G-quadruplex DNA and ligand interaction in living cells using NMR spectroscopy

Salgado, Gilmar F.; Cazenave, Christian; Kerkour, Abdelaziz; Mergny, Jean‐Louis

doi:10.1039/c4sc03853c

Cited by 91 publications

(74 citation statements)

References 42 publications

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“…More recently, several groups reported evidences of G4 formation in the genome of eukaryotic cells (5,6). The formation of G4s from exogenous G4 forming DNA sequences was also observed in live Xenopus laevis oocytes (7,8). In addition, a novel high-throughput sequencing technology allowed identifying a vast number of G4 structures and mapping their distribution throughout a human genome (9).…”

Section: Introductionmentioning

confidence: 71%

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

et al. 2016

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G-quadruplexes (G4s) are DNA secondary structures that are capable of forming and function in vivo. The propensity of G4s to exhibit extreme polymorphism and complex dynamics is likely to influence their cellular function, yet a clear microscopic picture of their folding process is lacking. Here we employed single-molecule FRET microscopy to obtain a direct view of the folding and underlying conformational dynamics of G4s formed by the human telomeric sequence in potassium containing solutions. Our experiments allowed detecting several folded states that are populated in the course of G4 folding and determining their folding energetics and timescales. Combining the single-molecule data with molecular dynamics simulations enabled obtaining a structural description of the experimentally observed folded states. Our work thus provides a comprehensive thermodynamic and kinetic description of the folding of G4s that proceeds through a complex multi-route pathway, involving several marginally stable conformational states.

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Section: Introductionmentioning

confidence: 71%

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

et al. 2016

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“…To this end, numerous small molecules have been developed to target G‐quadruplexes . However, given that the majority of small molecules bind non‐covalently and that G‐quadruplexes arise from reversible inter‐/intra‐molecular forces, it has been challenging to determine the extent to which these compounds interact with G‐quadruplexes in live cells …”

Section: Introductionmentioning

confidence: 99%

Trianguleniums as Optical Probes for G‐Quadruplexes: A Photophysical, Electrochemical, and Computational Study

Shivalingam

Vyšniauskas

Albrecht

et al. 2016

Chemistry A European J

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Nucleic acids can adopt non‐duplex topologies, such as G‐quadruplexes in vitro. Yet it has been challenging to establish their existence and function in vivo due to a lack of suitable tools. Recently, we identified the triangulenium compound DAOTA‐M2 as a unique fluorescence probe for such studies. This probe's emission lifetime is highly dependent on the topology of the DNA it interacts with opening up the possibility of carrying out live‐cell imaging studies. Herein, we describe the origin of its fluorescence selectivity for G‐quadruplexes. Cyclic voltammetry predicts that the appended morpholino groups can act as intra‐ molecular photo‐induced electron transfer (PET) quenchers. Photophysical studies show that a delicate balance between this effect and inter‐molecular PET with nucleobases is key to the overall fluorescence enhancement observed upon nucleic acid binding. We utilised computational modelling to demonstrate a conformational dependence of intra‐molecular PET. Finally, we performed orthogonal studies with a triangulenium compound, in which the morpholino groups were removed, and demonstrated that this change inverts triangulenium fluorescence selectivity from G‐quadruplex to duplex DNA, thus highlighting the importance of fine tuning the molecular structure not only for target affinity, but also for fluorescence response.

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“…[1–4] Such investigations mostly involve RNA sequences labeled with appropriate reporters as natural nucleosides are practically non-fluorescent and do not provide intrinsic labels that are suitable for analysis by spectroscopic and diffraction techniques. [5] Minimally perturbing fluorescent nucleoside analogs, [6] isotope- (e,g., 13 C, 15 N), [7] spin- (e.g., nitroxide) [8] and heavy atom-labeled (e.g., Br, Se) [9] nucleosides incorporated into oligonucleotides (ONs) have been applied in assays to study structure, dynamics and function of RNA. However, given the multitude and diversity of RNA transcripts, probing structure-function relationships of RNA sequences using established biochemical and biophysical methods remains a major challenge.…”

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confidence: 99%

Structure of the Ribosomal RNA Decoding Site Containing a Selenium‐Modified Responsive Fluorescent Ribonucleoside Probe

et al. 2017

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Comprehensive understanding of the structure–function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation‐sensitive fluorophore and an anomalous X‐ray diffraction label (5‐selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand‐induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.

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G-quadruplex DNA and ligand interaction in living cells using NMR spectroscopy

Abstract: Using in-cell NMR spectroscopy to probe ligand binding to a G-quadruplex nucleic acid.

Cited by 91 publications

References 42 publications

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

Trianguleniums as Optical Probes for G‐Quadruplexes: A Photophysical, Electrochemical, and Computational Study

Structure of the Ribosomal RNA Decoding Site Containing a Selenium‐Modified Responsive Fluorescent Ribonucleoside Probe

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