Biopolymers and cell. 1997; 13 (3): 177 - 184

The study of protein-nucleic acid recognition: Simulation of base and «model» amino acids complexes in DMSO by Monte Carlo method

V. I. Danilov, O. V. Mikhaleva, O. N. Slyusarch.uk, V. I. Poltcv, J. L, Alderfer

A computer simulation of gamine (G), cytosine (C), G-C base pair, protoned C (CH ), acetic acid in neutral (AcOH) and dcprotoned (AcO ) forms, G-AcO , C-AcOH, CH -AcO complexes salvation in DMSO was carried out by Monte Carlo method. It is shown that G-C base pair formation in DMSO is energetically favorable. G-AcO complex formation is comparable with the formation of G-C base pair in energetical favorability. In this case acetate union can replace C in G-C base pair. The formation of C-AcOH complex is much less favorable than the formation of G-C pair. However proton transfer from AcOH to C leads to the formation of CH -AcOH complex which is much more favorable than all of the complexes studied. Here acetic acid can replace G in G-C base pair. The formation of G-AcO and CH -AcO specific complexes detected in DMSO with the help of experiment and theory is a competitive process in respect to the formation of G-C base pairs and can be considered the primary step in the real mechanism of protein-nucleic acid recognition.