KFU. Card publication. Molecular Dynamics of Oligonucleotide DNA Complexes with Phosphatidylserine

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FEDERAL UNIVERSITY

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MOLECULAR DYNAMICS OF OLIGONUCLEOTIDE DNA COMPLEXES WITH PHOSPHATIDYLSERINE

Form of presentation

Articles in international journals and collections

Year of publication

2023

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Authors, employees of KFU

Ibragimova Milyausha Yakubovna, author

Bibliographic description in the original language

Ibragimova M.Y., Zaitsev S.Yu., Aupov R. Kh.., Andrianov G.V., Zhdanov R.I. Molecular Dynamics of Oligonucleotide DNA Complexes with Phosphatidylserine // Biointerface Research in Applied Chemistry. - 2023, V. 13, Issue 3. - P. 287-297. https://doi.org/10.33263/BRIAC133.287

Annotation

A formation of DNA-lipid complexes was studied by molecular docking and molecular dynamics methods using the interaction of DNA with phosphatidylserine (PS). We have previously shown that some fatty acids and phosphatidylglycerol can specifically bind to oligonucleotide DNA (dA)20?(dT)20. It is shown that (dA)20?(dT)20 and phosphatidylserine formed a stable complex with a 6.3 kcal/mol binding energy and the PS molecule located in the minor groove of DNA. This complex contains 342 groups of atoms, the distance between which is less than 3.4 Å. The types of bonds in the PS-DNA(oligonucleotide) complex are suggested as hydrogen bonds, van der Waals, and hydrophobic interactions. In our previous study, a similar arrangement with close binding energy of 5.8 kcal/mol was shown for phosphatidylglycerol complex with the same oligonucleotide (complex contained 354 groups of atoms). The present study is of interest due to the importance of such complexes for applied biochemistry and biotechnology, genetics and molecular biology, cytology and pharmacology, nanotechnology, and self-assembly smart materials.

Keywords

interfacial interactions; interatomic distances; phosphatidylserine; oligonucleotides; DNA-lipid complexes; docking; molecular dynamics

The name of the journal

Biointerface Research in Applied Chemistry

URL

https://doi.org/10.33263/BRIAC133.287

Please use this ID to quote from or refer to the card

https://repository.kpfu.ru/eng/?p_id=265839&p_lang=2

Full metadata record

Field DC	Value	Language
dc.contributor.author	Ibragimova Milyausha Yakubovna	ru_RU
dc.date.accessioned	2023-01-01T00:00:00Z	ru_RU
dc.date.available	2023-01-01T00:00:00Z	ru_RU
dc.date.issued	2023	ru_RU
dc.identifier.citation	Ibragimova M.Y., Zaitsev S.Yu., Aupov R. Kh.., Andrianov G.V., Zhdanov R.I. Molecular Dynamics of Oligonucleotide DNA Complexes with Phosphatidylserine // Biointerface Research in Applied Chemistry. - 2023, V. 13, Issue 3. - P. 287-297. https://doi.org/10.33263/BRIAC133.287	ru_RU
dc.identifier.uri	https://repository.kpfu.ru/eng/?p_id=265839&p_lang=2	ru_RU
dc.description.abstract	Biointerface Research in Applied Chemistry	ru_RU
dc.description.abstract	A formation of DNA-lipid complexes was studied by molecular docking and molecular dynamics methods using the interaction of DNA with phosphatidylserine (PS). We have previously shown that some fatty acids and phosphatidylglycerol can specifically bind to oligonucleotide DNA (dA)20?(dT)20. It is shown that (dA)20?(dT)20 and phosphatidylserine formed a stable complex with a 6.3 kcal/mol binding energy and the PS molecule located in the minor groove of DNA. This complex contains 342 groups of atoms, the distance between which is less than 3.4 Å. The types of bonds in the PS-DNA(oligonucleotide) complex are suggested as hydrogen bonds, van der Waals, and hydrophobic interactions. In our previous study, a similar arrangement with close binding energy of 5.8 kcal/mol was shown for phosphatidylglycerol complex with the same oligonucleotide (complex contained 354 groups of atoms). The present study is of interest due to the importance of such complexes for applied biochemistry and biotechnology, genetics and molecular biology, cytology and pharmacology, nanotechnology, and self-assembly smart materials.	ru_RU
dc.language.iso	ru	ru_RU
dc.subject		ru_RU
dc.title	Molecular Dynamics of Oligonucleotide DNA Complexes with Phosphatidylserine	ru_RU
dc.type	Articles in international journals and collections	ru_RU