Investigating the bent states of dsDNA defects with nunchucks

Structural defects in double-stranded DNA, like bulges or bubbles, occur naturally in dsDNA, can affect gene replication and transcription, and are common targets for DNA repair. These defects may be recognized by DNA-binding proteins not just based on structure, but also based on their dynamics. Understanding the dynamics of dsDNA defects is therefore crucial to understanding a variety of DNA processing and repair mechanisms.

Here we study the bent states of two different sizes of bulge and bubble defects using a DNA nunchuck - a pair of tiled DNA nanotubes nucleated from origami seeds that are connected by a 37 bp dsDNA linker. We find significant differences between the bend angle distributions of a 3-base bulge, a 6-base bulge or a 6-base bubble, and a 2-base bubble. For example, the linker with a 2-base bubble is stiffer than all other linkers, including defect-free ds DNA; a 3-base bulge has a predominant bent state near 80 degrees; and a 6-base bulge explores a plethora of bent states without having a predominant one.