DNA Nunchucks: Nanoinstrumentation for Dynamic, Single-Molecular Characterization of DNABending

The dynamic bending of a double-stranded DNA (dsDNA) sequence is an essential aspect of its structure and biological function that is rarely characterized because direct measurement, even at the single-molecule level, can be difficult and time consuming. The DNA nunchuck is an origami-based instrument that makes the single-molecule bend fluctuations of short dsDNA sequences visible using fluorescence microscopy. Nunchuck data reveal that even "generic" dsDNA, containing no special bend-inducing sequences, regularly explore meta-stable bent states. For dsDNA containing a bend-inducing sequence, such as the 6-thymine DNA "bulge", nunchucks reveal the complete landscape of bent states, and a significantly higher frequency of transitions between bent and straight states compared to well-paired dsDNA. Bent state duration distribution shows that nunchucks have the temporal resolution to detect bend states that persist for only a few seconds.