Somma 2006
Somma 2006
Somma 2006
Session 4
M. Somma
Table of Contents
Session 4
Introduction 3
Extraction methods 4
Purification methods 4
CTAB extraction and purification method 6
Quantification of DNA by spectrophotometry 9
Principles of spectrophotometric determination of DNA 9
Determination of the concentration of nucleic acids 11
Experimental 13
References 17
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 3
Introduction
Extraction and purification of nucleic acids is the first step in most molecular biology
studies and in all recombinant DNA techniques. Here the objective of nucleic acid
extraction methods is to obtain purified nucleic acids from various sources with the
aim of conducting a GM specific analysis using the Polymerase Chain Reaction
(PCR). Quality and purity of nucleic acids are some of the most critical factors for
PCR analysis. In order to obtain highly purified nucleic acids free from inhibiting
contaminants, suitable extraction methods should be applied. The possible
contaminants that could inhibit the performance of the PCR analysis are listed in
Table 1. In order to avoid the arising of a false negative result due to the presence of
PCR inhibitors in the sample, it is highly recommended to perform a control
experiment to test PCR inhibition. For this purpose, a plant-specific (eukaryote or
chloroplast) or species-specific PCR analysis is commonly used.
As a wide variety of methods exist for extraction and purification of nucleic acids, the
choice of the most suitable technique is generally based on the following criteria:
• Target nucleic acid
• Source organism
• Starting material (tissue, leaf, seed, processed material, etc.)
• Desired results (yield, purity, purification time required, etc.)
• Downstream application (PCR, cloning, labelling, blotting, RT-PCR, cDNA
synthesis, etc.)
The principles of some of the most common methodologies used today for the
extraction and purification of nucleic acids are described in the following sections.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 4
Extraction methods
The extraction of nucleic acids from biological material requires cell lysis, inactivation
of cellular nucleases and separation of the desired nucleic acid from cellular debris.
Often, the ideal lysis procedure is a compromise of techniques and must be rigorous
enough to disrupt the complex starting material (e.g. tissue), yet gentle enough to
preserve the target nucleic acid. Common lysis procedures include:
• Mechanical disruption (e.g. grinding, hypotonic lysis)
• Chemical treatment (e.g. detergent lysis, chaotropic agents, thiol reduction)
• Enzymatic digestion (e.g. proteinase K)
Cell membrane disruption and inactivation of intracellular nucleases may be
combined. For instance, a single solution may contain detergents to solubilise cell
membranes and strong chaotropic salts to inactivate intracellular enzymes. After cell
lysis and nuclease inactivation, cellular debris may easily be removed by filtration or
precipitation.
Purification methods
Methods for purifying nucleic acids from cell extracts are usually combinations of two
or more of the following techniques:
• Extraction/precipitation
• Chromatography
• Centrifugation
• Affinity separation
A brief description of these techniques will be given in the following paragraphs
(Zimmermann et al., 1998).
Extraction/Precipitation
Solvent extraction is often used to eliminate contaminants from nucleic acids. For
example, a combination of phenol and chloroform is frequently used to remove
proteins. Precipitation with isopropanol or ethanol is generally used to concentrate
nucleic acids. If the amount of target nucleic acid is low, an inert carrier (such as
glycogen) can be added to the mixture to increase precipitation efficiency. Other
precipitation methods of nucleic acids include selective precipitation using high
concentrations of salt (“salting out”) or precipitation of proteins using changes in pH.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 5
Chromatography
Centrifugation
Affinity separation
In recent years, more and more purification methods have combined affinity
immobilisation of nucleic acids with magnetic separation. For instance, poly(A) +
mRNA may be bound to streptavidin-coated magnetic particles by biotin-labelled
oligo(dT) and the particle complex removed from the solution (and unbound
contaminants) with a magnet. This solid phase technique simplifies nucleic acid
purification since it can replace several steps of centrifugation, organic extraction and
phase separation with a single, rapid magnetic separation step.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 6
Plant cells can be lysed with the ionic detergent cetyltrimethylammonium bromide
(CTAB), which forms an insoluble complex with nucleic acids in a low-salt
environment. Under these conditions, polysaccharides, phenolic compounds and
other contaminants remain in the supernatant and can be washed away. The DNA
complex is solubilised by raising the salt concentration and precipitated with ethanol
or isopropanol. In this section, the principles of these three main steps, lysis of the
cell membrane, extraction of the genomic DNA and its precipitation will be described.
Lysis of the cell membrane. As previously mentioned, the first step of the DNA
extraction is the rupture of the cell and nucleus wall. For this purpose, the
homogenised sample is first treated with the extraction buffer containing EDTA
Tris/HCl and CTAB. All biological membranes have a common overall structure
comprising lipid and protein molecules held together by non-covalent interactions.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 7
As shown in Figure 1, the lipid molecules are arranged as a continuous double layer
in which the protein molecules are “dissolved”. The lipid molecules are constituted
by hydrophilic ends called “heads” and hydrophobic ends called “tails”. In the CTAB
method the lysis of the membrane is accomplished by the detergent (CTAB)
contained in the extraction buffer. Because of the similar composition of both the
lipids and the detergent, the CTAB component of the extraction buffer has the
function of capturing the lipids constituting the cell and nucleus membrane. The
mechanism of solubilisation of the lipids using a detergent is shown in Figure 2.
