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

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 collision-induced dissociation tandem mass spectrometry and theoretical calculations. The major dissociations involved loss of nucleobase molecules and radicals, backbone cleavage, and cross-ring fragmentations that depended on the nature and position of the nucleobases. Mass identity in dissociations of symmetrical trinucleotide cation radicals of the (XXX+2H) and (XYX+2H) type was resolved by specific N labeling.

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

Dissociations of DNA trinucleotide codons as gas-phase singly and doubly protonated ions were studied by tandem mass spectrometry using N-labeling to resolve identity in the nucleobase loss and backbone cleavages. The monocations showed different distributions of nucleobase loss from the 5'-, middle, and 3'-positions depending on the nucleobase, favoring cytosine over guanine, adenine, and thymine in an ensemble-averaged 62:27:11:<1 ratio. The distribution for the loss of the 5'-, middle, and 3'-nucleobase was 49:18:33, favoring the 5'-nucleobase, but also depending on its nature.

Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization.

Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms.

Probing d- and l-Adrenaline Binding to β-Adrenoreceptor Peptide Motifs by Gas-Phase Photodissociation Cross-Linking and Ion Mobility Mass Spectrometry.

Diazirine-tagged d- and l-adrenaline derivatives formed abundant noncovalent gas-phase ion complexes with peptides -Ac-SSIVSFY-NH (peptide S) and -Ac-VYILLNWIGY-NH (peptide V) upon electrospray ionization. These peptide sequences represent the binding motifs in the β-adrenoreceptor. The structures of the gas-phase complexes were investigated by selective laser photodissociation of the diazirine chromophore at 354 nm, which resulted in a loss of N and formation of a transient carbene intermediate in the adrenaline ligand without causing its expulsion.

The Elusive Noncanonical Isomers of Ionized 9-Methyladenine and 2'-Deoxyadenosine.

Noncanonical nucleobases and nucleosides represent newly discovered species of relevance for DNA ionization. We report a targeted synthesis of gas-phase 9-methylene(1)adenine cation radical () as a low-energy isomer of ionized 9-methyladenine. Ion showed unique collision-induced dissociation and UV-vis photodissociation action spectra that distinguished it from other cation radical isomers.

Cation Radicals of Hachimoji Nucleobases P and Z: Generation in the Gas Phase and Characterization by UV-Vis Photodissociation Action Spectroscopy and Theory.

We report the generation of gas-phase cation radicals of unusual nucleobases 5-aza-7-deazaguanine (P) and 6-amino-5-nitro-()pyrid-2-one (Z) that have been used as building blocks of base-expanded (hachimoji) DNA. The cation radicals were generated by collision-induced intramolecular electron transfer and dissociation of ternary copper-terpyridine complexes. The cation radicals were characterized by deuterium labeling and tandem mass spectrometry including MS collision-induced dissociation, UV-vis photodissociation, and action spectroscopy.

Cation Radicals of Hachimoji Nucleobases. Canonical Purine and Noncanonical Pyrimidine Forms Generated in the Gas Phase and Characterized by UV-Vis Photodissociation Action Spectroscopy.

Oxidation of nontraditional nucleobases 1-methylcytosine (hachimoji base ) and isoguanine (hachimoji base ) in gas-phase ternary complexes with Cu(terpyridine) formed cation radicals that were characterized by tandem mass spectrometry, UV-vis photodissociation action spectroscopy in the 210-700 nm region, and calculations up to the CCSD(T)/complete basis set level of theory. Oxidation of was accompanied by exothermic isomerization in the 1-methylcytosine ion (), forming 1-methylene-2-hydroxy-4-aminopyrimidine cation radical () as a noncanonical distonic isomer of the nucleobase. Ion was characterized by deuterium exchange experiments and provided a matching UV-vis action spectrum with the vibronic absorption spectrum from time-dependent density functional theory calculations.

Guanine-adenine interactions in DNA tetranucleotide cation radicals revealed by UV/vis photodissociation action spectroscopy and theory.

