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

Abstract

Abstract 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.

Keywords

• Molecular dynamics study
• RNA
• Poly(rA)
• Poly(rU)
• Dopamine
• Neurotransmitter binding