Sonication Resource Center

Introduction

Sonicators transform electrical energy into ultrasonic energy which is transmitted to the samples being processed. The sound waves generated by a sonicator create alternating compression and expansion cycles, with rates depending on the frequency of the sound waves. During the low-pressure cycle, high-intensity ultrasonic waves create small vacuum bubbles. When the bubbles can no longer absorb energy, they collapse violently during a high-pressure cycle. This phenomenon is termed cavitation, and it is this cavitation force that results in DNA and chromatin being fragmented during sonication.

A multi-sample sonicator allows the sonication of several samples at the same time. Multi-sample sonicators use either water bath sonication technology or focused ultrasonic technology and display an integrated cooling system. This kind of device ensures reproducibility, effectiveness, and temperature monitoring. However, some multi-sample sonicators are quite expensive, and in particular plates for some commercially-available high-throughput sonicators can cost hundreds of dollars.

Sonication is a critical first step in most ChIP assays. If the sonication in your ChIP assay is not efficient or does not generate enough chromatin, there is nothing you can do to save the experiment, no matter how good the ChIP antibody is or how robust the rest of the ChIP protocol is. Without good sonication, you don’t stand a chance of being successful.

Chromatin sonication is crucial for several reasons. Sonication solubilizes and releases the chromatin, so this step must be efficient to obtain a good chromatin yield. Sonication is also required to generate DNA fragments that are the appropriate size (200-600 bp) to allow efficient immunoprecipitation and good peak resolution in ChIP-Seq assays.

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