Dna Sonication
Dna Sonication - Related Videos
07:24
Sonication Extraction of Lipid Biomarkers from Sediment
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2023
Source: Laboratory of Jeff Salacup - University of Massachusetts Amherst The material comprising the living "organic" share of any ecosystem (leaves, fungi, bark, tissue; Figure 1) differs fundamentally from the material of the non-living "inorganic" share (rocks and their constituent minerals, oxygen, water, metals). Organic material contains carbon linked to a series of other carbon and hydrogen molecules (Figure 2), which distinguishes it from inorganic material. Carbon's wide valency range...
09:31
Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Cited by 56 •
2016
We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.
09:05
Generation and Quantitative Analysis of Pulsed Low Frequency Ultrasound to Determine the Sonic Sensitivity of Untreated and Treated Neoplastic Cells
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2015
Selective damage of human leukemia cells can be achieved through a novel approach of applying low frequency ultrasound both with and without chemotherapeutic pretreatment of leukemic and normal hematopoietic cells.
03:22
Low Frequency Ultrasound Application: A Method to Determine the Effect of Sonication on Human Leukemia Cells
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2023
This video describes the selective damage of human leukemia cells by using low frequency ultrasound. This application of low frequency ultrasound in a preclinical in vitro condition demonstrates that cell destruction can be attained in order to examine and compare the effects of sonication on leukemia and normal cells.
10:35
Novel Diagnostics in Revision Arthroplasty: Implant Sonication and Multiplex Polymerase Chain Reaction
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Cited by 16 •
2017
Differential diagnostics in painful arthroplasty is crucial for treatment success. Joint aspiration is routinely performed preoperatively. Multiplex polymerase chain reaction of the joint aspirate and the sonication fluid, a feasible tool for quick pathogen detection from these samples is described.
FAQs
Ultrasonic energy creates cavitation bubbles in the DNA-containing solution. When these bubbles collapse, they generate localized mechanical shear forces that place stress on DNA molecules and can break their phosphodiester backbones. This physical mechanism allows fragmentation without relying on a sequence-specific chemical reaction, making the resulting pieces suitable for analyses that require controlled DNA fragment sizes.
Fragment size is shaped by sonication power, pulse duration, sample volume, and temperature. Increasing or changing these conditions alters the mechanical energy delivered to the solution and therefore affects the extent of backbone breakage. Because the variables interact, maintaining the same settings across samples is important when experiments require comparable DNA fragment distributions.
Temperature is one of the conditions that can change the outcome of DNA fragmentation. If temperature varies between samples or during processing, the same nominal sonication settings may not produce equivalent fragment sizes. Controlling temperature therefore supports reproducibility, which is especially important when fragmented material will be compared across chromatin, sequencing, or genomic analysis experiments.
The method can be applied to purified DNA or to chromatin, depending on the downstream biological analysis. Fragmenting chromatin supports chromatin immunoprecipitation, while fragmenting purified DNA supports next-generation sequencing, library preparation, and other genomic analyses. In each setting, controlled fragment sizes help align the prepared material with the resolution and measurement requirements of the experiment.
A reproducible workflow should keep sonication power, pulse duration, sample volume, and temperature consistent between samples. The DNA-containing solution is exposed to high-frequency ultrasonic energy under the selected conditions, and the resulting fragmentation is used for the intended downstream analysis. Standardization reduces variation in fragment size and makes measurements or comparisons more reliable.
In chromatin immunoprecipitation, controlled fragmentation prepares chromatin for an analysis that depends on resolving genomic material into smaller pieces. Sonication conditions influence the size of those pieces, so inconsistent power, timing, volume, or temperature can introduce differences between samples. Reproducible fragmentation consequently supports clearer comparison of chromatin-associated measurements.
Fragmented DNA provides material for next-generation sequencing, library preparation, and broader genomic analysis. Controlling fragment size helps produce input that is more consistent with the requirements of these downstream measurements and can improve analytical resolution. The value of the preparation therefore depends not only on breaking DNA, but also on doing so reproducibly across samples.