Presentation Type
Panel Discussion
Start Date
20-3-2021 11:30 AM
Abstract
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 Ca2+, Sr2+, and Ba2+ interact with a MUA monolayer. Using Gromacs, a computer software system, the behavior of these metal cations can be modeled over time using force fields. Force fields are mathematical equations that represent and model the behavior of different species. Tilt angles of metal ions such as calcium, strontium, and barium indicate that both Ca2+ and Ba2+ ions behave similarly; yet Sr2+ ions do not follow these same patterns. Direct and indirect binding tendencies were also analyzed using radial distribution functions to find patterns of how metals interact with the carboxylate in MUA. Results found that ions with larger atomic nuclei are more likely to bind directly compared to ions with smaller atomic nuclei. Looking specifically at direct binding, monodentate binding is more likely to happen for all ions, and larger ions have a higher probability of bidentate binding than smaller ions. Future research includes analyzing why Sr2+ ions do not follow the same patterns as Ca2+ and Ba2+ ions, enlarging the size of the MUA monolayer to fit a strand of DNA, and modeling how metal ions interact with both DNA and a MUA monolayer.
Keywords
Divalent, Cations, Monolayer, Tilt Angle, Binding, Simulation, Molecular dynamics, DNA
Modeling the Interactions of Divalent Metal Cations with a Monolayer
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 Ca2+, Sr2+, and Ba2+ interact with a MUA monolayer. Using Gromacs, a computer software system, the behavior of these metal cations can be modeled over time using force fields. Force fields are mathematical equations that represent and model the behavior of different species. Tilt angles of metal ions such as calcium, strontium, and barium indicate that both Ca2+ and Ba2+ ions behave similarly; yet Sr2+ ions do not follow these same patterns. Direct and indirect binding tendencies were also analyzed using radial distribution functions to find patterns of how metals interact with the carboxylate in MUA. Results found that ions with larger atomic nuclei are more likely to bind directly compared to ions with smaller atomic nuclei. Looking specifically at direct binding, monodentate binding is more likely to happen for all ions, and larger ions have a higher probability of bidentate binding than smaller ions. Future research includes analyzing why Sr2+ ions do not follow the same patterns as Ca2+ and Ba2+ ions, enlarging the size of the MUA monolayer to fit a strand of DNA, and modeling how metal ions interact with both DNA and a MUA monolayer.