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Related Concept Videos

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.
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...

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Related Experiment Video

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Improved Polymerase Chain Reaction-restriction Fragment Length Polymorphism Genotyping of Toxic Pufferfish by Liquid Chromatography/Mass Spectrometry
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Identifying Novel DNA Adducts in Amphipods and Developing Sample Preparation for Adductomics Using Dispersive

Zareen Khan1, Elena Gorokhova1, Giulia Martella1

  • 1Department of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden.

Environmental Science & Technology
|October 30, 2025
PubMed
Summary

Researchers developed new DNA adductomics methods for environmental exposure assessment using amphipods. Dispersive solid-phase extraction (d-SPE) improved sample cleanup and detection sensitivity for DNA adducts in challenging matrices.

Keywords:
DNA adductsdispersive solid-phase extractionexposure assessmenthigh-resolution mass spectrometrynontarget analysis

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Area of Science:

  • Environmental Science
  • Analytical Chemistry
  • Toxicology

Background:

  • Environmental DNA adductomics is crucial for exposure assessment but faces challenges with diverse sample types.
  • Existing methods for DNA adductome analysis using LC-HRMS struggle with sample cleanup, especially in nonmammalian species.
  • Chitinous and lipid-rich tissues of species like amphipods present a difficult matrix for DNA extraction and analysis.

Purpose of the Study:

  • To enhance structural identification of unknown DNA adducts by integrating software and databases.
  • To evaluate dispersive solid-phase extraction (d-SPE) as an effective cleanup method for DNA adductome analysis in crustacean samples.
  • To improve DNA adductomics methods for accurate exposure assessment in diverse environmental matrices.

Main Methods:

  • Integrated open-source software nLossFinder with a DNA adductomics database for structural identification of adducts.
  • Utilized accurate mass data and MS2-fragmentation for differentiating nucleoside adducts.
  • Introduced and evaluated dispersive solid-phase extraction (d-SPE) with Z-sep+ sorbent for sample cleanup.

Main Results:

  • Successfully identified 16 DNA adducts, including 10 novel modifications on amphipod DNA.
  • Demonstrated significant reduction in matrix interferences (e.g., phospholipids) using d-SPE.
  • Achieved up to a 170% enhancement in LC-HRMS signal response for DNA adducts, improving sensitivity.

Conclusions:

  • The combined data analysis workflow and d-SPE offer a robust approach for DNA adductomics in environmental monitoring.
  • d-SPE provides a simple, high-throughput alternative to conventional cleanup methods, suitable for challenging matrices.
  • These advancements enable more accurate and comprehensive exposure assessments across diverse species and environmental conditions.