DNA Extraction (Phenol–Chloroform)

Biology Assay / Lab Protocols Complexity: high

Description

Genomic DNA extraction: cells are lysed and proteins digested, then DNA is purified either by organic (phenol:chloroform) extraction or by silica-column binding, precipitated/eluted, and accepted only when the A260/A280 purity ratio is acceptable.

Process Flowchart

graph TD N1["Cell/tissue sample"] N2["Lysis buffer + proteinase K"] N3["Lyse cells; digest protein"] N4{"Purification method?"} N5["Phenol:chloroform extract"] N6["Bind DNA to silica column"] N7["Wash column"] N8["Ethanol precipitate"] N9["Elute / resuspend DNA"] N10{"A260/A280 ~ 1.8?"} N11["Purified genomic DNA"] N1 --> N3 N2 --> N3 N3 --> N4 N4 -->|organic| N5 N4 -->|column| N6 N5 --> N8 N6 --> N7 N7 --> N9 N8 --> N9 N9 --> N10 N10 -->|re-extract| N3 N10 -->|yes| N11 style N1 fill:#ff6b6b,color:#fff style N2 fill:#ffd43b,color:#000 style N3 fill:#51cf66,color:#fff style N4 fill:#74c0fc,color:#fff style N5 fill:#51cf66,color:#fff style N6 fill:#51cf66,color:#fff style N7 fill:#51cf66,color:#fff style N8 fill:#51cf66,color:#fff style N9 fill:#51cf66,color:#fff style N10 fill:#74c0fc,color:#fff style N11 fill:#b197fc,color:#fff

Node provenance

Each step below is grounded in a cited source (hover a citation for the full title).

StepRoleSource
Cell/tissue sampleTriggers & InputsSambrook, J. et al. 2001
Lysis buffer + proteinase KStructures & ObjectsSambrook, J. et al. 2001
Lyse cells; digest proteinProcessing & OperationsSambrook, J. et al. 2001
Purification method?Intermediates & StatesBoom, R. et al. 1990
Phenol:chloroform extractProcessing & OperationsGreen, M. R. et al. 2017
Bind DNA to silica columnProcessing & OperationsBoom, R. et al. 1990
Wash columnProcessing & OperationsBoom, R. et al. 1990
Ethanol precipitateProcessing & OperationsGreen, M. R. et al. 2017
Elute / resuspend DNAProcessing & OperationsSambrook, J. et al. 2001
A260/A280 ~ 1.8?Intermediates & StatesSambrook, J. et al. 2001
Purified genomic DNAProducts & OutputsSambrook, J. et al. 2001

🎨 Color Scheme (5-Color System)

Red
Triggers & Inputs
Yellow
Structures & Objects
Green
Processing & Operations
Blue
Intermediates & States
Violet
Products & Outputs

Process Statistics

  • Nodes: 11
  • Edges: 12
  • Conditionals: 2
  • AND Gates: 2
  • OR Gates: 2
  • Total Gates: 4

Keywords

  • dna extraction
  • lysis
  • phenol chloroform
  • silica column
  • purity

Sources & References

  • Molecular Cloning: A Laboratory Manual (3rd ed.)
    Sambrook, J.; Russell, D. W. , Cold Spring Harbor Laboratory Press (2001)
    View Source
  • Rapid and simple method for purification of nucleic acids
    Boom, R.; Sol, C. J.; Salimans, M. M.; Jansen, C. L.; Wertheim-van Dillen, P. M.; van der Noordaa, J. , Journal of Clinical Microbiology (1990)
    DOI: 10.1128/jcm.28.3.495-503.1990
  • Isolation of High-Molecular-Weight DNA Using Organic Solvents
    Green, M. R.; Sambrook, J. , Cold Spring Harbor Protocols (2017)
    DOI: 10.1101/pdb.prot093450