Conformations and N-glycosidic bond stabilities of sodium cationized 2′-deoxycytidine and cytidine: Solution conformation of [Cyd + Na]+ is preserved upon ESI

Zhu, Yanlong; Hamlow, L. A.; He, Chenchen; Roy, H. A.; Cunningham, N. A.; Munshi, Musleh Uddin; Berden, Giel; Oomens, Jos; Rodgers, M. T.

doi:10.1016/j.ijms.2017.04.005

Cited by 21 publications

(30 citation statements)

References 66 publications

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“…Protonation of 2a + was calculated to be entirely analogous to that of 1a + , giving the O2- and N3-protonated tautomers 2b 2+ and 2c 2+ with GB = 750 and 741 kJ mol –1 , respectively. The relative enthalpies and Gibbs energies, favoring the O2-protonated tautomer 2b 2+ , can be compared to those of singly charged cytidine and 2′-deoxycytidine ions that have been calculated to have very similar relative energies slightly favoring N3–H protomers . Both forms have been found to coexist in the gas phase. − Protonation of 2a + resulted in an unfolding of the side chain, as illustrated by the lowest-Gibbs-energy structures 2b 2+ and 2c 2+ (Scheme S2).…”

Section: Resultsmentioning

confidence: 99%

Charge-Tagged Nucleosides in the Gas Phase: UV–Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals

Liu

Nováková

et al. 2021

J. Phys. Chem. A

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Cytidine ribonucleosides were furnished at O5′ with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV−vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3-and O2protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3−H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1−C1′ glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born− Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.

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Section: Resultsmentioning

confidence: 99%

Charge-Tagged Nucleosides in the Gas Phase: UV–Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals

Liu

Nováková

et al. 2021

J. Phys. Chem. A

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“…In all ground Nuo, [Nuo+H] + , and [Nuo+Na] + conformers, either C2′-endo (also known as “South”) or C3′-endo (also known as “North”) sugar puckering 67,68 are favored. More specific sugar puckering designations based on pseudorotation phase angles 52–56,67,68 include 2 T 1 , 2 T 3 , and 2 1 T for the C2′-endo conformers, but only 3 T 2 for the C3′-endo conformers. All ground neutrals, including m 7 Guo, prefer C2′-endo ( 2 T 1 , 2 T 3 , and 2 1 T) sugar puckering.…”

Section: Resultsmentioning

confidence: 99%

“…N-glycosidic bond cleavage with retention of the cation by the nucleobase, the sole fragmentation channel observed in the reactions performed here, is often the intrinsically lowest energy unimolecular dissociation pathway observed in the CID of nucleosides (see the Supplementary Material for a more in-depth overview of the canonical nucleoside CID reaction products). [52][53][54][55][56][60][61][62][63][64] In previous work by Wu et al, 61 the fragmentation pathways observed for gas phase [GuoþH] þ and [dGuoþH] þ were mechanistically mapped to proceed through a stepwise E1 elimination reaction by electronic structure calculations and comparisons with guided ion beam mass spectrometry (GIBMS) TCID activation energy thresholds. These results suggest the solvent-free substitution reaction pathway to proceed first by the rate-limiting elongation/cleavage of the C1 0 -N9 glycosidic bond, forming an oxocarbenium ion-like transition state on the sugar and an interaction of the N9 heteroatom electron density with the C2 0 H hydrogen, followed by transfer of that C2 0 proton to the N9 atom of the nucleobase with the formation of a C1 0 ¼C2 0 p-bond and an unsaturated planar sugar moiety.…”

Section: Reaction Products and Mechanismsmentioning

confidence: 99%

“…Overall, the QIT MS ER-CID and GIBMS TCID reports on the canonical nucleosides consistently display two major trends: one, the RNA nucleoside glycosidic bonds are more stable than their DNA counterparts, and two, protonation activates the glycosidic bonds more effectively than sodium cationization. [52][53][54][55][56][60][61][62][63] For example, the RNA guanosine form, Guo, requires more energy to cleave its glycosidic bond than the DNA form, dGuo. 52,61 The TCID studies of [GuoþH] þ and [dGuoþH] þ yielded bond activation energies of 114.8 AE 2.9 and 93.6 AE 2.9 kJ/mol, respectively.…”

Section: Comparisons With Canonical Nucleoside Stability Measurementsmentioning

confidence: 99%

“…Tandem mass spectrometry (MS/MS) approaches have proven effective in providing insight into the intrinsic properties of nucleic acid constituents. Performing collision-induced dissociation (CID) in an energy-resolved fashion has also proved useful for a variety of purposes including the separation of isobaric compounds, 50 nucleic acid constituent proton affinity (PA) measurements, 51 relative stability measurements of canonical nucleosides, [52][53][54][55][56] glycosyl phosphates, 57 9-ethylguanine tetrads, 58 nucleic acid-drug complexes, 59 and accurate absolute glycosidic bond cleavage thermochemistry measurements via threshold collision-induced dissociation (TCID). [60][61][62][63] Here we use energy-resolved collisioninduced dissociation (ER-CID) MS/MS experiments performed in a quadrupole ion trap mass spectrometer (QIT MS) to elucidate the relative intrinsic N-glycosidic bond stabilities of the protonated and sodium cationized forms of canonical Guo and five methylguanosines (Guom, m 1 Guo, m 7 Guo, m 2 2 Guo, and m 2 2 Guom).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating

Devereaux

Zhu

Rodgers

2018

Eur J Mass Spectrom (Chichester)

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The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.

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Exploring Glycosylated Soy Isoflavones Affinities toward G‐tetrads as Studied by Survival Yield Method

2023

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Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G + Na] + ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrome-try (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G + Na] + interaction in the gas phase was determined from E com50 -the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G + Na] + interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.

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Conformations and N-glycosidic bond stabilities of sodium cationized 2′-deoxycytidine and cytidine: Solution conformation of [Cyd + Na]+ is preserved upon ESI

Cited by 21 publications

References 66 publications

Charge-Tagged Nucleosides in the Gas Phase: UV–Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals

Charge-Tagged Nucleosides in the Gas Phase: UV–Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals

Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating

Exploring Glycosylated Soy Isoflavones Affinities toward G‐tetrads as Studied by Survival Yield Method

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