Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction

Frańska, Magdalena; Stężycka, Olga; Jankowski, Wojciech; Hoffmann, Marcin

doi:10.1021/jasms.2c00071

Cited by 5 publications

(7 citation statements)

References 49 publications

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“…The gas‐phase decomposition of cytosine dimer resulted exclusively in the formation of protonated monomers. The gas‐phase decomposition of nucleoside dimers and mixed dimers resulted in the formation of protonated monomers followed by the loss of sugar moiety (loss of mass 132 for ribose moiety and loss of mass 116 for deoxyribose moiety 22,23 ).…”

Section: Methodsmentioning

confidence: 99%

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

Jankowski,

Hoffmann,

Półrul

et al. 2023

Rapid Comm Mass Spectrometry

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RationaleCytosine and its conjugates are prone to form protonated, triply‐bonded dimers. Therefore, the nucleic‐acid cytosine‐rich sequence forms the four‐stranded noncanonical secondary structure known as the intercalated motif (i‐motif). This process has resulted in studies on cytosine protonated dimers. This communication focuses on the protonated dimers of cytosine and its nucleoside using the survival yield (SY) method and quantum mechanics calculations.MethodsTo obtain the precursor ion fragmentation curve, the plot of SY against Ecomδ, the product ion spectra of the protonated dimers were obtained using a Waters/Micromass Q‐TOF Premier mass spectrometer. Quantum mechanics calculations were performed using GAUSSIAN 16, and full geometry optimizations and energy calculations were performed within the density functional theory framework at B3LYP/6‐31G(d,p).ResultsThe precursor ion fragmentation curve allowed the rating of the gas‐phase stabilities of the analyzed protonated dimers. Substitution of sugar moiety at N1 cytosine atom decreased the gas‐phase stabilities of the protonated dimers. The deoxycytidine dimer was found to be more stable than the cytidine dimer and cytidine–deoxycytidine dimer. Quantum chemical calculations indicated that cytosine aminohydroxy tautomer may be involved in the formation of protonated cytosine–cytosine nucleoside dimers but not in the formation of cytosine dimers.ConclusionsThe results obtained for nucleoside dimers indicated that the SY method may reflect the i‐motif stabilities observed under physiological conditions. Therefore, the analysis of other protonated dimers of variously substituted cytosine–cytosine nucleoside using the SY method may be important to study the effect of cytosine substitution on the i‐motif stabilities. Cytosine tautomer containing C2‐OH… N(2H)‐C4 moiety may be involved in the formation of protonated cytosine–cytosine nucleoside dimers.

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Section: Methodsmentioning

confidence: 99%

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

Jankowski,

Hoffmann,

Półrul

et al. 2023

Rapid Comm Mass Spectrometry

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“…With minimal input from the instructor, students elucidated that the lost sugar moiety most probably was 1,5-anhydro-β-D-ribofuranose (Figure 6). 27 Two issues were briefly discussed with the students:…”

Section: Product Ion Spectra Of Protonated and Sodiated Monomersmentioning

confidence: 99%

Nucleosides as Excellent Molecules for Teaching the Basics and Capabilities of Electrospray Ionization Mass Spectrometry

Frański

2024

J. Chem. Educ.

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The area of application of electrospray ionization mass spectrometry (ESI-MS), usually coupled with liquid chromatography, seems to be much larger than those of any other ionization method. It gives rise to the demand for new teaching methods that would effectively help students to master the principles of working with and making full use of the capabilities of ESI-MS. Herein, a simple demonstration of electrospray ionization mass spectrometry of nucleosides has been proposed in order to show students the basics and capabilities of this ionization method. Besides the simple molecular mass determination followed by analyzing the collision induced dissociation (CID) process, such issues as detection of supramolecular self-assemblies, fragmentation of glycosides, proton/ metal cation affinities, and isotope labeling have been discussed on the basis of the mass spectra obtained.

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“…, using aqueous-phase X-ray emission, infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies. The Mg 2+ –ATP coordination chemistry has been recently investigated in the gas phase using mass spectrometry (in particular, phosphate–Mg 2+ –adenine interactions) and in acetate solutions using NMR spectroscopy. Previous LJ-PES work focused on the ribose or adenine units in ATP (aq) , − or on inorganic phosphate aqueous solutions.…”

Section: Introductionmentioning

confidence: 99%

How Does Mg²⁺_(aq) Interact with ATP_(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy

Mudryk,

Lee,

Tomaník

et al. 2024

J. Am. Chem. Soc.

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Liquid-jet photoemission spectroscopy (LJ-PES) allows for a direct probing of electronic structure in aqueous solutions. We show the applicability of the approach to biomolecules in a complex environment, exploring site-specific information on the interaction of adenosine triphosphate in the aqueous phase (ATP (aq) ) with magnesium (Mg 2+ (aq) ), highlighting the synergy brought about by the simultaneous analysis of different regions in the photoelectron spectrum. In particular, we demonstrate intermolecular Coulombic decay (ICD) spectroscopy as a new and powerful addition to the arsenal of techniques for biomolecular structure investigation. We apply LJ-PES assisted by electronic-structure calculations to study ATP (aq) solutions with and without dissolved Mg 2+ . Valence photoelectron data reveal spectral changes in the phosphate and adenine features of ATP (aq) due to interactions with the divalent cation. Chemical shifts in Mg 2p, Mg 2s, P 2p, and P 2s core-level spectra as a function of the Mg 2+ /ATP concentration ratio are correlated to the formation of [Mg(ATP) 2 ] 6− (aq) , [MgATP] 2− (aq) , and [Mg 2 ATP] (aq) complexes, demonstrating the element sensitivity of the technique to Mg 2+ −phosphate interactions. The most direct probe of the intermolecular interactions between ATP (aq) and Mg 2+ (aq) is delivered by the emerging ICD electrons following ionization of Mg 1s electrons. ICD spectra are shown to sensitively probe ligand exchange in the Mg 2+ −ATP (aq) coordination environment. In addition, we report and compare P 2s data from ATP (aq) and adenosine mono-and diphosphate (AMP (aq) and ADP (aq) , respectively) solutions, probing the electronic structure of the phosphate chain and the local environment of individual phosphate units in ATP (aq) . Our results provide a comprehensive view of the electronic structure of ATP (aq) and Mg 2+ −ATP (aq) complexes relevant to phosphorylation and dephosphorylation reactions that are central to bioenergetics in living organisms.

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Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction

Cited by 5 publications

References 49 publications

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

Nucleosides as Excellent Molecules for Teaching the Basics and Capabilities of Electrospray Ionization Mass Spectrometry

How Does Mg²⁺_(aq) Interact with ATP_(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy

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Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction

Cited by 5 publications

References 49 publications

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

Nucleosides as Excellent Molecules for Teaching the Basics and Capabilities of Electrospray Ionization Mass Spectrometry

How Does Mg2+(aq) Interact with ATP(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy

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How Does Mg²⁺_(aq) Interact with ATP_(aq)? Biomolecular Structure through the Lens of Liquid-Jet Photoemission Spectroscopy