Phenol-Chloroform-Isoamyl Alcohol (PCI) Extraction
Definition
Organic extraction method using differential solubility to partition DNA into an aqueous phase while proteins and lipids accumulate at the organic-aqueous interface or in the organic phase. Highest inhibitor removal of the four methods; manual and safety-constrained.
- Method type
- Organic (liquid-liquid) DNA extraction
- Separation principle
- Differential solubility across aqueous/organic phases
- DNA yield location
- Aqueous (top) phase
- Inhibitor removal
- Highest among common extraction methods
- Handling
- Manual, requires fume-hood safety precautions
Common questions
Why is PCI extraction still used when safer kit-based methods exist?+
Its superior removal of PCR inhibitors makes it valuable for difficult substrates such as heavily degraded, soil-contaminated, or chemically treated evidence where silica-column or Chelex methods leave residual inhibition.
What safety concerns limit its routine use in a modern lab?+
Phenol and chloroform are toxic and corrosive, so the method needs a fume hood, protective equipment, and careful phase separation, which makes it slower and less automatable than silica-column or magnetic-bead workflows.
How does PCI extraction differ from Chelex in what it recovers?+
PCI yields double-stranded DNA suitable for quantification and downstream STR typing, while Chelex releases single-stranded template directly usable for PCR but not reliably quantifiable or storable long term.
Related terms
- Chaotropic Salt
- Guanidinium thiocyanate or hydrochloride at 4-6 M concentration. Disrupts the hydration shell of DNA and causes it to bind electrostatically to silica...
- Chelex-100
- Styrene-divinylbenzene ion-exchange resin with iminodiacetate chelating groups. Used at 5% w/v in forensic DNA extraction to bind divalent metal cations during boiling...
- Inhibition Index
- A quantitative measure of PCR inhibitor burden in a DNA extract, derived from the Ct shift of an internal positive control (IPC)...
- Maxwell RSC 48
- Promega cartridge-based magnetic-bead extraction instrument. Each cartridge is pre-loaded with all reagents; closed-format processing eliminates cross-contamination. Used at FBI Laboratory and AFMES.
- QIAcube Connect
- QIAGEN robotic workstation that automates spin-column extraction protocols (QIAamp DNA Investigator). Processes 12 samples per 60-minute run; used in UK, US and...