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Contour-clamped homogeneous electric field electrophoresis of Staphylococcus aureus.

Nature protocols · 2006 · Unclear · Insufficient evidence

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UnclearInsufficient evidencePaper 3494

This protocol describes CHEF electrophoresis, a pulsed-field gel electrophoresis method using controlled electric fields that change direction to separate large DNA fragments (approximately 10 kb to 9 Mb) in agarose gels. It outlines applications including ep…

Study snapshot

PublicationNature protocols · 2006
Study typeother
Reported directionUnclear
Evidence ratingInsufficient

Abstract

Contour-clamped homogeneous electric field (CHEF) electrophoresis is a technique of pulsed-field gel electrophoresis that enables the resolution of large fragments of DNA that cannot be resolved by conventional gel electrophoresis. The procedure involves the application of controlled electric fields that change direction at a predetermined angle to samples of DNA that have been embedded in an agarose gel matrix and digested with a restriction endonuclease. Adjustment of the electrophoresis conditions enables the separation of DNA fragments with lengths from 10 kilobases up to 9 megabases in a size-dependent manner in agarose gels. The banding patterns can be used for epidemiological typing, the separated DNA can be immobilized onto a membrane and used for genetic mapping, or individual fragments can be extracted and used for downstream genetic manipulations. The protocol requires specialized equipment and can be completed in a maximum of 7 days.

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AI evidence extraction

Structured fields below were generated from the paper’s abstract and metadata to make the evidence easier to inspect. Automated extraction may be incomplete or incorrect; verify important details against the original paper.

Study typeother
Effect directionunclear
PopulationNot supplied
Sample sizeNot supplied
Exposureprotocol can be completed in a maximum of 7 days
Evidence strengthInsufficientConfidence: 74% · Peer reviewed: yes

Main findings

This protocol describes CHEF electrophoresis, a pulsed-field gel electrophoresis method using controlled electric fields that change direction to separate large DNA fragments (approximately 10 kb to 9 Mb) in agarose gels. It outlines applications including epidemiological typing, genetic mapping, and extraction of fragments for downstream work.

Outcomes measured

  • Resolution/separation of large DNA fragments using contour-clamped homogeneous electric field (CHEF) electrophoresis
  • Generation of DNA banding patterns for epidemiological typing
  • Use of separated DNA for genetic mapping or downstream genetic manipulations

Limitations

  • Protocol description; no health or biological effect outcomes are reported in the abstract
  • No quantitative exposure parameters (e.g., field strength, pulse characteristics) are provided in the abstract
View raw extracted JSON
{
  "study_type": "other",
  "exposure": {
    "band": null,
    "source": "laboratory electrophoresis (controlled electric fields)",
    "frequency_mhz": null,
    "sar_wkg": null,
    "duration": "protocol can be completed in a maximum of 7 days"
  },
  "population": null,
  "sample_size": null,
  "outcomes": [
    "Resolution/separation of large DNA fragments using contour-clamped homogeneous electric field (CHEF) electrophoresis",
    "Generation of DNA banding patterns for epidemiological typing",
    "Use of separated DNA for genetic mapping or downstream genetic manipulations"
  ],
  "main_findings": "This protocol describes CHEF electrophoresis, a pulsed-field gel electrophoresis method using controlled electric fields that change direction to separate large DNA fragments (approximately 10 kb to 9 Mb) in agarose gels. It outlines applications including epidemiological typing, genetic mapping, and extraction of fragments for downstream work.",
  "effect_direction": "unclear",
  "limitations": [
    "Protocol description; no health or biological effect outcomes are reported in the abstract",
    "No quantitative exposure parameters (e.g., field strength, pulse characteristics) are provided in the abstract"
  ],
  "evidence_strength": "insufficient",
  "confidence": 0.74,
  "peer_reviewed_likely": "yes",
  "keywords": [
    "contour-clamped homogeneous electric field",
    "CHEF",
    "pulsed-field gel electrophoresis",
    "electric fields",
    "DNA separation",
    "Staphylococcus aureus",
    "agarose gel",
    "restriction endonuclease",
    "epidemiological typing",
    "genetic mapping"
  ],
  "suggested_hubs": []
}
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AI-extracted fields are generated from the abstract and metadata and may be incomplete or incorrect. This material is for informational purposes and is not medical advice.

Identifiers and source

DOI: 10.1038/nprot.2006.382
PubMed: 17406564

Read the original paper →

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