With the advancement and maturation of next-generation sequencing (NGS) technology, its applications in scientific research, diagnostics, and healthcare markets continue to expand. As the market grows, the pace of innovation in sequencing technology itself has gradually slowed, making sample preparation an increasingly prominent bottleneck in NGS. New reagents and instruments aimed at reducing processing time and increasing throughput are constantly emerging. Meanwhile, novel methods focusing on smaller sample volumes are also being developed. However, DNA fragmentation remains an unavoidable step in NGS library preparation.

▲ Basic process for high-throughput sequencing NGS

The primary reason for fragmenting long-chain DNA (typically chromosomal DNA) is that shorter DNA fragments facilitate rapid DNA hybridization and highly sensitive target detection, significantly improving sequencing efficiency. Currently, there are four main methods for chromosomal DNA fragmentation: restriction enzyme digestion, hydrodynamic shearing, ultrasonic shearing, and nebulization. Each method has its pros and cons.

▲ Molecular structure and morphology of DNA

Ultrasonic shearing, based on hydrodynamic and ultrasonic fragmentation, is the most common DNA fragmentation method. The principle involves liquid subjected to high-frequency pulses, generating countless high-pressure and low-pressure points. Cavitation bubbles form and collapse within milliseconds due to pressure changes, creating transient high-intensity shear forces in the liquid. These forces can lyse cells, disrupt proteins, and shear DNA. Here, we highly recommend a specialized product: the FT-3000FJ Ultrasonic DNA Shearing Instrument. It employs a non-contact working mode and can process up to 12 samples simultaneously, making it a standardized tool for Chromatin Immunoprecipitation (ChIP) and DNA shearing research platforms.

Product Advantages

The Ultrasonic DNA Shearing Instrument exposes DNA to a uniform ultrasonic system for unbiased shearing, producing large quantities of uniformly sized double-stranded DNA fragments. Its advantages include:

• Zero sample contamination: Non-contact, closed shearing reduces contamination risks.
• High processing efficiency: Processes up to 12 samples at once with fast handling speed.
• Unbiased shearing: Produces DNA fragments with consistent sizes and no preference.
• Isothermal processing: Equipped with a chiller for constant-temperature shearing, preventing protein denaturation in ChIP experiments.

Workflow

1. Sample Pre-treatment
   Use a high-speed disperser (e.g., S10 or S20) or grinder (e.g., FeiTong-24 or FeiTong-96) to homogenize biological samples under ice-bath conditions (e.g., IMS-50) to obtain a homogeneous solution.
2. Cell Lysis
   For the homogenized solution, typically use an ultrasonic cell disruptor (e.g., FYT-1800) or high-pressure cell disruptor (e.g., FT-1800L). Special samples may require an ice-bath environment to obtain a solution containing cellular contents.
3. Solution Centrifugation
   Centrifuge the lysed solution at low temperature (e.g., M16RS) and collect the supernatant for further use.
4. DNA Shearing
   1. Transfer the lysed solution into 0.2 mL or 0.5 mL EP tubes and secure them in the adapter by tightening the nuts.
   2. Place the adapter in a water bath and activate the chiller, setting the temperature to 6°C.
   3. Once the temperature stabilizes, set the DNA shearing parameters (e.g., 20 s on, 25 s off, 300 W power, total shearing time of 30 min) and start the program.
   4. After shearing, collect the DNA samples and store them at low temperature to prevent degradation for further research.

Application Examples

▲ Shearing effect on E. coli DNA

▲ Shearing effect on DNA at 50 ng/μL concentration

Conclusion

The FT-3000FJ Non-Contact Ultrasonic DNA Interrupter employs a constant-temperature, non-contact approach for sample shearing, homogenization, and mixing. It features sterile operation, non-destructive processing, and micro-volume shearing. Its ability to process multiple samples simultaneously makes it perfectly suited for second-generation sequencing. Suitable for a wide range of biological samples, it is an essential tool for ChIP and DNA shearing research platforms.