Eur. Phys. J. D 20, 421-430 (2002)
https://doi.org/10.1140/epjd/e2002-00144-9

Modeling of recognition sites of nucleic acid bases and amide side chains of amino acids. Combination of experimental and theoretical approaches

¹ Department of Molecular Biophysics, B. Verkin Institute for Low Temperature Physics and Engineering of the National Academy of Sciences of Ukraine, 47 Lenin avenue, Kharkov 61103, Ukraine
² IRSAMC, Laboratoire Physique Quantique (UMR 5626 du CNRS) , Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse Cedex, France and Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA

Corresponding author: ^a ludwik@u.arizona.edu

Received: 5 February 2002
Revised: 14 March 2002
Published online: 13 September 2002

Abstract

A combined experimental-theoretical approach to modeling of building blocks of recognition complexes formed by nucleic acid bases and the amino-acids side-chain amino group is reviewed. The approach includes the temperature dependent field-ionization mass spectrometry and ab initio quantum chemical calculations. The mass spectrometric technique allows determination of interaction enthalpies of biomolecules in the gas phase, and the results it produces are directly comparable to the results obtained through theoretical modeling. In our works we have analyzed both thermodynamic and structural aspects of the recognition complexes of four canonical nucleic acid bases and acrylamide, which models the side chain of asparagine and glutamine. It has been shown that all bases can interact with amide group of the amino acids via their Watson-Crick sites when being incorporated into a single strand DNA or RNA. Stability of the complexes studied, expressed as (kJ mole^-1) decreases as: m⁹Gua Cyt Ade Ura . We have determined that in the double stranded DNA only purine bases can be recognized.