Ion mobility spectrometry reveals intermediate states in temperature-resolved DNA unfolding

Hommersom, Bob; Porta, Tiffany; Heeren, Ron M. A.

doi:10.1016/j.ijms.2017.03.008

Cited by 8 publications

(8 citation statements)

References 20 publications

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“…To do so, we built a temperature-variable nanoelectrospray source, inspired by previous designs. [43][44][45][46] The nanospray emitter is embedded inside a temperature-controlled copper block ( Figure S 1). MS-melting experiments,…”

Section: T95-2t D(tt(gggt)4)mentioning

confidence: 99%

“…Here, we examined how these binding constants change with the solution temperature. To do so, we built a temperature-variable nanoelectrospray source, inspired by previous designs. − The nanospray emitter is embedded inside a temperature-controlled copper block (Figure S1). MS-melting experiments, i.e., the quantitation of each stoichiometry as a function of the solution temperature, allows a thorough thermodynamic characterization of binding enthalpies (Δ H °) and entropies (Δ S °), and we will show how these thermodynamic parameters can be interpreted in terms of structure.…”

Section: Introductionmentioning

confidence: 99%

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Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry

et al. 2018

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Designing ligands targeting G-quadruplex nucleic acid structures and affecting cellular processes is complicated because there are multiple target sequences and some are polymorphic. Further, structure alone does not reveal the driving forces for ligand binding. To know why a ligand binds, the thermodynamics of binding must be characterized. Electrospray mass spectrometry enables one to detect and quantify each specific stoichiometry (number of strands, cations, and ligands) and thus to simultaneously determine the equilibrium constants for each complex. Using a temperature-controlled nanoelectrospray source, we determined the temperature dependence of the equilibrium constants, and thus the enthalpic and entropic contributions to the formation of each stoichiometry. Enthalpy drives the formation of each quartet-K-quartet unit, whereas entropy drives the formation of quartet-K-triplet units. Consequently, slip-stranded structures can become more abundant as the temperature increases. In the presence of ligands (Phen-DC3, TrisQ, TMPyP4, Cu-ttpy), we observed that, even when only a 1:1 (ligand/quadruplex) complex is observed at room temperature, new states are populated at intermediate temperatures, including 2:1 complexes. In most cases, ligand-G4-quadruplex binding is entropically driven, and we discuss that this may have resulted from biases when ranking ligand potency using melting experiments. Other thermodynamic profiles could be linked to topology changes in terms of number of G-quartets (reflected in the number of specific K ions in the complex). The thermodynamics of ligand binding to each form, one ligand at a time, provides unprecedented detail on the interplay between ligand binding and topology changes in terms of number of G-quartets.

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Section: T95-2t D(tt(gggt)4)mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry

et al. 2018

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“…To do so, we built a temperature-variable nanoelectrospray source, inspired by previous designs. [40][41][42][43] The nanospray emitter is embedded inside a temperature-controlled copper block ( Figure S 1). MS-melting experiments,…”

Section: Abbreviationmentioning

confidence: 99%

Thermal Denaturation of DNA G-Quadruplexes and their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry

Marchand

Rosu

Zenobi

et al. 2018

Preprint

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As the idea that G-quadruplex nucleic acid structures are involved in cellular processes is gaining support, it becomes important to develop ligands that specifically target G-quadruplexes. However, ligand design is complicated because there are multiple G-quadruplex target sequences, some sequences are polymorphic, and very few ligand-quadruplex structures in solution were solved to date. Further, structure alone does not reveal the driving forces for ligand binding. To know why a ligand binds, the thermodynamics of binding must be characterized. Electrospray mass spectrometry makes it possible to detect and quantify each specific stoichiometry in terms of number of strands, number of specific cations, and number of ligands, and thus allows one to simultaneously determine the equilibrium constants for the formation of each complex. We designed and built a temperature-controlled nano-electrospray source to monitor thermal denaturation by mass spectrometry ("MS-melting"). We studied the thermal denaturation of G-quadruplexes, including the c-myc promoter and several telomeric sequence variants, and their complexes with popular ligands (Phen-DC3, TrisQ, TMPyP4, Cu-ttpy). From the temperature dependence of the equilibrium constants, we determined the enthalpic and entropic contributions to the formation of each stoichiometric state. In absence of ligand, we untangled the potassium-induced G-quadruplex folding thermodynamics, one potassium ion at a time. The formation of each quartet-K + -quartet units is strongly enthalpy driven, with entropy penalty. In contrast, the formation of quartet-K + -triplet units is entropically driven. For this reason, such misfolded structures can become more abundant as the temperature increases.In the presence of ligands, mass spectrometry also revealed new states at intermediate temperatures. For example, even in cases where only a 1:1 (ligand:quadruplex) is observed at room temperature, a 2:1 complex predominates at intermediate temperatures. Mass spectrometry also makes it easy to distinguish ligand bound to the 2-quartet structures (containing 1 K + ), the 3-quartet structures (containing 2 K + ) and to the unfolded strand (no specific K + ). We confirm that TrisQ binds preferably, but not exclusively, to 3quartet structures, Phen-DC3 binds to a 2-quartet structure, while the porphyrin ligand TMPyP4 is characterized as non-selective, because it binds to all forms including the unfolded one. The thermodynamics of ligand binding to each form, one ligand at a time, provides unprecedented detail on the interplay between ligand binding and changes in G-quadruplex topology.

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“… [57] The intermediate states of DNA complexes have been investigated using a similar design coupled with IMS by Hommersom et al. [58] This design has been shown to be a useful tool for probing the thermodynamics and ligand binding of non‐canonical nucleic acid structures, as shown in Marchand et al. The source modifications made in this latter study allowed for the real‐time control of temperature ramps, with one scan performed every second.…”

Section: Ion Source Designsmentioning

confidence: 99%

Temperature‐Controlled Electrospray Ionization: Recent Progress and Applications

Harrison

Pruška

Oganesyan

et al. 2021

Chemistry A European J

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Native electrospray ionization (ESI) and nanoelectrospray ionization (nESI) allow researchers to analyze intact biomolecules and their complexes by mass spectrometry (MS). The data acquired using these soft ionization techniques provide a snapshot of a given biomolecules structure in solution. Over the last thirty years, several nESI and ESI sources capable of controlling spray solution temperature have been developed. These sources can be used to elucidate the thermodynamics of a given analyte, as well as provide structural information that cannot be readily obtained by other, more commonly used techniques. This review highlights how the field of temperature‐controlled mass spectrometry has developed.

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Ion mobility spectrometry reveals intermediate states in temperature-resolved DNA unfolding

Cited by 8 publications

References 20 publications

Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry

Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry

Thermal Denaturation of DNA G-Quadruplexes and their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry

Temperature‐Controlled Electrospray Ionization: Recent Progress and Applications

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