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In the context of the problem of nucleic acid-protein interactions, thermodynamic and geometrical parameters of complexes of methylated nucleic acid bases with acrylamide (as a model of the side chains of asparagine and glutamine) were investigated. Enthalpies of formation of nucleic acid base-acrylamide complexes, determined experimentally by means of temperature-dependent field ionization mass spectrometry, were in reasonable agreement with the interaction energies calculated theoretically using atom-atom potential functions. A stability order for base-acrylamide complexes was determined: Nucleic acid-protein interactions, both specific and nonspecific, are important for all the biological functions of nucleic acids and for the molecular machinery of cells. 1,2Nonspecific interactions of proteins with nucleic acids can have hydrophobic or electrostatic nature (e.g. interactions of positively charged amino acids with negatively charged phosphate groups of the duplex backbone). The specific interactions arise as a result of mutual recognition of specially arranged moieties of the nucleic acid and protein via hydrogen bond formation. 3 They are important for promoter-operator interactions, and during biosynthesis of nucleic acids and proteins.Although several models of protein-nucleic acid complexes have been constructed using modern experimental and computational approaches, 4 only a few reliable data on the energetics of such complex formation exist. Evaluation of energies of nucleic acid base-amino acid residue interactions is of great importance for such model building. An efficient method of determination of the energetic parameters of intermolecular interactions in the complexes of biomolecules bound by weak non-valence interactions (van der Waals interactions and H-bonds), in the so-called vacuum approach (in the absence of the influence of a solvent), is provided by temperature-dependent field ionization (TD FI) mass spectrometry, developed at this Institute. 5,6 The method is based on the measurement of a relative association constant K ass of molecules in the gas phase, construction of the van't Hoff plots, and thus calculations of the enthalpies of formation (DH) of the complexes under study. This paper is a continuation of our systematic study of associations between biopolymer components in vacuum. 7,8,9 We have determined the enthalpies of complex formation for a series of methylated nucleic acid bases with acrylamide, considered to be a model compound for asparagine and glutamine side chains. These energy values have been attributed to certain configurations of acrylamide-base complexes, constructed using classical potential functions. This approach allowed us to determine the relative affinities of various functional groups of nucleic acid bases for asparagine and glutamine residues, and to suggest models of interactions of these residues with singlestranded and double-stranded nucleic acids. METHODSIn the present work experimental data on enthalpies of formation for complexes between various nitr...