Figure 3 illustrates how, when the cell membrane is exposed to the CTAB extraction
buffer, the detergent captures the lipids and the proteins allowing the release of the
genomic DNA. In a specific salt (NaCl) concentration, the detergent forms an
insoluble complex with the nucleic acids. EDTA is a chelating component that among
other metals binds magnesium. Magnesium is a cofactor for DNase. By binding Mg
with EDTA, the activity of present DNase is decreased. Tris/HCl gives the solution a
pH buffering capacity (a low or high pH damages DNA). It is important to notice that,
1
Pictures in current and following page: "Genetic Science Learning Center, University of Utah,
http://gslc.genetics.utah.edu."
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 8
since nucleic acids can easily degrade at this stage of the purification, the time
between the homogenisation of the sample and the addition of the CTAB buffer
solution should be minimised. After the cell and the organelle membranes (such as
those around the mitochondria and chloroplasts) have been broken apart, the
purification of DNA is performed.
Precipitation. In this final stage, the nucleic acid is liberated from the detergent. For
this purpose, the aqueous solution is first treated with a precipitation solution
comprising a mixture of CTAB and NaCl at elevated concentration (> 0.8 M NaCl).
The salt is needed for the formation of a nucleic acid precipitate. Sodium acetate may
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 9
be preferred over NaCl for its buffering capacity. Under these conditions, the
detergent, which is more soluble in alcohol than in water, can be washed out, while
the nucleic acid precipitates. The successive treatment with 70% ethanol allows an
additional purification, or wash, of the nucleic acid from the remaining salt.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 10
A = OD = εlc (1)
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 11
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 12
Table 2. Absorbance reading of highly purified calf thymus DNA in 1x TNE buffer
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 13
Experimental
Equipment
REMARK
All of the equipment used must be sterilised prior to use and any residue of DNA
must be removed. In order to avoid contamination, barrier pipette tips that are
protected against aerosol should be used.
Reagents
REMARK
All chemicals should be of molecular biology grade. Deionised water and buffers
should be autoclaved prior to use. In addition all chemicals should be DNA and
DNase free.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 14
• Proteinase K
• RNase A
• Tris[hydroxymethyl] aminomethane hydrochloride (Tris-HCl)
• Sterile deionised water
CTAB-buffer
20 g/l CTAB 4g
1.4 M NaCl 16.4 g
0.1 M Tris-HCl 3.15 g
20 mM Na2EDTA 1.5 g
• add 100 ml of deionised water
• adjust pH to a value of 8.0 with 1M NaOH
• fill up to 200 ml and autoclave
• store buffer at 4°C for max. 6 months
CTAB-precipitation solution
5 g/l CTAB 1g
0.04 M NaCl 0.5 g
• add 100 ml of deionised water
• adjust pH to a value of 8.0 with 1 M NaOH
• fill up to 200 ml and autoclave
• store solution at 4°C for max. 6 months
NaCl 1.2 M
Ethanol-solution 70 % (v/v)
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 15
Procedure
*
These additional optional steps are now commonly introduced to the CTAB extraction
method to enhance the yield of genomic DNA from highly complex matrices.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 16
The DNA solution may be stored in a refrigerator for a maximum of two weeks, or in
the freezer at - 20°C for longer periods.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 17
References
Hotzel, H., Müller, W. and Sachse, K. (1999). Recovery and characterization of
residual DNA from beer as a prerequisite for the detection of genetically modified
ingredients. European Food Research Technology 209, 192-196.
Hupfer, C., Hotzel, H., Sachse, K. and Engel, K.H. (1998). Detection of the genetic
modification in heat-treated products of Bt maize by polymerase chain reaction.
Zeitschrift für Lebensmittel-Untersuchung und -Forschung A 206, 203-207.
Lipp, M., Bluth, A., Eyquem, F., Kruse, L., Schimmel, H., Van den Eede, G. and
Anklam, E. (2001). Validation of a method based on polymerase chain reaction
for the detection of genetically modified organisms in various processed
foodstuffs. European Food Research Technology 212, 497-504.
Lipp, M., Brodmann, P., Pietsch, K., Pauwels, J. and Anklam, E. (1999). IUPAC
collaborative trial study of a method to detect genetically modified soy beans and
maize in dried powder. Journal of AOAC International 82, 923–928.
Murray, M.G. and Thompson, W.F. (1980). Rapid isolation of high molecular weight
plant DNA. Nucleic Acids Research 8, 4321–4325.
Poms, R.E., Glössl, J. and Foissy, H. (2001). Increased sensitivity for detection of
specific target DNA in milk by concentration in milk fat. European Food Research
Technology 213, 361-365.
Wagner, D.B., Furnier, G.R., Saghay-Maroof, M.A., Williams, S.M., Dancik, B.P. and
Allard, R.W. (1987). Chloroplast DNA polymorphisms in lodgepole and jack pines
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4
Extraction and Purification of DNA 18
and their hybrids. Proceedings of the National Academy of Science USA 84,
2097–2100.
The Analysis of Food Samples for the Presence of Genetically Modified Organisms Session 4