Matrical SonicMan™

Small-insert random DNA fragments are necessary to create efficient libraries for genomic sequencing projects. The success and efficiency of sequencing a large genome is dependent on the randomness of the fragments generated by the shearing of target DNA. Physical shearing methods (i.e., sonication, nebulization, and hydrodynamic shearing; references 1,2,3) are preferentially chosen over enzymatic digestion due to the randomness and size of the fragments produced resulting in a suitable overlapping collection of fragments for sub-cloning. The SonicManTM offers these properties in a high-throughput sonication format allowing for a straightforward, user-friendly, customizable method to generate random DNA fragments.

• Fragment size is correlated with sonication settings (power/time) and is controllable by the user
• Fragments centered around a desired length can be repeatedly generated in seconds
• Samples may be sonicated in volumes ranging from 25uL to 1.5mL per well and is scalable to 96 well format and 384 well formats
• Unlike enzyme based digestion, the random fragments generated by sonication are suitable for the sequencing of large genomes and sonication procedures allow for an uncomplicated, quick process as opposed to techniques like hydrodynamic shearing
• No specialized reagents are needed minimizing solution variation and allowing for easy carryover to downstream applications

• time: SonicMan can shear 96 samples to fragment sizes of 150, with nothing above 250 base pairs, in 4 hours
• fragment size: correlated with power/time settings, desired length distribution can be repeatedly generated in seconds
• samples volumes 25ul to 1.5ml per well, 96-well and 384-well plates formats
• fragent type: unlike enzyme based digestion, random fragments are generated - suitable for the sequencing of large genomes
• process: sonication is a quick and simple process compared with hydrodynamic shearing, typical sonication time 30 second pulses
• no specialized reagents are needed
• sonication pin lifetime: new design of stainless steel pins last 30 minutes of sonication, compared to 100 seconds with gold pins

1. Deininger PL 1983. Anal. Biochem. 129: 216-223.
2. Bodenteich AS, Chissoe S, Wang Y-F, and Roe BA 1994. In Automated DNA sequencing and analysis techniques (ed. MD Adams, C Fields, and C Venter), pp.42-50. Academic Press, London, UK.
3. Thorstenson YR, Hunicke-Smith SP, Oefner PJ, Davis RW 1998. Genome Res. 8:848-55.

1. What deepwell plates are suitable for use with the Sonicman, especially are there any restrictions on materials (PP, PS etc)? There are no restrictions on the deepwell plate types that can be used, they have to match the height of the pins. Obviously we would prefer you to use Matrical Deepwell plates but most manufacturers plates will be fine.
2. Can the Sonicman heads be autoclaved or rinsed in a dishwasher ? The heads can certainly be rinsed in a dishwasher but we have never autoclaved the heads. If you do this we would be curious to see how it holds up.
3. How do we stop cross contamination between sample plates? During sonication, we do not get cross contamination because of the silicone seal. If they use the same pin head for multiple samples you can wash between uses. Our standard QA test for contamination is to sonicate in a 100uM Fluorescein solution checker board on a plate and then look to see if we get Fluorescein in the surrounding wells. You can then wash the pin head and sonicate a plate with just water in to see if you have any carryover of the Fluorescein.
4. What would the typical longevity of the probes be? For a standard DMSO mix how many plates would they typically be able to process before we needed to change the head? - With the new SS pins, the pins will last for about 30-60 minutes of sonication time. A typical mix cycle takes only 10-20 seconds so if you wash the lids they will last a very long time (approx 180 - 240 plates).
5. Can we automate the pin head change? Yes this is quite simple, the robot arm will be able to pick up the pin head, place it on the mix plate and then add it to the Sonicman.
6. What is the best way to wash the pin heads between samples? The best way is for the robot arm to remove the pin head and dip the pins in DMSO, then in water followed by an ethanol dry. This will avoid using any of the sonication time for pin cleaning.
7. DNA shearing size - what size ranges can be produced, and how reproducible is this (run-run variation; well to well variation within a single run)? In 4 hours of sonication, we have been able to create a DNA band from 50-250 base pairs with a peak at about 150bp. By changing the power and time, we have been able to create other size ranges as well. There is minimal variation from well to well or run to run. During the early part of the sonication cycle, we see some variability, well to well, but this goes away with longer sonication times. We think this is due to inefficient coupling between the horn and some of the pins. However, during sonication, the pins “seat” themselves into the lid and make better contact with the horn and the wells that we lagging catch up. Consequently, we see about a 15% well to well variation in short time sonications (less than a couple minutes) but this decreases to negligible variation over several minutes.
8. Effect of DNA concentration - any data on which DNA concentration ranges can be effectively sonicated in the low volumes of 96 and 384-well plates? The DNA concentration does not seem to have any effect on the shearing by sonication, although, we have not tested this exhaustively.
9. Material loss. Upon sonication of genomic DNA to low MW size (eg 100-500 bp range) how much material is lost? Our data indicates a recovery of >70% on 4 hours sonication to a DNA fragement size of 50-250bp.
10. Chromatin research: Any data / publications detailing the use of the SonicMan for the Chromatin Immunprecipitation technique? We did one experiment for a group in Sweden and it seemed to work just fine. But one experiment is not definitive so I would suggest that if you have a customer who wants to do this, that they send us samples so that we can validate the process.
11. Time required for sonication. I heard that sonication of DNA to less than 250 bp was possible in 4 hours - quite a long time for sonication. Not really that long of time. DNA is basically a brick and you’re trying to break it down into sand. It’s easy to break a brick in half but it takes a lot longer to make sand.
12. Is the process faster with fewer than 96 samples? No, since our system does all 96 samples at once, it will take the same amount of time to do 1 or 96 samples.
13. Is faster sonication possible, for example with higher power, at the cost of sample loss? No, we are using 100% power currently. Heating would be an issue if we went even higher. Time should not be an issue since we can make fragments much faster than they can be sequenced. We can produce 576 samples per day for DNA sequencing so you would need a lot of sequencers to keep up.

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Matrical SonicMan sonicator for dna fragmentation

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High‐Throughput DNA Shearing Using the Matrical SonicMan™