doi.org/10.1093/nar/gkp549openalex-snapshot

Discovering ligands for a microRNA precursor with peptoid microarrays

inferred← citeshttps://doi.org/10.1093/nar/gkp594openalex-snapshot

Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside–RNA hairpin loop interactions

inferred← citeshttps://doi.org/10.1093/nar/gkq793openalex-snapshot

Structural characterization of naturally occurring RNA single mismatches

inferred← citeshttps://doi.org/10.1101/263509openalex-snapshot

LinearFold: Linear-Time Prediction of RNA Secondary Structures

inferred← citeshttps://doi.org/10.1101/cshperspect.a003665openalex-snapshot

Folding and Finding RNA Secondary Structure

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Approaches to Validate and Manipulate RNA Targets with Small Molecules in Cells

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Target-Directed Approaches for Screening Small Molecules against RNA Targets

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Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA

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Identification of potential conserved RNA secondary structure throughout influenza A coding regions

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A simple ligation-based method to increase the information density in sequencing reactions used to deconvolute nucleic acid selections

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Small Molecule Inhibitors of MicroRNA

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MBNL derivatives for therapeutic application in myotonic dystrophy

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