There are 3 basic steps involved in DNA extraction, that is, lysis, precipitation and purification. In lysis, the nucleus and the cell are broken open, thus releasing DNA. This process involves mechanical disruption and uses enzymes and detergents like Proteinase K to dissolve the cellular proteins and free DNA.
The other step, which is known as precipitation, separates the freed DNA from the cellular debris. It involves use of sodium (Na+) ions to neutralize any negative charge in DNA molecules, making them less water soluble and more stable. Alcohol (e.g isopropanol or ethanol) is then added, causes precipitation of DNA from the aqueous solution since it does not dissolve in alcohol.
After separation of DNA from aqueous solution, it is then rinsed with alcohol, a process known as purification. Purification removes all the remaining cellular debris and unwanted material. Once the DNA is completely purified, it is usually dissolved in water again for convenient storage and handling.
The following is a sample protocol for the extraction of genomic DNA from cell culture. Sample Size: Start with 1 x 105 to 5 x 106 cells.
DNA concentration can be determined either by absorbance or fluorescence. To determine DNA concentrations using the UV-absorbance method measure the absorbance of the DNA sample at 260 nm with a spectrophotometer.
Fluorescence methods determine DNA concentration by using double-stranded DNA binding dyes, such as Helixyte™ Green (AAT Bioquest Cat No.
17597) that fluoresce when bound to dsDNA, or DNA quantitation kits, such as the Portelite™ Fluorimetric High Sensitivity DNA Quantitation Kit (Cat No.
17661) or the Portelite™ Fluorimetric DNA Quantitation Kit with Broad Dynamic Range (Cat No.
17665). The fluorescence intensity is measured using a fluorometer, such as the CytoCite™ BG100 portable fluorometer from AAT Bioquest (Cat No.
CBG100). Of the two methods, fluorescence-based DNA quantitation is more sensitive and generally used to quantify DNA for next generation sequencing.
Helixyte™ Green Purity of DNA and RNA samples can be assessed by taking the ratio of absorbance at 260 nm and 280 nm (A260/A280). A ratio of ∼1.8 indicates a pure DNA sample, while a ratio of ∼2.0 indicates a pure RNA sample. If the ratio is higher or lower, it may indicate the presence of contaminates (e.g. protein, phenol, etc.) which also absorb at or near 280 nm. Strong absorbance around 230 nm can indicate that organic compounds or chaotropic salts are present in the purified DNA. A ratio of 260 nm to 230 nm can help evaluate the level of salt carryover in the purified DNA. The lower the ratio, the greater the amount of thiocyanate salt is present, for example. As a guideline, the A260/A230 is best if greater than 1.5.