Lighting Up of Thiazole Orange on G-Quadruplex DNA by High Pressure

Bhowmik, Sudipta; Takahashi, Shuntaro; Sugimoto, Naoki

doi:10.1021/acsomega.8b03430

Cited by 5 publications

(1 citation statement)

References 31 publications

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“…Hemicyanines have also been utilized to stain G-quadruplex (GQ) structures, − which contain stacked G-tetrads connected by loop residues that are stabilized by cation coordination within the central cavity. , GQs can exhibit structural polymorphism and produce parallel, hybrid, or antiparallel topologies. They also represent a common recognition element for the construction of nucleic acid-based biosensors (aptasensors) that afford a specific GQ topology in response to target binding .…”

Section: Introductionmentioning

confidence: 99%

Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching

et al. 2020

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Fluorescent nucleobases represent an important class of molecular reporters of nucleic acid interactions. In this work, the advantages of utilizing a noncanonical fluorescent nucleobase surrogate for monitoring thrombin binding by the 15-mer thrombin binding aptamer (TBA) is presented. TBA folds into an antiparallel G-quadruplex (GQ) with loop thymidine (T) residues interacting directly with the protein in the thrombin−TBA complex. In the free GQ, T3 is solventexposed and does not form canonical base-pairs within the antiparallel GQ motif. Upon thrombin binding, T3 interacts directly with a hydrophobic protein binding pocket. Replacing T3 with a cyanine-indole-quinolinium (4QI) hemicyanine dye tethered to an acyclic 1,2-propanediol linker is shown to have minimal impact on GQ stability and structure with the internal 4QI displaying a 40-fold increase in emission intensity at 586 nm (excitation 508 nm) compared to the free dye in solution. Molecular dynamics (MD) simulations demonstrate that the 4QI label π-stacks with T4 and T13 within the antiparallel GQ fold, which is supported by strong energy transfer (ET) fluorescence from the GQ (donor) to the 4QI label (acceptor). Thrombin binding to 4QI-TBA diminishes π-stacking interactions between 4QI and the GQ structure to cause a turn-off emission intensity response with an apparent dissociation constant (K d ) of 650 nM and a limit of detection (LoD) of 150 nM. These features highlight the utility of internal noncanonical fluorescent surrogates for monitoring protein binding by GQfolding aptamers in the absence of DNA topology switching.

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Section: Introductionmentioning

confidence: 99%

Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching

et al. 2020

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Meeting report: Seventh International Meeting on Quadruplex Nucleic Acids (Changchun, P.R. China, September 6–9, 2019)

Mergny

2020

Biochimie

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Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation

Oliva

Mukherjee

Winter

2021

Sci Rep

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Recently, non-canonical DNA structures, such as G-quadruplexes (GQs), were found to be highly pressure sensitive, suggesting that pressure modulation studies can provide additional mechanistic details of such biomolecular systems. Using FRET and CD spectroscopy as well as binding equilibrium measurements, we investigated the effect of pressure on the binding reaction of the ligand ThT to the quadruplex 22AG in solutions containing different ionic species and a crowding agent mimicking the intracellular milieu. Pressure modulation helped us to identify the different conformational substates adopted by the quadruplex at the different solution conditions and to determine the volumetric changes during complex formation and the conformational transitions involved. The magnitudes of the binding volumes are a hallmark of packing defects and hydrational changes upon ligand binding. The conformational substates of the GQ as well as the binding strength and the stoichiometry of complex formation depend strongly on the solution conditions as well as on pressure. High hydrostatic pressure can also impact GQs inside living cells and thus affect expression of genetic information in deep sea organisms. We show that sub-kbar pressures do not only affect the conformational dynamics and structures of GQs, but also their ligand binding reactions.

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Lighting Up of Thiazole Orange on G-Quadruplex DNA by High Pressure

Cited by 5 publications

References 31 publications

Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching

Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching

Meeting report: Seventh International Meeting on Quadruplex Nucleic Acids (Changchun, P.R. China, September 6–9, 2019)

Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation

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