DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity
mrDNA simulation of the DNA origami plate designed as a sensor of transmembrane potentials. The coarse-grained simulation starts with the caDNAno design of the origami plate which is first mapped into a 5-bp/bead model followed by a 1-bead/bp model. Finally, the all-atom model of the system was obtained by averaging equilibrated conformations in coarse-grained simulation. At the end, the all-atom model was simulated for couple of nanoseconds in vacuum using the network of elastic restraints.
All-atom molecular dynamics simulation of ATTO532 (yellow) and ATTO647N (red) dye molecules conjugated to dsDNA in purely aqueous solution. The movie illustrates MD trajectories of two independent simulation runs (run 1 and run 2) starting from the same initial configuration. Water and ions are not shown for clarity.
All-atom molecular dynamics simulation of ATTO532 (yellow) and ATTO647N (red) dye molecules conjugated to dsDNA anchored in DOPC lipid bilayer membrane. The movie illustrates MD trajectories of two independent simulation runs (run 1 and run 2) starting from the same initial configuration. Water and ions are not shown for clarity.