The primary structure under investigation is a DNA origami 'claw' consisting of three rigid 'prongs' joined by three flexible linkages. This structure is composed of one long circular 'backbone' strand of ssDNA (m13p18 plasmid) held in shape by many short linear 'staple' strands. The overall structure can be diagrammed in two dimensions:
For FRET analysis, we add fluorescent dyes to the ends of some of the 'staple' strands. By varying the strand to which these dyes are added, we can change the location and orientation of the tags on the macrostructure.
Origami Triangle Rigid Control Structure
This DO triangle presents a surface area similar to that of the claw and can be functionalized with single-stranded binding elements. It differs from the claw in that it is rigid, so binding with the substrate should not cause a change in conformation.
Model Virus Capsid
We used wild type bacteriophage MS2 as the control ("blunt") molecule
We used MS2 functionalized with single-stranded DNA - with a sequence of either T21 or (TCA)7 - as the "sticky" target structure.