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Molecular simulation study of RNA/dopamine complex dynamics at varying concentrations.

Fuente: PubMed

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Detalles Bibliográficos
Autores principales:	Poghosyan, Armen H, Mamasakhlisov, Yevgeni S, Parsadanyan, Marine A, Shahinyan, Mariam A, Movsisyan, Zvart H, Vardevanyan, Poghos O
Formato:	Artículo científico
Lenguaje:	en
Publicado:	Scientific reports 2025
Materias:	Dopamine Molecular Dynamics Simulation RNA Hydrogen Bonding Nucleic Acid Conformation Poly A
Acceso en línea:	Acceder al recurso
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author	Poghosyan, Armen H Mamasakhlisov, Yevgeni S Parsadanyan, Marine A Shahinyan, Mariam A Movsisyan, Zvart H Vardevanyan, Poghos O
author_facet	Poghosyan, Armen H Mamasakhlisov, Yevgeni S Parsadanyan, Marine A Shahinyan, Mariam A Movsisyan, Zvart H Vardevanyan, Poghos O Poghosyan, Armen H Mamasakhlisov, Yevgeni S Parsadanyan, Marine A Shahinyan, Mariam A Movsisyan, Zvart H Vardevanyan, Poghos O
collection	PubMed - marine biology
contents	Molecular simulation study of RNA/dopamine complex dynamics at varying concentrations. Poghosyan, Armen H Mamasakhlisov, Yevgeni S Parsadanyan, Marine A Shahinyan, Mariam A Movsisyan, Zvart H Vardevanyan, Poghos O Dopamine Molecular Dynamics Simulation RNA Hydrogen Bonding Nucleic Acid Conformation Poly A The interaction between dopamine and RNA structures holds significant potential for understanding neurotransmitter-driven RNA modulation and biosensor design. Here, we employ all-atom molecular dynamics (MD) simulations to investigate the concentration-dependent binding of dopamine to poly(rA)/poly(rU) complex. We reveal that the dopamine molecules are preferentially trapped by poly(A)/poly(U) complex where the dopamine catechol rings became oriented parallel towards to RNA amine rings, although with the increase of dopamine concentration we track a multi-mode binding of dopamine molecules, i.e., different configurations can be found. The increasing of dopamine concentration leads to the dense packing of poly(A)/poly(U) complex, where more than half of dopamine molecules are strongly bound. We argue that the dopamine shows mainly intercalation mechanism of stabilization of poly(A)-poly(U) complexes governed by the hydrogen bonds network formation. These findings offer new insights relevant to RNA-based biosensors and the interplay between neurotransmitters and nucleic acids.
format	Artículo científico
id	pubmed_40593137
institution	PubMed
language	en
publishDate	2025
publisher	Scientific reports
record_format	pubmed
spellingShingle	Molecular simulation study of RNA/dopamine complex dynamics at varying concentrations. Poghosyan, Armen H Mamasakhlisov, Yevgeni S Parsadanyan, Marine A Shahinyan, Mariam A Movsisyan, Zvart H Vardevanyan, Poghos O Dopamine Molecular Dynamics Simulation RNA Hydrogen Bonding Nucleic Acid Conformation Poly A Molecular simulation study of RNA/dopamine complex dynamics at varying concentrations. Poghosyan, Armen H Mamasakhlisov, Yevgeni S Parsadanyan, Marine A Shahinyan, Mariam A Movsisyan, Zvart H Vardevanyan, Poghos O Dopamine Molecular Dynamics Simulation RNA Hydrogen Bonding Nucleic Acid Conformation Poly A The interaction between dopamine and RNA structures holds significant potential for understanding neurotransmitter-driven RNA modulation and biosensor design. Here, we employ all-atom molecular dynamics (MD) simulations to investigate the concentration-dependent binding of dopamine to poly(rA)/poly(rU) complex. We reveal that the dopamine molecules are preferentially trapped by poly(A)/poly(U) complex where the dopamine catechol rings became oriented parallel towards to RNA amine rings, although with the increase of dopamine concentration we track a multi-mode binding of dopamine molecules, i.e., different configurations can be found. The increasing of dopamine concentration leads to the dense packing of poly(A)/poly(U) complex, where more than half of dopamine molecules are strongly bound. We argue that the dopamine shows mainly intercalation mechanism of stabilization of poly(A)-poly(U) complexes governed by the hydrogen bonds network formation. These findings offer new insights relevant to RNA-based biosensors and the interplay between neurotransmitters and nucleic acids.
title	Molecular simulation study of RNA/dopamine complex dynamics at varying concentrations.
topic	Dopamine Molecular Dynamics Simulation RNA Hydrogen Bonding Nucleic Acid Conformation Poly A
url	https://pubmed.ncbi.nlm.nih.gov/40593137/