A two-quartet G-quadruplex topology of human KIT2 is conformationally selected by a perylene derivative

Ceschi, Silvia; Largy, Eric; Gabelica, Valérie; Sissi, Claudia

doi:10.1016/j.biochi.2020.09.015

Cited by 11 publications

(13 citation statements)

References 34 publications

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“…Another interesting aspect of this work refers to the application of SM-FRET experiments on freely diffusing molecules to kinetic analyses. Interestingly, the kinetic parameters describing the folding process of kit2_SHORT and kit2_LONG derived herein are in good agreement with those previously reported for the short sequence without labelling groups ( 30 , 38 ). As such, we can attribute S1 to the intermediate folding species that has been reported to present a higher antiparallel content.…”

Section: Discussionsupporting

confidence: 90%

“…Among them, the most polymorphic appears to be c-kit2. In solution, it can fold into a monomeric and a dimeric G4 structures according to a folding pathway that comprises several kinetic intermediates as recently probed by native electrospray ionization mass spectrometry (ESI-MS), stopped-flow UV-Vis and CD experiments ( 30 , 38 ). Noteworthy, addition of a single base at the 3′ terminal of c-kit2 largely suppresses formation of the dimeric G4 in solution.…”

Section: Introductionmentioning

confidence: 99%

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Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene

Vesco

Lamperti

Salerno

et al. 2021

Nucleic Acids Research

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G-quadruplexes embedded within promoters play a crucial role in regulating the gene expression. KIT is a widely studied oncogene, whose promoter contains three G-quadruplex forming sequences, c-kit1, c-kit2 and c-kit*. For these sequences available studies cover ensemble and single-molecule analyses, although for kit* the latter were limited to a study on a promoter domain comprising all of them. Recently, c-kit2 has been reported to fold according to a multi-step process involving folding intermediates. Here, by exploiting fluorescence resonance energy transfer, both in ensemble and at the single molecule level, we investigated the folding of expressly designed constructs in which, alike in the physiological context, either c-kit2 or c-kit* are flanked by double stranded DNA segments. To assess whether the presence of flanking ends at the borders of the G-quadruplex affects the folding, we studied under the same protocols oligonucleotides corresponding to the minimal G-quadruplex forming sequences. Data suggest that addition of flanking ends results in biasing both the final equilibrium state and the folding kinetics. A previously unconsidered aspect is thereby unravelled, which ought to be taken into account to achieve a deeper insight of the complex relationships underlying the fine tuning of the gene-regulatory properties of these fascinating DNA structures.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene

Vesco

Lamperti

Salerno

et al. 2021

Nucleic Acids Research

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“…Ceschi et al employed ESI-MS to study the binding of perylene derivatives, PIPER and K20, to KIT2 G4 [ 190 ]. Their results revealed a binding stoichiometry of 1:1 on both ligands.…”

Section: Methods To Characterize G4/ligand Interactionsmentioning

confidence: 99%

“…Their results revealed a binding stoichiometry of 1:1 on both ligands. They also demonstrated the incapacity of the ligand to bind the unfolded oligonucleotide [ 190 ]. Moreover, the preferential binding of K20 to a two-quartet topology was demonstrated, since the most represented complex was the one having a single selectively coordinated K + ion, while only a small amount of the complex having two K + was detected [ 190 ].…”

Section: Methods To Characterize G4/ligand Interactionsmentioning

confidence: 99%

“…They also demonstrated the incapacity of the ligand to bind the unfolded oligonucleotide [ 190 ]. Moreover, the preferential binding of K20 to a two-quartet topology was demonstrated, since the most represented complex was the one having a single selectively coordinated K + ion, while only a small amount of the complex having two K + was detected [ 190 ]. On the other hand, PIPER showed a reduced preference for a two-quartet topology since the complexes with one and two K + ions were equally represented [ 190 ].…”

Section: Methods To Characterize G4/ligand Interactionsmentioning

confidence: 99%

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G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions

et al. 2021

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Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.

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G‐quadruplex as a Platform for New Perspectives in Nucleic Acid Targeting for Therapeutic Applications

Palumbo¹,

Sissi²

2022

Nucleic Acids in Medicinal Chemistry and Chemical Biology

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A two-quartet G-quadruplex topology of human KIT2 is conformationally selected by a perylene derivative

Cited by 11 publications

References 34 publications

Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene

Double-stranded flanking ends affect the folding kinetics and conformational equilibrium of G-quadruplexes forming sequences within the promoter of KIT oncogene

G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions

G‐quadruplex as a Platform for New Perspectives in Nucleic Acid Targeting for Therapeutic Applications

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