Fig 1.
Nanodroplets persisted in solution longer than microbubbles.
A) Flow chart outlining method for production of nanodroplets. B) A persistence study was performed in the ultrasonic bath to compare nanodroplets and microbubbles. An Accusizer particle sizing system (Particle Sizing Systems, Port Richey, FL) was used to measure the microbubble and nanodroplet concentrations at specific time points between 0 and 300 seconds (5 minutes). Nanodroplets maintained between 10–20% of their initial concentration as far out as 3 minutes into the sonication treatment, while the microbubble concentration dropped to 10% after 1 second.
Fig 2.
Nanodroplets were an effective cavitation agent for use in DNA fragmentation.
A) The effectiveness of nanodroplets as a cavitation enhancement agent after multiple freeze-thaw cycles was tested. DNA ladder size is indicated in base pairs. Input is DNA prior to sonication with nanodroplets. B) Comparison of DNA fragmentation efficiency after two minutes in glass (Lanes 1–3) versus plastic (Lanes 4–6) tubes in the Covaris E110 sonicator. The addition of nanodroplets to Covaris microTUBES produces a DNA fragment size distribution comparable to the microTUBES used with the supplied rod (compare Lanes 1 and 3). DNA fragmented in glass microTUBES had a smaller DNA size distribution compared to plastic 0.2 mL PCR tubes (compare Lanes 3 and 5–6). DNA ladder size is indicated in base pairs.
Fig 3.
Nanodroplet-mediated DNA fragmentation compared to a commercial method.
(A) Flow chart outlining method for comparing DNA fragmentation methods. (B) False gel picture from Agilent D1000 ScreenTape system showing DNA fragment size distribution in base pairs for samples fragmented in the Covaris E110 sonicator. Purple bars indicate the upper (1,500 bp) molecular weight marker and green bars indicate the lower (25 bp) molecular weight marker in each lane.
Fig 4.
Saccharomyces cerevisiae gDNA (BY4741) fragmented with nanodroplets in an ultrasonic bath was comparable in quality to DNA fragmented using a commercial method.
(A) Agilent D1000 ScreenTape system traces for DNA samples in microTUBES with the rod (left panel) or microTUBES with nanodroplets (right panel) that were subjected to sequencing. Average size is indicated in base pairs (bp). DNA size markers are denoted by Upper and Lower. (B) Traces showing similar size distribution of DNA after sequencing library preparation. Average size is indicated in base pairs (bp). DNA size markers are denoted by Upper and Lower. (C) Mapping sequencing reads to the Saccharomyces cerevisiae (S288c) reference genome is comparable in detection of single nucleotide variations, insertions, and deletions. Abundance and profile of relative errors in sequencing reads does not indicate a difference in the presence of error bias in the data.
Fig 5.
The use of nanodroplets allowed an ultrasonic water bath to fragment genomic DNA.
(A) Schematic showing the ultrasonic bath used for sonication. Samples were immobilized in the water bath using a stand with a tube rack attached. The circulating water chiller was optional. Water chilled to four degrees Centigrade can be added just prior to sonication, with no loss in DNA fragmentation efficiency. (B) A time-titration was performed with samples with and without nanodroplets. Following fragmentation, samples were run on a 1.5% agarose gel and visualized using SYBR green. DNA ladder sizes are indicated in base pairs. (C) Arrangement of DNA samples fragmented in the ultrasonic bath with and without samples to produce (D) an acoustic field map of the bath. The fragmentation ability (base pair size) is visualized with the s1color bar, where red indicates complete fragmentation in the 200–500 bp range.
Fig 6.
DNA fragmentation in an ultrasonic water bath compared to a commercially available device.
(A) Flow chart outlining method for comparing DNA fragmentation methods.
Fig 7.
Saccharomyces cerevisiae gDNA (BY4741) fragmented with nanodroplets in an ultrasonic water bath was comparable in quality to DNA fragmented in a commercially available device.
(A) Agilent D1000 ScreenTape data showing size distribution of DNA fragmented in tubes without (left panel) or tubes with nanodroplets (right panel). Average size is indicated in base pairs (bp). DNA size markers are denoted by Upper and Lower. (B) False gel picture indicating that DNA fragmented without nanodroplets had an average fragment size >1,500 bp. Purple bars indicate the upper (1,500 bp) molecular weight marker and green bars indicate the lower (25 bp) molecular weight marker in each lane. (C) Size distribution of DNA after sequencing library preparation. Average size is shown in base pairs (bp). DNA size markers are denoted by Upper and Lower. (D) Mapping sequencing reads to the Saccharomyces cerevisiae (S288c) reference genome is comparable in detection of single nucleotide variations and indels in Fig 4C. Abundance and profile of relative errors in sequencing reads does not indicate a difference in the presence of error bias in the data compared to data in Fig 4C.