Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions

scientific article

Recognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1093/NAR/28.15.2935
P932PMC publication ID102689
P698PubMed publication ID10908357
P5875ResearchGate publication ID277497109

P2093author name stringD Wang
J A Cowan
K Natarajan
T Ohyama
P2860cites workSaccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamerQ27619183
Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE RNA complexQ27733230
Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptideQ27734487
Paromomycin binding induces a local conformational change in the A-site of 16 S rRNAQ27748953
Synthesis of small RNAs using T7 RNA polymeraseQ29615997
Interaction of antibiotics with functional sites in 16S ribosomal RNAQ29616813
RNA structure and NMR spectroscopyQ36713130
Specific binding of aminoglycoside antibiotics to RNA.Q36893237
1H NMR studies of the high-affinity Rev binding site of the Rev responsive element of HIV-1 mRNA: base pairing in the core binding elementQ38308302
Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactionsQ38358047
In vitro selection analysis of neomycin binding RNAs with a mutagenized pool of variants of the 16S rRNA decoding regionQ38359224
Small molecules that selectively block RNA binding of HIV-1 Rev protein inhibit Rev function and viral productionQ41526627
In vitro selection of a viomycin-binding RNA pseudoknotQ42658806
The binding site of a specific aminoglycoside binding RNA moleculeQ42675535
Inhibition of the hammerhead ribozyme by neomycin.Q43205493
Synthesis and purification of large amounts of RNA oligonucleotides.Q46185103
Direct observation of aminoglycoside-RNA interactions by surface plasmon resonanceQ46281462
Ion effects on ligand-nucleic acid interactionsQ46833485
Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C-heteronuclear NMR.Q53999593
Preparation of isotopically enriched RNAs for heteronuclear NMR.Q54619928
Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunitQ59062684
Modeling RNA-ligand interactions: the Rev-binding element RNA-aminoglycoside complex.Q64946919
Non-competitive inhibition of group I intron RNA self-splicing by aminoglycoside antibioticsQ68034802
Neomycin inhibition of the hammerhead ribozyme involves ionic interactionsQ72046600
A novel RNA motif for neomycin recognitionQ73909515
Minimal RNA constructs that specifically bind aminoglycoside antibiotics with high affinitiesQ74024094
Binding of neomycin-class aminoglycoside antibiotics to the A-site of 16 S rRNAQ74352573
Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNAQ74496312
P433issue15
P407language of work or nameEnglishQ1860
P304page(s)2935-2942
P577publication date2000-08-01
P1433published inNucleic Acids ResearchQ135122
P1476titleRecognition of a cognate RNA aptamer by neomycin B: quantitative evaluation of hydrogen bonding and electrostatic interactions
P478volume28

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cites work (P2860)
Q37661656An RNA aptamer possessing a novel monovalent cation-mediated fold inhibits lysozyme catalysis by inhibiting the binding of long natural substrates
Q38307602An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures
Q51578933An investigation on the interaction modes of a single-strand DNA aptamer and RBP4 protein: a molecular dynamic simulations approach.
Q35761658Aptamers for pharmaceuticals and their application in environmental analytics
Q33871203Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA
Q38077027Binding sugars: from natural lectins to synthetic receptors and engineered neolectins
Q47389545Capreomycin and hygromycin B modulate the catalytic activity of the delta ribozyme in a manner that depends on the protonation and complexation with Cu2+ ions of these antibiotics
Q33691290Carbohydrate recognition by boronolectins, small molecules, and lectins
Q28484847Challenges and opportunities for small molecule aptamer development
Q34459868Chemical nucleases
Q34354156Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study.
Q31058286DNA aptamers against the Lup an 1 food allergen.
Q38341396Defining a Stem Length-Dependent Binding Mechanism for the Cocaine-Binding Aptamer. A Combined NMR and Calorimetry Study
Q38335658Entropy and Mg2+ control ligand affinity and specificity in the malachite green binding RNA aptamer
Q58717959G-Quadruplex-Forming DNA Aptamers Inhibit the DNA-Binding Function of HupB and Mycobacteriumtuberculosis Entry into Host Cells
Q34693492Kinetics and Mechanisms of Oxidative Cleavage of HIV RRE RNA by Rev-Coupled Transition Metal Chelates
Q90241067No Structure-Switching Required: A Generalizable Exonuclease-Mediated Aptamer-Based Assay for Small-Molecule Detection
Q38306204Probing the shielding properties of aptameric protective groups.
Q37024725RNA as a versatile and powerful platform for engineering genetic regulatory tools
Q34796685RNA-acting antibiotics: in-vitro selection of RNA aptamers for the design of new bioactive molecules less susceptible to bacterial resistance
Q38318269Salt bridge exchange binding mechanism between streptavidin and its DNA aptamer--thermodynamics and spectroscopic evidences
Q38289590Salt-mediated two-site ligand binding by the cocaine-binding aptamer.
Q54327282Selective transformations of complex molecules are enabled by aptameric protective groups.
Q33228631Study of binding stoichiometries of the human immunodeficiency virus type 1 reverse transcriptase by capillary electrophoresis and laser-induced fluorescence polarization using aptamers as probes.
Q36070170Targeted cleavage of HIV RRE RNA by Rev-coupled transition metal chelates
Q42112131Toggled RNA aptamers against aminoglycosides allowing facile detection of antibiotics using gold nanoparticle assays

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