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Article
Structural and Energetic Effects of O2′-Ribose Methylation of Protonated Pyrimidine Nucleosides
The 2′-substituents distinguish DNA from RNA nucleosides. 2′-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2′-modifications may alter the hydrogen-bonding intera...
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Article
Open AccessAmino acid-linked platinum(II) compounds: non-canonical nucleoside preferences and influence on glycosidic bond stabilities
Nucleobases serve as ideal targets where drugs bind and exert their anticancer activities. Cisplatin (cisPt) preferentially coordinates to 2′-deoxyguanosine (dGuo) residues within DNA. The dGuo adducts that ar...
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Article
Impact of Sodium Cationization on Gas-Phase Conformations of DNA and RNA Cytidine Mononucleotides
Gas-phase conformations of the sodium-cationized forms of the 2′-deoxycytidine and cytidine mononucleotides, [pdCyd+Na]+ and [pCyd+Na]+, are examined by infrared multiple photon dissociation action spectroscopy. ...
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Article
Structures and Relative Glycosidic Bond Stabilities of Protonated 2′-Fluoro-Substituted Purine Nucleosides
The 2′-substituent is the primary distinguishing feature between DNA and RNA nucleosides. Modifications to this critical position, both naturally occurring and synthetic, can produce biologically valuable nucl...
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Article
Impact of the 2′- and 3′-Sugar Hydroxyl Moieties on Gas-Phase Nucleoside Structure
Modified nucleosides have been an important target for pharmaceutical development for the treatment of cancer, herpes simplex virus, and the human immunodeficiency virus (HIV). Amongst these nucleoside analogu...
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Article
Protonated Asparaginyl-Alanine Decomposition: a TCID, SORI-CID, and Computational Analysis
Deamidation of asparagine residues, one of the fastest known post-translational modifications in proteins, plays a significant role in various biological functions and degenerative, aging diseases. Here, we pr...
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Article
Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines
Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillato...
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Article
Influence of Linkage Stereochemistry and Protecting Groups on Glycosidic Bond Stability of Sodium Cationized Glycosyl Phosphates
Energy-resolved collision-induced dissociation (ER-CID) experiments of sodium cationized glycosyl phosphate complexes, [GP x +Na]+, are performed to elucidate the effects of link...
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Article
Influence of Transition Metal Cationization versus Sodium Cationization and Protonation on the Gas-Phase Tautomeric Conformations and Stability of Uracil: Application to [Ura+Cu]+ and [Ura+Ag]+
The gas-phase conformations of transition metal cation-uracil complexes, [Ura+Cu]+ and [Ura+Ag]+, were examined via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical calculations. ...
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Article
IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Studies of Sodium Cationized Thymidine and 5-Methyluridine: Kinetic Trap** During the ESI Desolvation Process Preserves the Solution Structure of [Thd+Na]+
Thymidine (dThd) is a fundamental building block of DNA nucleic acids, whereas 5-methyluridine (Thd) is a common modified nucleoside found in tRNA. In order to determine the conformations of the sodium cationi...
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Article
N3 and O2 Protonated Conformers of the Cytosine Mononucleotides Coexist in the Gas Phase
The gas-phase conformations of the protonated forms of the DNA and RNA cytosine mononucleotides, [pdCyd+H]+ and [pCyd+H]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy over th...
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Article
2,4-Dihydroxy and O2 Protonated Tautomers of dThd and Thd Coexist in the Gas Phase: Methylation Alters Protonation Preferences versus dUrd and Urd
The gas-phase structures of protonated thymidine, [dThd + H]+, and its modified form, protonated 5-methyluridine, [Thd + H]+, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy comb...
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Article
Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif
(CCG)n•(CGG)n trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)n•(CGG)n repeats adopt i-motif conformat...
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Article
Base-Pairing Energies of Protonated Nucleoside Base Pairs of dCyd and m5dCyd: Implications for the Stability of DNA i-Motif Conformations
Hypermethylation of cytosine in expanded (CCG)n•(CGG)n trinucleotide repeats results in Fragile X syndrome, the most common cause of inherited mental retardation. The (CCG)n•(CGG)n repeats adopt i-motif conformat...
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Article
Structural and Energetic Effects in the Molecular Recognition of Acetylated Amino Acids by 18-Crown-6
Absolute 18-crown-6 (18C6) binding affinities of four protonated acetylated amino acids (AcAAs) are determined using guided ion beam tandem mass spectrometry techniques. The AcAAs examined in this work include...
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Article
Protonation Preferentially Stabilizes Minor Tautomers of the Halouracils: IRMPD Action Spectroscopy and Theoretical Studies
Tautomerization induced by protonation of halouracils may increase their efficacy as anti-cancer drugs by altering their reactivity and hydrogen bonding characteristics, potentially inducing errors during DNA ...
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Article
Sodium Cation Affinities of Commonly Used MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry
The sodium cation affinities of six commonly used MALDI matrices are determined here using guided ion beam tandem mass spectrometry techniques. The collision-induced dissociation behavior of six sodium cationi...
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Article
Infrared Multiple Photon Dissociation Action Spectroscopy and Theoretical Studies of Triethyl Phosphate Complexes: Effects of Protonation and Sodium Cationization on Structure
The gas-phase structures of protonated and sodium cationized complexes of triethyl phosphate, [TEP + H]+ and [TEP + Na]+, are examined via infrared multiple photon dissociation (IRMPD) action spectroscopy using t...
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Article
Open AccessInfrared Multiple Photon Dissociation Action Spectroscopy and Theoretical Studies of Diethyl Phosphate Complexes: Effects of Protonation and Sodium Cationization on Structure
The gas-phase structures of deprotonated, protonated, and sodium-cationized complexes of diethyl phosphate (DEP) including [DEP − H]−, [DEP + H]+, [DEP + Na]+, and [DEP − H + 2Na]+ are examined via infrared multi...
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Article
A simple model for metal cation-phosphate interactions in nucleic acids in the gas phase: Alkali metal cations and trimethyl phosphate
Threshold collision-induced dissociation techniques are employed to determine the bond dissociation energies (BDEs) of complexes of alkali metal cations to trimethyl phosphate, TMP. Endothermic loss of the int...
