Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

Chou, Chau-Wen; Limbach, Patrick A.; Cole, Richard B.

doi:10.1016/s1044-0305(02)00649-9

Cited by 12 publications

(16 citation statements)

References 60 publications

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“…Several previous H/DX-MS studies of DNA fragmentation have been conducted on nucleotide tetramers with one or two high proton affinity (PA) bases (adenine, guanine, and cytosine) in a low PA base (thymine) environment [5][6][7]13]. To obtain comparable dataset, DNA tetramers of similar compositions were analyzed.…”

Section: Resultsmentioning

confidence: 99%

“…As supporting evidence for the charge-controlled mechanism presented in Scheme 6, Chou et al [13] did not observe any 5=-COO cleavage fragments in fragmentation of 3=-or 5=-charge-tagged oligodeoxyribonucleotides. This is in contrast to the fragmentation pattern observed in the current study for untagged DNA tetramers, where z-and z-derived ions were frequently observed as intense peaks.…”

mentioning

confidence: 78%

“…Albeit disfavored, the latter reaction is possible in positive ions. This may explain why Chou et al [13] still observed (a-B)-and w-ions for positive DNA-ions with charge tagged 5=-or 3=-termini.…”

Section: Nucleobase Loss Drives Subsequent Site-specific 3=-coo Cleavagementioning

confidence: 99%

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RNA fragmentation in MALDI mass spectrometry studied by H/D-exchange: Mechanisms of general applicability to nucleic acids

Andersen

Kirpekar

Haselmann

2006

J. Am. Soc. Mass Spectrom.

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To reveal the gas-phase chemistry of RNA and DNA fragmentation during MALDI mass spectrometry in positive ion mode, we performed hydrogen/deuterium exchange on a series of RNA and DNA tetranucleotides and studied their fragmentation patterns on a highresolution MALDI TOF-TOF instrument. We were specifically interested in elucidating the remarkably different fragmentation behavior of RNA and DNA, i.e., the characteristic and abundant production of c-and y-ions from RNA versus a dominating generation of (a-B)-and w-ions from DNA analytes. The analysis yielded important information on all significant backbone cleavages as well as nucleobase losses. Based on this, we suggest common fragmentation mechanisms for RNA and DNA as well as an important RNA-specific reaction requiring a 2=-hydroxyl group, leading to c-and y-ions. The data is viewed and discussed in the context of previously published data to obtain a coherent picture of the fragmentation of singly protonated nucleic acids. (J Am Soc Mass Spectrom 2006, 17, 1353-1368

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Section: Resultsmentioning

confidence: 99%

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confidence: 78%

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RNA fragmentation in MALDI mass spectrometry studied by H/D-exchange: Mechanisms of general applicability to nucleic acids

Andersen

Kirpekar

Haselmann

2006

J. Am. Soc. Mass Spectrom.

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“…1. 1 The modification of sugar in the nucleosides is important for therapeutic applications. For example, arabino-uridine (with 2 0 -OH anti relative to the 3 0 -OH group) was used in the development of new anti-leukemia agents 2 and 2 0 ,3 0 -dideoxyuridine (without the 2 0 -and 3 0 -hydroxyl groups)…”

Section: Introductionmentioning

confidence: 99%

“…solvent, salt presence and pH), it is possible to study these systems in the gas phase by use of mass spectrometry. Indeed, the thermochemical state function such as gas-phase basicities (GB D G° T for Eqn (1)) and proton affinities (PA D H° T for the same reaction) of natural or synthetic modified nucleosides can be determined. can occur under either metastable 5 or low-energy collisional activation conditions:…”

Section: Introductionmentioning

confidence: 99%

Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformation

Mezzache¹,

Alvès²,

Pèpe³

et al. 2005

J. Mass Spectrom.

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A ladder of relative proton affinities (PA) for a series of modified uridines (e.g. araU, ddU, 5BrU, 5BrdU and 5IU) was established from competitive dissociations of proton-bound heterodimers using Cooks and co-workers' kinetic method. The studied heterodimers are constituted of a modified nucleoside and either an amino acid or a nucleoside with known PA value. These non-covalent heterodimers were prepared under electrospray conditions to be selected and dissociated into the ion-trap analyzer. These results allowed our PA ladder of uridine and deoxyuridine analogs substituted at the C-5 position in the uracil ring to be extended. From this scale, it was showed that the substitution of hydrogen atom at the C-2' position in the sugar ring by a hydroxyl group involves a decrease of about 7 kJ mol(-1). The experimental values for U, 5MeU, dU, 5MedU, ddU and araU are consistent with those obtained by DFT calculations (B3P86/6-31+G//B3LYP/6-31G(.)). Several neutral and protonated conformations of these compounds were considered, in particular the ring conformation of furanose and the orientation of the base with respect to the sugar ring. These calculated results showed the influence of sugar substituent on the conformation of the neutral form of theses nucleosides. However, the most stable protonated structure is the same for all the studied nucleosides except for araU, where the position of the anti 2'-OH group imposes a specific conformation.

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Current literature in mass spectrometry

2003

J. Mass Spectrom.

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In order to keep subscribers up‐to‐date with the latest developments in their field, John Wiley & Sons are providing a current awareness service in each issue of the journal. The bibliography contains newly published material in the field of mass spectrometry. Each bibliography is divided into 11 sections: 1 Books, Reviews & Symposia; 2 Instrumental Techniques & Methods; 3 Gas Phase Ion Chemistry; 4 Biology/Biochemistry: Amino Acids, Peptides & Proteins; Carbohydrates; Lipids; Nucleic Acids; 5 Pharmacology/Toxicology; 6 Natural Products; 7 Analysis of Organic Compounds; 8 Analysis of Inorganics/Organometallics; 9 Surface Analysis; 10 Environmental Analysis; 11 Elemental Analysis. Within each section, articles are listed in alphabetical order with respect to author (5 Weeks journals ‐ Search completed at 19th. February. 2003)

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Fragmentation pathway studies of oligonucleotides in matrix-assisted laser desorption/ionization mass spectrometry by charge tagging and H/D exchange

Cited by 12 publications

References 60 publications

RNA fragmentation in MALDI mass spectrometry studied by H/D-exchange: Mechanisms of general applicability to nucleic acids

RNA fragmentation in MALDI mass spectrometry studied by H/D-exchange: Mechanisms of general applicability to nucleic acids

Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformation

Current literature in mass spectrometry

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