Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer.

No abstract is available for this paper.

• Publication year

  2000

• Venue

  RNA: A publication of the RNA Society

• Publication date

  2000-05-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1017/S1355838200000169PMID 10836787PMCID PMC1369946
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme.

  1999cited by this paper
• In vitro selection of functional nucleic acids.

  1999cited by this paper
• A semiconserved residue inhibits complex formation by stabilizing interactions in the free state of a theophylline-binding RNA.

  1998cited by this paper
• Solution structure of the tobramycin–RNA aptamer complex

  1998cited by this paper
• Solution structure of an ATP-binding RNA aptamer reveals a novel fold.

  1997cited by this paper
• Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA

  1997cited by this paper
• Structural analysis of nucleic acid aptamers.

  1997cited by this paper
• RNA aptamers

  1997cited by this paper
• Nucleic Acid Selection and the Challenge of Combinatorial Chemistry.

  1997cited by this paper
• Aptamer structures from A to zeta.

  1996cited by this paper
• Aptamer structures from A to ζ

  1996cited by this paper
• Structural basis of RNA folding and recognition in an AMP–RNA aptamer complex

  1996cited by this paper
• Structural Basis of Ligand Discrimination by Two Related RNA Aptamers Resolved by NMR Spectroscopy

  1996cited by this paper
• Molecular recognition in the FMN-RNA aptamer complex.

  1996cited by this paper
• A network of heterogeneous hydrogen bonds in GNRA tetraloops.

  1996cited by this paper
• Divalent metal ion binding to a conserved wobble pair defining the upstream site of cleavage of group I self-splicing introns.

  1995cited by this paper
• Diversity of oligonucleotide functions.

  1995cited by this paper
• GNRA tetraloops make a U-turn.

  1995cited by this paper
• Stabilization of RNA structure by Mg ions. Specific and non-specific effects.

  1994cited by this paper
• High-resolution molecular discrimination by RNA.

  1994cited by this paper
• Proton NMR studies of manganese ion binding to tRNA-derived acceptor arm duplexes.

  1993cited by this paper
• Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA.

  1992cited by this paper
• Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies.

  1992cited by this paper
• Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin.

  1992cited by this paper
• Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops.

  1991cited by this paper
• In vitro selection of RNA molecules that bind specific ligands

  1990cited by this paper
• Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

  1990cited by this paper
• Binding and Linkage: Functional Chemistry of Biological Macromolecules

  1990cited by this paper
• Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins

  1989cited by this paper
• Synthesis of small RNAs using T7 RNA polymerase.

  1989cited by this paper
• Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.

  1987cited by this paper
• NMR of paramagnetic molecules in biological systems

  1986cited by this paper
• Transfer RNA in solution: selected topics.

  1980cited by this paper
• Structural domains of transfer RNA molecules.

  1976influential reference

• NMR and SPR Fragment-Based Screening Can Produce Novel High Affinity Small Molecule Hits against Structured RNAs.

  2025cites this paper
• How to Design Genetic Biosensors for Medical Purposes?

  2025cites this paper
• Mechanism of Ligand Binding to Theophylline RNA Aptamer

  2024cites this paper
• Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from Theophylline-Binding RNA Aptamer

  2024cites this paper
• Essential Considerations for Free Energy Calculations of RNA–Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer

  2024cites this paper
• START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances

  2024cites this paper
• Different Strategies for the Microfluidic Purification of Antibiotics from Food: A Comparative Study

  2023cites this paper
• Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering.

  2023cites this paper
• A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer

  2022cites this paper
• Discovery of small molecules that target a tertiary-structured RNA

  2022cites this paper
• Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions.

  2022cites this paper
• What defines a synthetic riboswitch? – Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials

  2021cites this paper
• Ligand-dependent tRNA processing by a rationally designed RNase P riboswitch

  2021cites this paper
• Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation

  2021cites this paper
• A malachite green light-up aptasensor for the detection of theophylline.

  2021cites this paper
• Systematic Review of Aptamer Sequence Reporting in the Literature Reveals Widespread Unexplained Sequence Alterations

  2021cites this paper
• The theophylline aptamer: 25 years as an important tool in cellular engineering research.

