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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.
DNA Agarose Gel Electrophoresis02:35

DNA Agarose Gel Electrophoresis

Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify DNA fragments using a gel extraction protocol.
Gel extraction follows five major steps: running gel electrophoresis to separate fragments, isolating the individual bands, extracting DNA from those bands, and removing the dye and salts from the extracted mixture to obtain pure DNA.
In cloning experiments, both the insert and vector DNA...

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Related Experiment Video

Updated: May 16, 2026

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
12:33

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

Efficient high-quality and high molecular weight plant DNA extraction protocol using Percoll™.

Kanae Nishii1,2, Michelle L Hart1, Nathan Kelso1

  • 1Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, Scotland, UK.

Plant Biotechnology (Tokyo, Japan)
|May 15, 2026
PubMed
Summary

This study presents a new protocol for extracting high-quality, high molecular weight (HMW) DNA from recalcitrant plants. This method utilizes a Percoll™ gradient and CTAB lysis, enabling successful long-read sequencing for de novo genome assembly projects.

Keywords:
Percoll™Streptocarpushigh-molecular weight DNA extractionlong-read sequencingnext generation sequencing

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Last Updated: May 16, 2026

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Published on: July 28, 2017

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Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • High-quality, high molecular weight (HMW) DNA is crucial for de novo genome assembly using long-read sequencing technologies.
  • Certain plant species, like *Streptocarpus schliebenii*, are recalcitrant to DNA extraction due to high secondary metabolite content, hindering genomic studies.
  • Previous DNA extraction protocols have repeatedly failed for these challenging plant materials.

Purpose of the Study:

  • To develop and optimize a robust protocol for extracting HMW DNA from recalcitrant plants suitable for long-read sequencing.
  • To adapt and improve existing Percoll™ gradient methods for efficient plant DNA isolation.
  • To assess the applicability of the new protocol across diverse plant lineages.

Main Methods:

  • Developed a novel HMW DNA extraction protocol incorporating a Percoll™ gradient step.
  • Modified buffer compositions and procedural steps from established Percoll™ protocols.
  • Replaced the agarose plug method with CTAB lysis followed by Qiagen Genomic-Tips for DNA purification.

Main Results:

  • The optimized protocol successfully extracted optimal quality and HMW DNA from three *Streptocarpus* species.
  • The method demonstrated broad applicability, yielding HMW DNA from seven out of twelve tested species across various plant lineages.
  • Four species, *Iris pseudacorus*, *Pulmonaria affinis*, *Corytoplectus speciosus*, and *Ilex aquifolium*, yielded both HMW and high-quality DNA.

Conclusions:

  • The developed Percoll™ gradient-based protocol is effective for obtaining high-quality HMW DNA from diverse and recalcitrant plant species.
  • This protocol serves as a valuable resource for researchers undertaking de novo plant genome projects, particularly with challenging genetic material.
  • The findings facilitate advancements in plant genomics by enabling successful long-read sequencing of previously inaccessible species.