ArticleNucleic acids research2009
Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe Ç.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 67 citations in OpenAlex.
- Explaining the Decay of Nucleic Acid-Based Sensors under Continuous Voltammetric Interrogation.Analytical chemistry · 2023Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Reduction in Dynamics of Base pair Opening upon Ligand Binding by the Cocaine-Binding Aptamer.Biophysical journal · 2020Article
- Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors.Nucleic acids research · 2020Review
- Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer.Nucleic acids research · 2019Article
- Aptamer-functionalized neural recording electrodes for the direct measurement of cocaine in vivo.Journal of materials chemistry. B · 2017Article
- General Strategy to Introduce pH-Induced Allostery in DNA-Based Receptors to Achieve Controlled Release of Ligands.Nano letters · 2015Article
- Recent advances in immunosensor for narcotic drug detection.BioImpacts : BI · 2015Article
- A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.BMC biophysics · 2015Article
- Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe.Nucleic acids research · 2014Article
- A comparison of the folding kinetics of a small, artificially selected DNA aptamer with those of equivalently simple naturally occurring proteins.Protein science : a publication of the Protein Society · 2014Article
- Nanopore force spectroscopy of aptamer-ligand complexes.Biophysical journal · 2013Article
- Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR.Nucleic acids research · 2013Article
- Using distal-site mutations and allosteric inhibition to tune, extend, and narrow the useful dynamic range of aptamer-based sensors.Journal of the American Chemical Society · 2012Article
- Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.The journal of physical chemistry. B · 2012Article
- Aptamers for pharmaceuticals and their application in environmental analytics.Bioanalytical reviews · 2012Article
- Electrochemical impedance spectroscopic sensing of methamphetamine by a specific aptamer.BioImpacts : BI · 2012Article
- Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe C.Nucleic acids research · 2011Article
- Precise mapping of RNA tertiary structure via nanometer distance measurements with double electron-electron resonance spectroscopy.Journal of the American Chemical Society · 2010Article
- RNA dynamics: perspectives from spin labels.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The cocaine aptamer is a DNA molecule that binds cocaine at the junction of three helices. The bifunctional spectroscopic probe Ç was incorporated independently into three different positions of the aptamer and changes in structure and dynamics upon addition of the cocaine ligand were studied. Nucleoside Ç contains a rigid nitroxide spin label and can be studied directly by electron paramagnetic resonance (EPR) spectroscopy and fluorescence spectroscopy after reduction of the nitroxide to yield the fluoroside Ç(f). Both the EPR and the fluorescence data for aptamer 2 indicate that helix III is formed before cocaine binding. Upon addition of cocaine, increased fluorescence of a fully base-paired Ç(f), placed at the three-way junction in helix III, was observed and is consistent with a helical tilt from a coaxial stack of helices II and III. EPR and fluorescence data clearly show that helix I is formed upon addition of cocaine, concomitant with the formation of the Y-shaped three-way helical junction. The EPR data indicate that nucleotides in helix I are more mobile than nucleotides in regular duplex regions and may reflect increased dynamics due to the short length of helix I.
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