Abstract
A perfluorocarbon nanodroplet formulation is shown to be an effective cavitation enhancement agent, enabling rapid and consistent fragmentation of genomic DNA in a standard ultrasonic water bath. This nanodroplet-enhanced method produces genomic DNA libraries and next-generation sequencing results indistinguishable from DNA samples fragmented in dedicated commercial acoustic sonication equipment, and with higher throughput. This technique thus enables widespread access to fast bench-top genomic DNA fragmentation.
Highlights
Next-generation sequencing is an attractive technology for detecting genetic disorders and characterizing the underlying molecular signature of disease to determine therapeutic options
We investigated whether a biologically inert agent could be added to DNA samples to amplify cavitation in a sonication device and improve the consistency and speed of genomic DNA fragmentation
We show that nanodroplets perform as an effective cavitation enhancement agent for the fragmentation of genomic DNA, decreasing sonication time while preserving DNA fragment size distribution and yield
Summary
Next-generation sequencing is an attractive technology for detecting genetic disorders and characterizing the underlying molecular signature of disease to determine therapeutic options. It is not yet, a routine diagnostic tool due to a lack of standardization in DNA sample preparation, cost, and difficulties in data interpretation [1, 2]. Random, unbiased fragmentation of DNA is a bottleneck in next-generation sequencing sample preparation pipelines due to serial processing of samples, cost limitations, poor DNA sample quality, and lack of reproducibility of fragment size between sample types [3, 4]
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