Natural polyamines play a fundamental role in the cell cycle. Despite being recognized as the most abundant organic counterions of DNA in the cell nucleus, their interactions with DNA have not been fully characterized. In a recent work [S. Perepelytsya, T. Vasiliu, A. Laaksonen, L. Engelbrecht, G. Brancato, and F. Mocci, J. Molec. Liq. 389, 122828 (2023)], we have shown how the interactions between spermidine3+ and the DNA double helix induce significant conformational variations in the polyamine molecule. Specifically, we found that DNA induces conformations that are not observed in solution. Following that study, we present here a detailed investigation of the most compact conformation of the polyamine, analyzing its connection to the interaction with the DNA duplex. The analysis reveals that anomalous bent conformations of the spermidine3+ molecule result from the interaction of all three amino groups of the polyamine with the DNA phosphate groups on the minor groove side of the double helix. The changes in dihedral angles of the bent spermidine3+ molecule can be explained in terms of conformational transformations of six- and seven-membered rings, analogous to cyclohexane and cycloheptane. The analysis of the position of spermidine3+ molecule along the DNA surface reveals a sequence specificity of this binding mode with a marked preference for the narrow minor groove of A-tracts. The formation of the anomalous bent conformations of spermidine3+ in the complex with the DNA double helix is expected to be of paramount importance in understanding the mechanisms underlying DNA’s biological function.
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March 2024
Research Article|
March 01 2024
Unusual bending patterns of spermidine3+ bound to DNA double helix
Sergiy Perepelytsya
;
Sergiy Perepelytsya
a)
1
Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine
, Kyiv 03143, Ukraine
a)Authors to whom correspondence should be addressed: [email protected]; [email protected]; and [email protected]
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Tudor Vasiliu
;
Tudor Vasiliu
2
Center of Advanced Research in Bionanoconjugates and Biopolymers, “Petru Poni” Institute of Macromolecular Chemistry
, Romania
3
The Research Institute of the University of Bucharest (ICUB)
, Romania
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Aatto Laaksonen
;
Aatto Laaksonen
a)
2
Center of Advanced Research in Bionanoconjugates and Biopolymers, “Petru Poni” Institute of Macromolecular Chemistry
, Romania
4
Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory Stockholm University
, Sweden
5
State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University
, P. R. China
6
Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology
, Sweden
a)Authors to whom correspondence should be addressed: [email protected]; [email protected]; and [email protected]
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Leon De Villiers Engelbrecht;
Leon De Villiers Engelbrecht
6
Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology
, Sweden
7
Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari
, Italy
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Francesca Mocci
Francesca Mocci
a)
7
Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari
, Italy
a)Authors to whom correspondence should be addressed: [email protected]; [email protected]; and [email protected]
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a)Authors to whom correspondence should be addressed: [email protected]; [email protected]; and [email protected]
Fiz. Nizk. Temp. 50, 219–230 (March 2024)
Low Temp. Phys. 50, 204–214 (2024)
Article history
Received:
January 30 2024
Citation
Sergiy Perepelytsya, Tudor Vasiliu, Aatto Laaksonen, Leon De Villiers Engelbrecht, Francesca Mocci; Unusual bending patterns of spermidine3+ bound to DNA double helix. Low Temp. Phys. 1 March 2024; 50 (3): 204–214. https://doi.org/10.1063/10.0024969
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