Molecular Dynamics Simulations on DNA-Chromophore Complexes
Abstract
Molecular dynamics simulations are performed to study the effects of the hydrophobic constituents of cyanine dye, Cy5, on the binding propensity. The umbrella sampling method, one of several advanced sampling techniques, is employed to compute the potential of mean force between dyes in solution and to establish the relationship between the chemical and structural properties of dyes and the binding propensity. It is demonstrated that the binding strengths of dyes are highly correlated to the hydrophobicity values. More detailed free energy landscape of the dye-dye interactions is generated by the extensive two-dimensional umbrella sampling simulations, which showed the dyes predominantly interacting via stacked conformation. The method can easily be applied to more complex DNA-chromophore systems to study the effect of DNA scaffold on the dye-dye interactions.
Document Details
- Document Type
- Technical Report
- Publication Date
- Jan 27, 2023
- Accession Number
- AD1192212
Entities
People
- Youngchan Kim
Organizations
- Boise State University
- United States Naval Research Laboratory