High yield DNA fragmentation using cyclical hydrodynamic shearing

Abstract

We report a new DNA fragmentation technique that significantly simplifies conventional hydrodynamic shearing fragmentation by eliminating the need for sample recirculation while maintaining high fragmentation yield and low fragment length variation, and therefore, reduces instrument complexity and cost, increases fragmentation throughput and is well suited for integration in a lab-on-a-chip platform. The new DNA shearing technique is realized in a microfluidic lab on a chip (LOC) consisting of a chain of series-connected constriction channels that are each separated by a long spacer channel with much larger cross-sectional area. A sample injected to the microfluidic structure undergoes multiple acceleration–deceleration cycles at each constriction channel where the fluid induces strain to the DNA molecules necessary to induce the double chain scission fragmentation, which has a similar effect as multiple recirculation cycles. Experimental results show that the new fragmentation technique improves the fragmentation yield of genomic DNA from 10% for single constriction channels up to 90% for multiple series connected constriction channels.