Direct Visualization of Flow-induced Scission of DNA

Scission of DNA into smaller fragments is an important step in next-generation sequencing, with hydrodynamic breakage being a preferred method. Previous studies on flow-induced scission of DNA (and polymers in general) have focused on observing the distribution of scission products to infer the breakage mechanism and kinetics. Few studies have directly visualized the breakage of individual molecules in a flow of controlled type. Here, we employ fluorescence microscopy to image the breakage of labelled DNA molecules in a microfluidic four-roll mill, which can generate different flow types. We focus on extensional flow with a stagnation point, where we observe the breakage dynamics of DNA and measure its breakage probability versus the local extensional strain rate. We compare these results with simple shear and examine how the rotational component of the flow affects breakage. Our findings shed light onto the flow-induced breakage dynamics of polymer molecules and are helpful in guiding the design of microfluidic devices for tunable fragment lengths.