ArticleNucleic acids research2012
Conformational dynamics of the tetracycline-binding aptamer.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 59 citations in OpenAlex.
- Mechanism underlying the high regulatory performance of the doxycycline riboswitch G12.Nature communications · 2026Article
- A Small-Molecule Approach Enables RNA Aptamers to Function as Sensors for Reactive Inorganic Targets.Angewandte Chemie (International ed. in English) · 2025Article
- Rational design of eukaryotic riboswitches that up-regulate IRES-mediated translation initiation with high switching efficiency through a kinetic trapping mechanism in vitro.RNA (New York, N.Y.) · 2023Article
- Development of a novel tobramycin dependent riboswitch.Nucleic acids research · 2023Article
- Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer.RNA biology · 2023Review
- Article
- What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials.Nucleic acids research · 2021Article
- Aptamers, Riboswitches, and Ribozymes inLife (Basel, Switzerland) · 2021Review
- Perspective on the Future Role of Aptamers in Analytical Chemistry.Analytical chemistry · 2019Article
- Influence of MgRNA (New York, N.Y.) · 2019Article
- Conditional Regulation of Gene Expression by Ligand-Induced Occlusion of a MicroRNA Target Sequence.Molecular therapy : the journal of the American Society of Gene Therapy · 2018Article
- Riboswitching with ciprofloxacin-development and characterization of a novel RNA regulator.Nucleic acids research · 2018Article
- Design of Artificial Riboswitches as Biosensors.Sensors (Basel, Switzerland) · 2017Review
- Applicability of a computational design approach for synthetic riboswitches.Nucleic acids research · 2017Article
- Tetracycline determines the conformation of its aptamer at physiological magnesium concentrations.Biophysical journal · 2014Article
- An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures.RNA (New York, N.Y.) · 2014Article
- A family of synthetic riboswitches adopts a kinetic trapping mechanism.Nucleic acids research · 2014Article
- Nanopore force spectroscopy of aptamer-ligand complexes.Biophysical journal · 2013Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The conformational dynamics induced by ligand binding to the tetracycline-binding aptamer is monitored via stopped-flow fluorescence spectroscopy and time-correlated single photon counting experiments. The fluorescence of the ligand is sensitive to changes within the tertiary structure of the aptamer during and after the binding process. In addition to the wild-type aptamer, the mutants A9G, A13U and A50U are examined, where bases important for regulation are changed to inhibit the aptamer's function. Our results suggest a very fast two-step-mechanism for the binding of the ligand to the aptamer that can be interpreted as a binding step followed by a reorganization of the aptamer to accommodate the ligand. Binding to the two direct contact points A13 and A50 was found to occur in the first binding step. The exchange of the structurally important base A9 for guanine induces an enormous deceleration of the overall binding process, which is mainly rooted in an enhancement of the back reaction of the first binding step by several orders of magnitude. This indicates a significant loss of tertiary structure of the aptamer in the absence of the base A9, and underlines the importance of pre-organization on the overall binding process of the tetracycline-binding aptamer.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.