Influence of Sodium Cationization versus Protonation on the Gas-Phase Conformations and Glycosidic Bond Stabilities of 2′-Deoxyadenosine and Adenosine

2016 ◽  
Vol 120 (34) ◽  
pp. 8892-8904 ◽  
Author(s):  
Y. Zhu ◽  
L. A. Hamlow ◽  
C. C. He ◽  
S. F. Strobehn ◽  
J. K. Lee ◽  
...  
Keyword(s):  
Gas Phase ◽  
Glycosidic Bond ◽  
Sodium Cationization

Evidence of gas-phase pyranose-to-furanose isomerization in protonated peptidoglycans

2021 ◽  
Author(s):  
Shanshan Guan ◽  
Benjamin J. Bythell
Keyword(s):  
Gas Phase ◽  
Bond Cleavage ◽  
Glycosidic Bond ◽  
Glycosidic Bond Cleavage

Protonated peptidoglycans isomerize prior to glycosidic bond cleavage.

Effects of sodium cationization versus protonation on the conformations and N-glycosidic bond stabilities of sodium cationized Urd and dUrd: solution conformation of [Urd+Na]+ is preserved upon ESI

2017 ◽  
Vol 19 (27) ◽  
pp. 17637-17652 ◽  
Author(s):  
Y. Zhu ◽  
H. A. Roy ◽  
N. A. Cunningham ◽  
S. F. Strobehn ◽  
J. Gao ◽  
...  
Keyword(s):  
Glycosidic Bond ◽  
Solution Conformation ◽  
Action Spectroscopy ◽  
Sodium Cationization ◽  
Spectroscopy Studies

The conformations of sodium cationized uridine and 2′-deoxyuridine are sensitive to the presence (or absence) of the 2′-hydroxyl substituent. IRMPD action spectroscopy studies suggest that the solution conformation of [Urd+Na]+ is preserved upon ESI.

Influence of 2′-fluoro modification on glycosidic bond stabilities and gas-phase ion structures of protonated pyrimidine nucleosides

2019 ◽  
Vol 219 ◽  
pp. 10-22 ◽  
Author(s):  
Zachary J. Devereaux ◽  
H.A. Roy ◽  
C.C. He ◽  
Y. Zhu ◽  
N.A. Cunningham ◽  
...  
Keyword(s):  
Gas Phase ◽  
Glycosidic Bond ◽  
Pyrimidine Nucleosides ◽  
Gas Phase Ion

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

2018 ◽  
Vol 25 (1) ◽  
pp. 16-29 ◽  
Author(s):  
Zachary J Devereaux ◽  
Y Zhu ◽  
MT Rodgers
Keyword(s):  
Nucleic Acid ◽  
Gas Phase ◽  
Excision Repair ◽  
Inverse Correlation ◽  
Sodium Cation ◽  
Cation Binding ◽  
Glycosidic Bond ◽  
Proton Affinities ◽  
Chemical Complexity ◽  
Naturally Occurring

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.

Impact of Sodium Cationization on Gas-Phase Conformations of DNA and RNA Cytidine Mononucleotides

2019 ◽  
Vol 30 (9) ◽  
pp. 1758-1767 ◽  
Author(s):  
L. A. Hamlow ◽  
Y.-w. Nei ◽  
R. R. Wu ◽  
J. Gao ◽  
J. D. Steill ◽  
...  
Keyword(s):  
Gas Phase ◽  
Dna And Rna ◽  
Sodium Cationization

Residual Gas Reactions in the Electron Microscope: I. Qualitative Observations on the Water Gas Reaction

1968 ◽  
Vol 26 ◽  
pp. 292-293
Author(s):  
Richard E. Hartman ◽  
Roberta S. Hartman ◽  
Peter L. Ramos
Keyword(s):  
Electron Beam ◽  
Electron Microscope ◽  
Gas Phase ◽  
Absolute Temperature ◽  
Residual Gas ◽  
Gas Reactions ◽  
Image Position ◽  
The Right ◽  
Water Gas ◽  
Thinning Rate

The action of water and the electron beam on organic specimens in the electron microscope results in the removal of oxidizable material (primarily hydrogen and carbon) by reactions similar to the water gas reaction .which has the form:The energy required to force the reaction to the right is supplied by the interaction of the electron beam with the specimen.The mass of water striking the specimen is given by:where u = gH2O/cm2 sec, PH2O = partial pressure of water in Torr, & T = absolute temperature of the gas phase. If it is assumed that mass is removed from the specimen by a reaction approximated by (1) and that the specimen is uniformly thinned by the reaction, then the thinning rate in A/ min iswhere x = thickness of the specimen in A, t = time in minutes, & E = efficiency (the fraction of the water striking the specimen which reacts with it).

Integration of Core-Edge Spectroscopy Methods for the Study of Polymers

1996 ◽  
Vol 54 ◽  
pp. 154-155
Author(s):  
E. G. Rightor
Keyword(s):  
Excited State ◽  
Polymer Blends ◽  
Gas Phase ◽  
Spatial Resolution ◽  
High Spatial Resolution ◽  
Electronic States ◽  
Core Electron ◽  
Bulk Solids ◽  
Development Application

Core edge spectroscopy methods are versatile tools for investigating a wide variety of materials. They can be used to probe the electronic states of materials in bulk solids, on surfaces, or in the gas phase. This family of methods involves promoting an inner shell (core) electron to an excited state and recording either the primary excitation or secondary decay of the excited state. The techniques are complimentary and have different strengths and limitations for studying challenging aspects of materials. The need to identify components in polymers or polymer blends at high spatial resolution has driven development, application, and integration of results from several of these methods.

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