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

Abstract

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.

Amino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities

“…Unstable glycosidic bonds accelerate depurination and formation of abasic sites on nucleic acids, which may ultimately contribute to cell cytotoxicity [67]. Destabilization of the glycosidic bond can be caused by a change in chemical composition of the nucleoside due to certain modifications such as methylation [45, 47, 68]. Previous evaluation of the effects of cisPt modification on guanosine residues indicated that platination has no significant effect on glycosidic bond stability [52].…”

“…The ligands of AlaPt or OrnPt likely cause electron-density withdrawal at the N9 position in a manner that is dependent on proximity of the platinum atom. Further tandem mass spectrometry and spectroscopic studies, including computational analysis, are ongoing in an effort to elucidate detailed mechanisms for glycosidic bond cleavage of the N7 and N1/N3 AlaPt and OrnPt adduct species, as done previously with both standard and modified nucleosides [42, 46, 68].…”

5-Halogenation of Uridine Suppresses Protonation-Induced Tautomerization and Enhances Glycosidic Bond Stability of Protonated Uridine: Investigations via IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Calculations

“…Survival yield analysis is a robust method to determine the relative stabilities of precursor ions. ,− For the ER-CID experiments of protonated uridine and the 5-halouridine nucleoside analogues, the survival yield of the precursor ion was calculated at each rf excitation amplitude examined using eq , Survival yield = I p / ( I p + ∑ i I f i ) where I p and ( I p + ∑ i I f i ) are defined as in eq . The survival yields were calculated using custom software developed in our laboratory.…”

Structures and Relative Glycosidic Bond Stabilities of Protonated 2′-Fluoro-Substituted Purine Nucleosides

“…CID MS/MS spectra for [Adofl+H] + and [Guofl+H] + acquired at an rf EA near their CID 50% value are shown in Figure 2. Previously published [39,40] [39,40,53,54,67,68], as well as for the protonated noncanonical purine 2′-O-methylnucleosides, [Adom+H] + and [Guom+H] + [44], and other protonated and sodium cationized noncanonical methylguanosines [45]. The pyrimidine [Nuofl+H] + , [Nuo+H] + , and [dNuo+H] + also primarily undergo N-glycosidic bond cleavage [41][42][43][69][70][71]; however, several competing neutral loss pathways are also observed for the protonated uracil and thymine nucleoside analogues.…”

“…The solvent-free and controllable chemical environment of tandem mass spectrometry (MS/MS) experiments has proven an invaluable asset in the study of various aspects of the canonical and noncanonical DNA and RNA constituents. For example, energy-resolved collisioninduced dissociation (ER-CID) experiments performed under multiple collision conditions in trapping mass spectrometers have been used to study the relative stability of various nucleosides [9,[39][40][41][42][43][44][45]. Additionally, threshold analysis of ER-CID experiments performed under nominally single collision conditions on guided ion beam mass spectrometers (GIBMS) have provided thermodynamically accurate dissociation energetics for various noncovalent [46][47][48][49][50][51][52] and covalent [53][54][55][56] interactions of nucleobases and nucleosides.…”