  2020cites this paper
• Parallel Implementation of String-Based Clustering for HT-SELEX Data

  2020cites this paper
• Amniotic fluid peptides predict postnatal kidney survival in developmental kidney disease.

  2020cites this paper
• FSBC: fast string-based clustering for HT-SELEX data

  2020cites this paper
• Alchemical free energy calculations via metadynamics: Application to the theophylline‐RNA aptamer complex

  2020cites this paper
• Parallel Implementation of Motif-Based Clustering for HT-SELEX Dataset

  2019cites this paper
• Low‐methoxyl pectin–zeolite hydrogels controlling drug release promote in vitro wound healing

  2019cites this paper
• 7,8‐Dihydro‐8‐oxoguanosine Lesions Inhibit the Theophylline Aptamer or Change Its Selectivity

  2019cites this paper
• Second-harmonic generation-based methods to detect and characterize ligand-induced RNA conformational changes.

  2019cites this paper
• Oligonucleotides

  2019cites this paper
• Thermodynamic and first-principles biomolecular simulations applied to synthetic biology: promoter and aptamer designs

  2018cites this paper
• Bioengineered Noncoding RNAs Selectively Change Cellular miRNome Profiles for Cancer Therapy

  2018cites this paper
• Riboswitches and synthetic aptamers : a head-to-head comparison

  2018cites this paper
• Design of Ligand‐Controlled Genetic Switches Based on RNA Interference

  2018cites this paper
• Investigations on the interface of nucleic acid aptamers and binding targets.

  2018cites this paper
• Regulation of T cell proliferation with drug-responsive microRNA switches

  2017cites this paper
• Detection of Ligand-Induced Conformational Changes in Oligonucleotides by Second-Harmonic Generation at a Supported Lipid Bilayer Interface.

  2016cites this paper
• Site-Specific Fluorescent Labeling of Nucleic Acids by Genetic Alphabet Expansion Using Unnatural Base Pair Systems

  2016cites this paper
• Twister ribozyme : from synthetic biology to in vivo function

  2016cites this paper
• Aberrant overexpression of ADAR1 promotes gastric cancer progression by activating mTOR/p70S6K signaling

  2016cites this paper
• A fast click-slow release strategy towards the HPLC-free synthesis of RNA.

  2016cites this paper
• Rational design of a synthetic mammalian riboswitch as a ligand-responsive -1 ribosomal frame-shifting stimulator

  2016cites this paper
• aptazymes as genetic regulatory switches

  2015cites this paper
• Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression

  2015cites this paper
• Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling.

  2015cites this paper
• A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae.

  2015cites this paper
• Magnetic microparticle-based SELEX process for the identification of highly specific aptamers of heart marker--brain natriuretic peptide

  2014cites this paper
• Nucléases cas9 commutables et leurs utilisations

  2014cites this paper
• Biosensor Design with Molecular Engineering and Nanotechnology

  2014cites this paper
• Aptamer‐Based Universal Fluorometric Sensors Based on Allosteric Modulation of RNA–Peptide Interactions

  2014cites this paper
• Synergetic regulation of translational reading-frame switch by ligand-responsive RNAs in mammalian cells

  2014cites this paper
• Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations.

  2014cites this paper
• Recent trends in SELEX technique and its application to food safety monitoring

  2014cites this paper
• Selection of RNAs for Constructing “Lighting-UP” Biomolecular Switches in Response to Specific Small Molecules

  2013cites this paper
• NMR Localization of Divalent Cations at the Active Site of the Neurospora VS Ribozyme Provides Insights into RNA–Metal-Ion Interactions

  2013cites this paper
• A novel dengue virus detection method that couples DNAzyme and gold nanoparticle approaches

  2013cites this paper
• Aptamers and Their Potential to Selectively Target Aspects of EGF, Wnt/β-Catenin and TGFβ–Smad Family Signaling

  2013cites this paper
• Cyclically amplified fluorescent detection of theophylline and thiamine pyrophosphate by coupling self-cleaving RNA ribozyme with endonuclease.

  2013cites this paper
• Computational design and biosensor applications of small molecule-sensing allosteric ribozymes.

