Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures
1 µs long MD simulation trajectories (two independent runs) of the ATTO 647N dye-conjugated to the DNA backbone in sample 1 having two unpaired bases near the dye in the DNA origami design. The scaffold strand of the DNA origami structure is shown in cyan, the staple strand carrying the dye molecule is shown in red and the other staple strand is shown in orange. The atoms of the dye molecule are shown using green spheres whereas the atoms of C6 molecules (anchor between the dye and DNA) are shown using magenta spheres. Water and counter ions are not shown for clarity.
1 µs long MD simulation trajectories (two independent runs) of the ATTO 647N dye-conjugated to the backbone of DNA systems in sample 2, having no unpaired bases in the DNA origiami. The scaffold strand of the DNA origami structure is shown in cyan, the staple strand carrying the dye molecule is shown in red and the other staple strand is shown in orange. The atoms of the dye molecule are shown using green spheres whereas the atoms of C6 molecules (anchor between the dye and DNA) are shown using magenta spheres. Water and counter ions are not shown for clarity.
1 µs long MD simulation trajectories (two independent runs) of the ATTO 647N dye-conjugated to a DNA base in sample 3, having no unpaired bases in the DNA origiami. The scaffold strand of the DNA origami structure is shown in cyan, the staple strand carrying the dye molecule is shown in red and the other staple strand is shown in orange. The atoms of the dye molecule are shown using green spheres whereas the atoms of C6 molecules (anchor between the dye and DNA) are shown using magenta spheres. Water and counter ions are not shown for clarity.
1 µs long MD simulation trajectories (two independent runs) of the Cy5 dye-conjugated to a DNA base in sample 1, having two unpaired bases near dye in the DNA origiami. The scaffold strand of the DNA origami structure is shown in cyan, the staple strand carrying the dye molecule is shown in red and the other staple strand is shown in orange. The atoms of the dye molecule are shown using green spheres whereas the atoms of C6 molecules (anchor between the dye and DNA) are shown using magenta spheres. Water and, counter ions are not shown for clarity.
1 µs long MD simulation trajectories (two independent runs) of the Cy5 dye-conjugated to a DNA base in sample 2, having no unpaired bases in the DNA origiami. The scaffold strand of the DNA origami structure is shown in cyan, the staple strand carrying the dye molecule is shown in red and the other staple strand is shown in orange. The atoms of the dye molecule are shown using green spheres whereas the atoms of C6 molecules (anchor between the dye and DNA) are shown using magenta spheres. Water and, counter ions are not shown for clarity.