Experimental and Theoretical Study of Energetics of Complex Formation Between Nucleic Acid Bases and the Bases with Amide Group

Abstract

A number of nucleic acid base pairs and complexes between the bases and the amide group of acrylamide have been studied experimentally by using mass spectrometry and theoretically by the method of atom-atom potential function calculations. It has been found from temperature dependencies of peak intensities in mass spectra of m2.2.9(3) Gua.m1Ura, m9 Ade.m1Cyt, m2.2.9(3) Gua.m1Gua.m1Cyt pairs that enthalpy values, delta H, of the complex formation are equal to 14.2 +/- 1.1, 13.5 +/- 1.3 and 16.4 +/- 1.4 kcal/M, respectively, and those of acrylamide with m1.3(2) Ura and m1Thy corresponds to 9.7 +/- 1.0 and 6.8 +/- 0.6 kcal/M. There is a good agreement of the experimental data with calculations when taking into account both the amino-oxo and the amino-hydroxy tautomeric forms of guanine. A combined use of the data allows us to determine the energy, the modes of interaction and the structure of the complexes. The results are discussed in connection with the modelling of molecular structure of biopolymers by the method of classical potential functions, protein-nucleic acids recognition and fidelity of nucleic acids biosynthesis.

Mass spectrometric and computational study of complex formation of nucleic acid bases with acrylamide as a surrogate for asparagine and glutamine residues

“…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.…”