  2013cites this paper
• Combining Rational and Evolutionary Approaches to Optimize Enzyme Activity in Saccharomyces cerevisiae

  2012cites this paper
• Probing Translation Initiation through Ligand Binding to the 5′ mRNA Coding Region

  2012cites this paper
• Quantitative and sensitive protein detection strategies based on aptamers

  2012cites this paper
• Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects.

  2012cites this paper
• Nucleinsäure- und Peptidaptamere: Grundlagen und bioanalytische Aspekte

  2012cites this paper
• High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch.

  2012cites this paper
• Nanomedicine Technologies for Cell-based Drug Screening

  2012cites this paper
• Self-assembled Peptide and Protein Nanostructures in Diagnosis

  2012cites this paper
• Gene Regulation System with an Artificial RNA Switch Operating in Human Cells

  2011cites this paper
• Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules

  2011cites this paper
• APTAMER SELECTION FOR JX-594

  2011cites this paper
• Riboswitches: structures and mechanisms.

  2011cites this paper
• Polymer Based Biosensors for Pathogen Diagnostics

  2011cites this paper
• Prevalence of syn nucleobases in the active sites of functional RNAs.

  2011cites this paper
• NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site

  2011cites this paper
• RNA recurrent motifs : identification and characterization

  2011cites this paper
• Evolution and protein packaging of small-molecule RNA aptamers.

  2011cites this paper
• Explicitly solvated ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer.

  2010cites this paper
• Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands.

  2010cites this paper
• Theophylline IMAGEtags (Intracellular Multi Aptamer Genetic tags): the development and evaluation of an RNA reporter system based on the theophylline aptamer

  2009influential citation
• Detection of bioactive small molecules by fluorescent resonance energy transfer (FRET) in RNA-protein conjugates.

  2009cites this paper
• Construction of intragenic synthetic riboswitches for detection of a small molecule

  2009cites this paper
• Design Principles for Riboswitch Function

  2009cites this paper
• Artificial Functional Nucleic Acids: Aptamers, Ribozymes, and Deoxyribozymes Identified by In Vitro Selection

  2009influential citation
• Use of a Riboswitch-controlled Conditional Hypomorphic Mutation to Uncover a Role for the Essential csrA Gene in Bacterial Autoaggregation*

  2009cites this paper
• In silico selection of RNA aptamers

  2009cites this paper
• Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme.

  2008cites this paper
• Development of an RNA-based theophylline-specific microarray biosensor

  2008cites this paper
• Characterization of PEGylated Anti-VEGF aptamers using surface plasmon resonance

  2008cites this paper
• Allosterisch regulierte Diels-Alder Ribozyme als maßgeschneiderte Werkzeuge in der Arzneistoffanalytik

  2008cites this paper
• Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing

  2008influential citation
• Model-guided design of ligand-regulated RNAi for programmable control of gene expression

  2008influential citation
• A flow cytometry-based screen for synthetic riboswitches

  2008cites this paper
• Higher-Order RNA Structural Requirements and Small-Molecule Induction of Tombusvirus Subgenomic mRNA Transcription

  2008influential citation
• A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function.

  2007cites this paper
• Calculation of absolute free energy of binding for theophylline and its analogs to RNA aptamer using nonequilibrium work values

  2007cites this paper
• A Novel Branch-Type PEGylation of Aptamer Therapeutics

  2007cites this paper
• Insight into the functional versatility of RNA through model-making with applications to data fitting

  2007cites this paper
• Aptamers as molecular recognition elements for electrical nanobiosensors

  2007cites this paper
• Riboswitching on RNA virus replication

  2007cites this paper
• Fluorescent energy transfer readout of an aptazyme-based biosensor.

  2006cites this paper
• Quenching of fluorophore-labeled DNA oligonucleotides by divalent metal ions: implications for selection, design, and applications of signaling aptamers and signaling deoxyribozymes.

  2006cites this paper
• Towards the discovery of drug-like RNA ligands?

  2006cites this paper
• Polymeric sensor materials: toward an alliance of combinatorial and rational design tools?

  2006cites this paper
• A Simple Fluorescent Biosensor for Theophylline Based on its RNA Aptamer

  2006cites this paper