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Related Concept Videos

DNA Isolation01:24

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
DNA Isolation01:34

DNA Isolation

DNA from cells is required for many biotechnology and research applications, such as molecular cloning. To remove and purify DNA from cells, researchers use various methods of DNA extraction. While the specifics of different protocols may vary, some general concepts underlie the process of DNA extraction.
Tissue Homogenization and Cell Lysis01:32

Tissue Homogenization and Cell Lysis

Tissue homogenization involves disintegrating tissue architecture and lysing cells, and is an early step in isolating and analyzing cellular components. The method used for homogenization depends on the sample type, the amount of sample available, the analyte to be obtained, and the sensitivity of the method. These methods are broadly classified as mechanical and non-mechanical methods.
Mechanical methods of tissue homogenization
These methods rely on applying external physical force to disrupt...
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

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Related Experiment Video

Updated: May 23, 2026

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
21:55

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation

Published on: April 30, 2012

Fragmentation of DNA by sonication.

Joseph Sambrook, David W Russell

    CSH Protocols
    |April 10, 2012
    PubMed
    Summary

    DNA fragmentation via sonication is crucial for DNA sequencing library preparation. Stopping sonication when DNA fragments reach approximately 700 bp optimizes subclone yield, avoiding excessive shearing.

    Area of Science:

    • Molecular Biology
    • Genomics
    • Biotechnology

    Background:

    • DNA fragmentation is a key preparatory step for DNA sequencing, library construction, and subcloning.
    • Sonication is a common method for achieving DNA fragmentation through hydrodynamic shearing.

    Purpose of the Study:

    • To describe a protocol for DNA fragmentation using sonication.
    • To identify optimal sonication parameters for maximizing subclone yield.

    Main Methods:

    • DNA samples subjected to controlled sonication.
    • Hydrodynamic shearing applied to induce DNA fragmentation.
    • Fragment size monitored to determine optimal sonication endpoint.

    Main Results:

    • Excessive sonication leads to DNA fragments that are difficult to clone.

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    Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
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    Published on: April 30, 2012

    Capturing Chromosome Conformation Across Length Scales
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    Capturing Chromosome Conformation Across Length Scales

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  • Most sonicators produce fragments between 300-500 bp with prolonged sonication.
  • Stopping sonication when fragments initially reach ~700 bp enhances subclone yield.

    • Conclusions:

    • Controlled sonication is effective for DNA fragmentation.
    • Optimizing sonication duration is critical for successful DNA cloning and library construction.