Structures and interaction energies of nucleic acid base-amino acid complexes. Methylcytosines-acrylamide model

The interaction energies between the cytosine methylated derivatives (m¹Cyt, m₂^1,NCyt, m₃^1,N,NCyt) and acrylamide, which models the side chains of natural amino acids asparagine and glutamine, were measured using the temperature-dependent field ionization mass spectrometry method. The experimental enthalpies of the dimer formation are -57.0 kJ mol^-1 for the acrylamide-m¹Cyt dimer, -58.7 kJ mol^-1 for the acrylamidem₂^1,NCyt dimer and -45.7 kJ mol^-1 for the acrylamide-m₃^1,N,NCyt dimer. The dimer structures were determined using quantum-chemical calculations. The calculated structures are almost planar with antiparallel orientations of the monomer dipoles and they are stabilized by intermolecular N-H⋯O and N-H⋯N H-bonds. The calculated interaction energies are in good agreement with the experimental data. The results indicate that the interaction energy between acrylamide and m¹Cyt is significantly higher than that between acrylamide and m¹Uracil. This result is relevant to the mechanism of the protein-nucleic acid recognition.