Covalent Crosslinking in Gas-Phase Biomolecular Ions. An Account and  Perspective. Photochemical and Collision-Induced Crosslinking in Stereochemically Distinct Scaffolds of Peptides and Nitrile-Imine Conjugate Ions in the Gas-Phase

Gas-phase ion complexes of dinucleotides and trinucleotides with a diaryltetrazole-tagged peptide undergo covalent cross-linking upon UV photodissociation (UVPD) at 213 nm.  The cross-linking reaction involves nitrile-imine intermediates produced by loss of N₂ from the tetrazole, whereby cross-linking between the complex components competes with internal cross-linking within the peptide.  The propensity for UVPD-induced cross-linking of DNA nucleobases was established for complexes of dinucleotides dAA, dCC, dGG, and dTT.  UVPD-CID-MS³ of isomeric trinucleotide-peptide complexes of dCGA, dAGC,  dCAG, dACG,  and dGCA showed nearly quantitative cross-linking that favored guanine regardless of its position in the sequence. Binding energies for the gas-phase ion complexes were obtained by Born-Oppenheimer molecular dynamics and density functional theory calculations at the M06-2X/def2qzvpp level. These calculations showed similar binding energies for the dAA, dCC, and dCAG complexes that were in the 195-221 kJ mol^-1 range, whereas binding to dGG and dTT was weaker.  A mechanism for the novel cross-linking reaction between the nitrile imine and guanine was elucidated with a riboguanosine conjugate that was tagged with a diaryltetrazole group at 5’-O.  Product analysis as well as the calculated structures and energies suggested that cross-links resulted from an attack on the aromatic ring of an imine intermediate by the guanine carbonyl oxygen, followed by proton migrations.