Understanding how divalent metal cations affect DNA binding to an 11-mercaptoundecanoic acid (MUA) monolayer, allows us to improve the specificity and efficiency of DNA-based nanodevices. Applications of DNA-based nanoscale devices include, but are not limited to biosensing, imaging, catalysis, and energy conversion. Classical molecular dynamics is used to model how the metal cations Mg2+, Ca2+, Sr2+, and Ba2+ interact with a MUA monolayer and DNA. Using Gromacs, a computer software system, the behavior of these elements can be modeled over time using force fields. Force fields are mathematical equations that represent and model the behavior of different species. Previous research analyzed smaller monolayers to determine their interactions with each metal cation. Using this information we are now able to quadruple the size of the monolayer in order to accommodate the DNA strand. Using the known patterns of the metal cations and monolayer we will determine the differences in interactions that the DNA causes. Physical properties such as tilt angles and binding energies will be analyzed to determine the patterns of how the MUA monolayer, divalent metal cations, and the DNA strand interact.

Modeling the interactions of DNA with divalent metal cations and a monolayer

ACS Spring 2022

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