Abstract
The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.
Highlights
DNA base pairing in motifs other than the well-known Watson– Crick structure have been under thorough study in recent years, where in particular the G-quadruplex and i-motif structures have received considerable attention
The canonical keto-amino C1 tautomer is very close in energy to the enol-amino tautomer C2; which of the two is lower in energy depends on the level of theory that is used.[11]
In contrast to the alkali metal ion, our spectra clearly show that a bidentate (N3 and O atoms) and a monodentate (O-atom) coordination motif occur in coexistence for copper
Summary
DNA base pairing in motifs other than the well-known Watson– Crick structure have been under thorough study in recent years, where in particular the G-quadruplex and i-motif structures have received considerable attention. The barrier to transfer was computed at 6.7 kJ molÀ1.5 The hemiprotonated dimer is further stabilized by two HNHÁ Á ÁOQC hydrogen bonds between the amino and carbonyl groups of each of the cytosine bases. Gas-phase IR photodissociation spectroscopy of charged species in ion trapping devices has been applied frequently in recent years to reveal the tautomeric structure of protonated and metalated nucleobases.[7,11,12,13,14,15,16,17,18,19,20,21] We present here the first IR spectra of mass selected C–M+–C complexes, where M = Cu, Li, Na and K, and derive their coordination geometries by comparison with computed spectra. The gas-phase IR spectrum of monomeric Ag+–C was very recently reported by Pino et al.[14]
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