Paper Citing NAMD - Abstract
Zobnina, V.G.; Chagovets, V.V.; Boryak, O.A.; Kosevich, M.V.
Mass spectrometric study and computer modeling of noncovalent interactions of cytosine with polyethylene glycol oligomers
Mass-spektrometriya, 11:97-106, 2014
Data on noncovalent intermolecular interactions of nitrogen bases as nucleic acid components with organic polyethers are of interest both for fundamental molecular biophysics and applied tasks of production of pharmaceutical organic nanoparticles. In the present work systems composed of pyrimidine nitrogen base cytosine (Cyt) or its methylderivatives and polyethylene glycol PEG-400 oligomers M n are examined by mass spectrometry with electrospray ionization (ESI) and fast atom bombardment. Recording of a set of associates of M n СytH + type ( n = 3-17) in the ESI mass spectra evidences formation of protonated complexes of the base with oligomers of various chain length in all systems studied. Computer modeling by means of molecular dynamics provided answers to questions concerning stability and structure of these complexes under different conditions. It is shown that M n СytH + clusters in the gas phase (vacuum) adopt a compact structure with a quasi-cyclic or quasi-helical self-organization of a polymeric chain around the protonated base. It is established that the compact structure of M 8СytH + complex characteristic of its gas phase state is preserved in liquid medium of methanol (utilized as a solvent in ESI). The results of simulation of evolution of methanol droplet in vacuum, which mimics the droplet disintegration under ESI conditions, have shown that the M 8СytH + complex initially present in the droplet does not disintegrate in the process of droplet evaporation. After completion of desolvation the complex returns to the conformation characteristic of the gas phase state. Thus, the evidence is found to the fact that M 8СytH + clusters recorded on the ESI mass spectra reflect adequately the presence of the corresponding noncovalent complexes in the analyzed liquid solution.
