The DNA Radical Code. Resolution of Identity in Dissociations of Trinucleotide Codon Cation Radicals in the Gas Phase

J Wan, B Broz, Y Liu, SR Huang, A Marek… - Journal of the …, 2023 - ACS Publications
Sixty DNA trinucleotide cation radicals covering a large part of the genetic code alphabet
were generated by electron transfer in the gas phase, and their chemistry was studied by …

The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry

E Fuchs, C Falschlunger, R Micura… - Nucleic Acids …, 2019 - academic.oup.com
The catalytic strategies of small self-cleaving ribozymes often involve interactions between
nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply …

Resolution of Identity in Gas-Phase Dissociations of Mono- and Diprotonated DNA Trinucleotide Codons by 15N-Labeling and Computational Structure Analysis

J Wan, B Broz, Y Liu, SR Huang, A Marek… - Journal of the …, 2022 - ACS Publications
Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions
were studied by tandem mass spectrometry using 15N-labeling to resolve identity in the …

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

RE Van Outersterp, J Martens, G Berden… - Physical Chemistry …, 2018 - pubs.rsc.org
The molecular family of nucleotide triphosphates (NTPs), with adenosine 5′-triphosphate
(ATP) as its best-known member, is of high biochemical importance as their phosphodiester …

Structural and energetic effects of O2′-ribose methylation of protonated purine nucleosides

CC He, LA Hamlow, ZJ Devereaux, Y Zhu… - The Journal of …, 2018 - ACS Publications
The chemical difference between DNA and RNA nucleosides is their 2′-hydrogen versus
2′-hydroxyl substituents. Modification of the ribosyl moiety at the 2′-position and 2′-O …

Excited State Deactivation Mechanism in Protonated Uracil: New Insights from Theoretical Studies

R Omidyan, F Abedini, L Shahrokh… - The Journal of Physical …, 2020 - ACS Publications
We have conducted here a theoretical exploration, discussing the distinct excited state
lifetimes reported experimentally for the two lowest lying protonated isomers of uracil. In this …

Influence of 5-fluorination on the structure and glycosidic bond stability of the protonated canonical DNA and RNA cytidine nucleosides: Oh, what a difference the 2 …

ZJ Devereaux, EO Soley, G Berden, J Oomens… - International Journal of …, 2024 - Elsevier
Fluorinated nucleosides are well-established as anticancer and antiviral medications. As
with many pharmaceuticals, the effects of fluorine modifications are often only partially …

Protonation-induced tautomerization lowers the activation barriers for N-glycosidic bond cleavage of thymidine and 5-methyluridine

RR Wu, MT Rodgers - International Journal of Mass Spectrometry, 2025 - Elsevier
Synergistic infrared multiple photon dissociation (IRMPD) action spectroscopy experiments
and electronic structure calculations revealed that both 2, 4-dihydroxy tautomers and O2 …

Formation of n→ π+ interaction facilitating dissociative electron transfer in isolated tyrosine-containing molecular peptide radical cations

WK Tang, X Mu, M Li, J Martens, G Berden… - Physical Chemistry …, 2020 - pubs.rsc.org
Long-range electron transfer in proteins can be rationalized as a sequential short-distance
electron-hopping processes via amino acid residues having low ionization energy as relay …

Structural and Energetic Effects of O2′-Ribose Methylation of Protonated Pyrimidine Nucleosides

CC He, LA Hamlow, Y Zhu, Y Nei, L Fan… - Journal of The …, 2019 - ACS Publications
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 …