Hydrogen-rich cation radicals (GATT + 2H)˙ and (AGTT + 2H)˙ represent oligonucleotide models of charged hydrogen atom adducts to DNA. These tetranucleotide cation radicals were generated in the gas phase by one-electron reduction of the respective (GATT + 2H) and (AGTT + 2H) dications in which the charging protons were placed on the guanine and adenine nucleobases. We used wavelength-dependent UV/Vis photodissociation in the valence-electron excitation region of 210-700 nm to produce action spectra of (GATT + 2H)˙ and (AGTT + 2H)˙ that showed radical-associated absorption bands in the near-UV (330 nm) and visible (400-440 nm) regions.

Ground and Excited States of Gas-Phase DNA Nucleobase Cation-Radicals. A UV-vis Photodisociation Action Spectroscopy and Computational Study of Adenine and 9-Methyladenine.

Cation radicals of adenine (A) and 9-methyladenine (MA) were generated in the gas phase by collision-induced intramolecular electron transfer in copper-terpyridine-nucleobase ternary complexes and characterized by collision-induced dissociation (CID) mass spectra and UV-vis photodissociation action spectroscopy in the 210-700 nm wavelength region. The action spectra of both A and MA displayed characteristic absorption bands in the near-UV and visible regions. Another tautomer of A was generated as a minor product by multistep CID of protonated 9-(2-bromoethyl)adenine.

UV-vis Photodissociation Action Spectroscopy Reveals Cytosine-Guanine Hydrogen Transfer in DNA Tetranucleotide Cation Radicals upon One-Electron Reduction.

We report the generation and spectroscopic study of hydrogen-rich DNA tetranucleotide cation radicals (GATC+2H) and (AGTC+2H). The radicals were generated in the gas phase by one-electron reduction of the respective dications (GATC+2H) and (AGTC+2H) and characterized by collision-induced dissociation and photodissociation tandem mass spectrometry and UV-vis photodissociation action spectroscopy. Among several absorption bands observed for (GATC+2H), the bands at 340 and 450 nm were assigned to radical chromophores.

Non-covalent complexes of the peptide fragment Gly-Asn-Asn-Gln-Gln-Asn-Tyr in the gas-phase. Photodissociative cross-linking, Born-Oppenheimer molecular dynamics, and ab initio computational binding study.

Non-covalent complexes of the short amyloid peptide motif Gly-Asn-Asn-Gln-Gln-Asn-Tyr (GNNQQNY) with peptide counterparts that were tagged with a diazirine ring at the N-termini (*GNNQQNY) were generated as singly charged ions in the gas phase. Specific laser photodissociation (UVPD) of the diazirine tag in the gas-phase complexes at 355 nm generated transient carbene intermediates that underwent covalent cross-linking with the target GNNQQNY peptide. The crosslinking yields ranged between 0.

High-resolution two-dimensional liquid chromatography analysis of key linker drug intermediate used in antibody drug conjugates.

In this manuscript, the application of high-resolution sampling (HRS) two-dimensional liquid chromatography (2D-LC) in the detailed analysis of key linker drug intermediate is presented. Using HRS, selected regions of the primary column eluent were transferred to a secondary column with fidelity enabling qualitative and quantitative analysis of linker drugs. The primary column purity of linker drug intermediate ranged from 88.

Effects of inflammatory factors including plasma tumor necrosis factor-α in the clinical treatment of acute respiratory distress syndrome.

The present study investigated the association between the levels of plasma tumor necrosis factor-α (TNF-α), interleukin (IL)-6, IL-8, high-sensitivity C-reactive protein and fibrinogen levels of patients with acute respiratory distress syndrome (ARDS) with ARDS treatment outcome and duration of mechanical ventilation, with the aim of improving the efficacy of ARDS therapy. A total of 140 patients with ARDS were randomly divided into groups A and B, with 70 patients in each group. The patients in group A received a combination of conventional treatment and comprehensive treatment (test group) and the patients in group B were treated with conventional therapy only (control group).