DNA: Extraction & Purification By Amr S. Moustafa, M.D.; Ph.D. Assistant Prof. & Consultant, Medical Biochemistry Dept. College of Medicine, KSU
Objectives The principle of standard method The comparison of the standard Vs other methods The evaluation of the purification procedure The experimental protocol for DNA purification
DNA Extraction & Purification: Key Steps Removal of contaminants Proteins RNA Other macromolecules Lysis of the cells Concentration of purified DNA (if required)
DNA Extraction & Purification: The Standard Method-1 (1) Lysis of cells: Lysis buffer: SDS and/or 8.0 M urea (2) Removal of contaminants: Proteinase K Phenol:chloroform extraction (3) Concentration of DNA: Ethanol precipitation
DNA Extraction & Purification: The Standard Method-2 Phenol:chloroform:isoamyl alcohol mixture: Denatures proteins Solubilizes denatured proteins Denatures proteins Stabilizes the aqueous/organic boundary Isoamyl alcohol: Separation of aqueous/organic phases Prevents foaming upon vortexing Phenol: Chloroform:
DNA Extraction & Purification: The Standard Method-3 Tris-buffered, redistilled phenol, pH 8.0: Oxidation products can damage DNA chains Addition of 8-hydroxyquinolone:antioxidant yellow color of phenol DNA is found in the upper aqueous layer Exceptions: high salt content, the aqueous phase forms lower layer If phenol is not equilibrated, DNA in the organic phase
DNA Extraction & Purification: The Standard Method-4 Ethanol precipitation: Concentration DNA solutions Removal of residual organic solvents DNA-free solutes Ethanol induces a structural transition in DNA precipitation High monovalent cation conc. (0.1 – 0.5 M) Most salts are soluble in 70% ethanol, precipitation and washing desalt DNA
DNA Extraction & Purification: The Standard Method-5 Time-consuming Hazardous organic solvents Residual amounts of organic solvents interfere with accurate measurement of DNA conc. with enzymatic manipulations of DNA Disadvantages:
DNA Extraction & Purification: The Standard Vs other Methods Key Differences: Sample: Type Quantity/volume Requirement: Time for extraction Equipments and reagents Cost/sample DNA: Yield & conc. Purity
DNA Extraction & Purification: QIAamp DNA mini kits-1 (1) Lysis of cells (2) Spin column: DNA adsorption to silica-gel membrane (3) Two-different wash steps: Removal of contaminants (4) Elution: Pure and concentrated DNA
DNA Extraction & Purification: QIAamp DNA mini kits-2 Advantages Sample: versatile Simple and rapid No use of organic solvents Pure and concentrated DNA
DNA Extraction & Purification: Evaluation DNA purity: A260/A280 ratio 1.7 – 1.9 DNA concentration (μg/ml): A260 X 50 DNA yield: DNA conc. X Total volume of DNA solution