Biopolym. Cell. 1997; 13(3):177-184.
Structure and Function of Biopolymers
The study of protein-nucleic acid recognition: Simulation of base and «model» amino acids complexes in DMSO by Monte Carlo method
1Danilov V. I., 1Mikhaleva O. V., 1Slyusarchuk O. N., 2Poltev V. I., 3Alderfer J. L.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. Institute of Theoretical and Experimental Biophysics
    3, Institutska, Pushchino, Moscow region, Russian Federation, 142290
  3. Roswell Park Cancer Institute
    Elm and Carlton Str., Buffalo, New-York, USA, 14263


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.


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