2,4-Dihydroxy and O2 Protonated Tautomers of dThd and Thd Coexist in the Gas Phase: Methylation Alters Protonation Preferences versus dUrd and Urd

Abstract

Abstract. The gas-phase structures of protonated thymidine, [ Comparison of this work to our previous IRMPD spectroscopy study of protonated 2'-deoxyuridine and uridine suggests that the 5-methyl substituent alters the preferences of O2 versus O4 protonation.

Structural characterization of nucleotide 5′-triphosphates by infrared ion spectroscopy and theoretical studies

“…Previous IRMPD spectroscopy studies by Rodgers and coworkers have provided a large body of data on metal-complexed nucleobases and nucleosides. [41][42][43][44][45][46][47][48] IRMPD spectra of metal-complexed NTPs have thus far not been reported and are an important next step in the characterization of the intrinsic interactions of specific NTPs.…”

“…Collision-induced dissociation (CID) is performed to evaluate the fragmentation behaviour of the systems, while infrared multiple-photon dissociation (IRMPD) spectroscopy in combination with quantum-chemical calculations is used to map intramolecular hydrogen bond interactions and deprotonation sites. Related systems such as protonated and deprotonated mononucleotides, [35][36][37][38][39] mononucleotide clusters, 40 protonated and metal-complexed nucleobases [41][42][43][44][45][46][47][48] and phosphate-metal complexes 49,50 have recently been successfully characterized using these methodologies.…”

Protonation of methyluracils in the gas phase: The particular case of 3-methyluracil

“…The second one is the development of structure-sensitive activation techniques, which enables one to obtain direct structural information on gaseous ions. Among those, Infrared Multiple Photon Dissociation spectroscopy (IRMPD) of mass-selected ions, is now established as a very powerful approach to probe the structure of gaseous ions of moderate size, [7][8][9][10], and different groups have used IRMPD spectroscopy to study the structure and tautomerization of protonated DNA and RNA building blocks generated by electrospray [11][12][13][14][15][16][17][18][19][20][21][22][23][24]. In our continuing effort to study the structure and unimolecular reactivity of gaseous nucleobases, either protonated [11][12][13]25,26] or complexed to metals [27][28][29][30][31][32], the present paper reports the IRMPD study in the fingerprint region between 1000 and 2000 cm -1 of three protonated methyluracils, namely 1-Me, 3-Me and 6-Me-uracil (Scheme 1), generated by electrospray ionization and trapped in a quadrupole ion trap.…”

O2 Protonation Controls Threshold Behavior for N-Glycosidic Bond Cleavage of Protonated Cytosine Nucleosides

“…In contrast, O2 protonation of cytosine occurs for the A•C + base pairs observed in oligonucleotide duplexes . Because the N3 and O2 atoms of cytosine exhibit similar proton affinities, and protonation plays an important role in facilitating the formation of noncanonical base pairing interactions that greatly influence the biochemical properties of nucleic acids, studies of the protonated cytosine nucleosides, protonated 2′-deoxycytidine and cytidine, [dCyd+H] + and [Cyd+H] + , have been performed in the gas phase to probe their intrinsic properties. − IRMPD action spectroscopy has been firmly established as a highly potent approach for examining the gas-phase conformations of protonated DNA and RNA nucleosides. ,,− In particular, we have examined the structures and relative stabilities of [dCyd+H] + and [Cyd+H] + in the gas phase using IRMPD action spectroscopy . Both N3 and O2 protonated conformers were found to coexist in the experimental population in roughly equal abundance, consistent with that reported by Filippi et al in a parallel IRMPD study.…”