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AVVISO DI SEMINARIO

Il 24 luglio 2019, h 15:00,
Sala Riunioni primo piano
Dipartimento di Scienze Chimiche e Geologiche,
Blocco D, Cittadella Universitaria di Monserrato

Il Dr Sergiy Perepelytsya
Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine

terrà un seminario dal titolo
Dynamics of counterions in the hydration shell of DNA double helix
(segue abstract)

Tutti gli interessati sono invitati a partecipare,

Francesca Mocci

--------------Abstract--------------

Dynamics of counterions in the hydration shell of DNA double helix

Sergiy Perepelytsya
Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine,

DNA is a polyelectrolyte macromolecule, shaped as the double helix with the negatively charged sugar-phosphate backbone outside and nucleic bases inside. The charge of DNA is neutralized by positively charged ions (counterions) that together with water molecules form an ion-hydration shell, stabilizing the structure of the double helix. Under the natural conditions the counterions may be the metallic ions (K+ or Mg2+) and organic molecules (polyamines). The counterions determine the structure and dynamics of the double helix in many respects that makes the study of interaction of different counterions with DNA macromolecule very important for the understanding mechanisms of DNA biological functioning.
In the developed theoretical approach the structure of DNA with counterions was considered as ordered system, resembling the lattice of ionic type (ion-phosphate lattice) [1-5]. The low-frequency spectra (<200 cm−1) of DNA with counterions for right-handed B-and D-, A-forms, and left-handed Z-form of the double helix with Na+, K+, Rb+, Cs+, and Mg2+ counterions were  studied to find the mode of ion-phosphate vibrations. The results show that in the case of alkali metals the frequencies of ion-phosphate vibrations decrease from 180 to 100 cm−1 and the Raman intensities increase as the counterion mass increases. In the case of Z-DNA the mode of ion-phosphate vibrations (near 150 cm−1) appear due to the motions of Mg2+ counterions in minor grove of the double helix. The results describe the experimental low-frequency Raman spectra of DNA confirming the existence of dynamical ordered structure of counterions around the double helix.
To study the impact of water molecules on counterions distribution around the double helix the atomistic molecular dynamics simulations have been carried out for DNA fragment d(CGCGAATTCGCG) in water solution with the counterions Na+, K+, Cs+ or Mg2+ [6]. The results show that due to the interaction with DNA at list two hydration shells of the counterions undergo changes. The Mg2+ and Na+ counterions, constraining water molecules of the first hydration shell, form with DNA water-mediated contacts mostly. The Cs+ and K+ counterions that do not constrain surrounding water molecules may be easily dehydrated and due to this can squeeze through the hydration shell of DNA to the bottom of the double helix grooves and be there up to 10 ns. In this timescale the counterions may be accumulated in the minor groove forming a regular structure along DNA.
The interactions of natural polyamines (putrescine2+, spermidine3+, and spermine4+) with DNA double helix have been studied using atomistic molecular dynamics simulation [7]. The results show that polyamine molecules are localized with recognizable patterns along the double helix with different residence times. The longest residence time (ca 100ns) is in the minor groove. The analysis of the sequence dependence shows that polyamine molecules prefer the A-tract regions of the minor groove – in its narrowest part. The preferable localization of putrescine2+, spermidine3+, and spermine4+ in the minor groove with A-tract motifs is correlated with modulation of the groove width by a specific nucleotide sequences. The developed toy model of DNA-polyamine interaction shows that the electrostatic interactions are the most important driving force in this phenomenon, making it even more prominent for polyamines with higher charges. The results of the study explain the specificity of polyamine interactions with A-tract region of the DNA double helix which is observed in experiments.

1.- Perepelytsya S., Volkov S.N. Ukrainian Journal of Physics 49, 1072 (2004)
2.- Perepelytsya S., Volkov S.N. European Physical Journal E 24, 261 (2007)
3.- Perepelytsya S., Volkov S.N. European Physical Journal E 31, 201 (2010)
4.- Perepelytsya S., Volkov S.N. Journal of Molecular Liquids 164, 113 (2011)
5.- Perepelytsya S., Volkov S.N. Journal of Physics: Conference Series 438, 012013 (2013)
6.- Perepelytsya S. Journal of Molecular Modeling 24,171 (2018)
7.- Perepelytsya S., Uli?ný J., Laaksonen A., Mocci F. Nucleic Acids Research. 47, 6084 (2019)