4. DNA extraction
and quantification
DNA extraction has two main aims: first, to maximizing the yield of DNA from a
sample and in sufficient quantity to permit a full DNA profile to be obtained – this
is increasingly important as the sample size diminishes; and, second, to extract DNA
that is pure enough for subsequent analysis: the level of difficulty here depends very
much on the nature of the sample. Once the DNA has been extracted, quantifying
the DNA is important for subsequent analysis.
DNA extraction
There are many methods available for extracting DNA. The choice of which method
to use depends on a number of factors, including the sample type and quantity;
the speed and in some cases ability to automate the extraction procedure [1–5]; the
success rate with forensic samples, which is a result of extracting the maximum
amount of DNA from a sample and at the same time removing any PCR inhibitors
that will prevent successful profiling [2, 6–8]; the chemicals that are used in the
extraction – most laboratories go to great lengths to avoid using hazardous chemicals;
and the cost of the procedure. Another important factor is the experience of the
laboratory staff.
General principles of DNA extraction
The three stages of DNA extraction can be classified as (i) disruption of the cellular
membranes, resulting in cell lysis, (ii) protein denaturation and (iii) the separation
of DNA from the denatured protein and other cellular components. Some of the
extraction methods commonly used in forensic laboratories are described below.
Chelex 100 resin
The Chelex 100 method was one of the first extraction techniques adopted
by the forensic community. Chelex 100 is a resin that is composed of styrene–
divinylbenzene copolymers containing paired iminodiacetate ions [9]. The resin has a very high affinity for polyvalent metal ions, such as magnesium (Mg2+); it
chelates the polyvalent metal ions and effectively removes them from solution.
The
extraction procedure is very simple, the Chelex 100 resin, which is supplied as
beads, is made into a 5% suspension using distilled water. The cellular material
is incubated with the Chelex 100 suspension at 56 ◦C for up to 30 minutes.
Proteinase K, which digests most cellular protein, is often added at this point. This
incubation is followed by 8–10 minutes at 100 ◦C to ensure that all the cells have
ruptured and that the protein has denatured. The tube is then simply centrifuged to
pellet the Chelex 100 resin and the denatured protein at the bottom of the tube,
leaving the aqueous solution containing the DNA to be used in PCR (Figure 4.1).
The Chelex 100 suspension is alkaline, between pH 9.0 and 11.0, and as a result
DNA that is isolated using this procedure is single-stranded.
DNA EXTRACTION AND QUANTIFICATION
Figure 4.1 The Chelex 100 extraction is quick and easy to perform. (a) The cellular material
is added to 1 ml of TE (1 mm EDTA, 10 mm Tris: pH 8.0) and incubated at room temperature for
10–15 minutes. (b) The tube is centrifuged at high speed to pellet the cellular material and the
supernatant is removed. (c) The pellet of cellular material is resuspended in 5% Chelex, the tube
is incubated at 56 ◦C for 15–30 minutes and then placed in a boiling water bath for 8 minutes.
The tube is centrifuged at high speed for 2–3 minutes to pellet precipitated protein. (d) The
supernatant contains the DNA and can be used directly in a PCR
The major advantages of this method are it is quick, taking around a hour; it is
simple and does not involve the movement of liquid between tubes, thereby reducing
the possibility of accidentally mixing samples; the cost is very low; and it avoids the
use of harmful chemicals. Importantly, it is amenable to a wide range of forensic
samples [9]. The DNA extract produced using this method is relatively crude but
sufficiently clean in most cases to generate a DNA profile.
Silica-based DNA extraction
Within molecular biology generally, the ‘salting out’ procedure has been widely
used [1]. The first stage of the extraction involves incubating the cellular material
in a lysis buffer that contains a detergent along with proteinase K. The commonly
used detergents are sodium dodecyl sulphate (SDS), Tween 20, Triton X-100 and Nonidet P-40. The lysis buffer destabilizes the cell membranes, leading to the breakdown of cellular structure.
The addition of a chaotropic salt, for example 6 M guanidine thiocyanate [10]
or 6 M sodium chloride, during or after cell lysis, disrupts the protein structure
by interfering with hydrogen bonding, Van der Waals interactions and hydrophobic
interactions. Cellular proteins are largely insoluble in the presence of the chaotropic
agent and can be removed by centrifugation or filtration. The reduced solubility of the
cellular protein is caused by the excess of ions in the high concentration of salt competing with the proteins for the aqueous solvent, effectively dehydrating the protein.
Commonly used commercial kits, for example the Qiagen kits, exploit the salting-out
procedure; the methods to isolate the DNA after the cellular disruption vary widely.
Several DNA extraction methods are based on the binding properties of silica or
glass particles. DNA will bind to silica or glass particles with a high affinity in the
presence of a chaotropic salt [10, 11]. After the other cellular components have been
removed the DNA can be released from the silica/glass particles by suspending them
in water (Figure 4.2). In the absence of the chaotropic salt the DNA no longer binds
to the silica/glass and is released into solution. The silica method, in particular, has
been shown to be robust when extracting DNA from forensic samples [2]; it is also
amenable to automation [2–4].
The advantage of the silica-based salting-out methods are that they yield high
molecular weight DNA that is cleaner than DNA from Chelex 100 extractions. As
with Chelex 100 extractions, no highly toxic chemicals are involved. The process
takes longer than the Chelex 100 and involves more than one change of tube and
so increases the possibility of sample mixing and cross-contamination.
Phenol–chloroform-based DNA extraction
The phenol–chloroform method has been widely used in molecular biology but has
been slowly phased out since the mid-1990s, largely because of the toxic nature of
phenol. It is still used in some forensic laboratories; in particular, it is still widely
used for the extraction of DNA from bone samples and soils.
Cell lysis is performed as in the previous method. Phenol–chloroform is added
to the cell lysate and mixed – the phenol denatures the protein. The extract is then
centrifuged and the precipitated protein forms a pellicle at the interface between the
organic phenol–chloroform phase and the aqueous phase; this process is repeated two
to three times or until there is no visible pellicle [12]. The DNA is then purified from
the aqueous phase by ethanol precipitation or filter centrifugation (Figure 4.3). The
method produces clean DNA but has some drawbacks: in addition to the toxic nature
of phenol, multiple tube changes are required and the process is labour intensive.
FTA paper
In Chapter 3 FTA paper was described as a method for sample collection and
storage, particularly from buccal swabs and fresh blood samples. Once a sample is applied to the FTA paper it is stable at room temperature for several years. Cellular
material lyses on contact with the FTA paper and the DNA becomes bound to the
paper, which has been treated with chemicals to inhibit the growth of microorganisms
that might otherwise break down the DNA.
DNA EXTRACTION AND QUANTIFICATION
Figure 4.2 DNA extraction from buccal cells using a salting-out method based on the QIAamp
Blood Mini Kit. (a) Cellular material is added to a lysis buffer and proteinase K and incubated
at 56 ◦C for at least 15 minutes. (b) Ethanol is added to the solution before it is transferred in
order to provide the optimum DNA binding conditions. (c) The lysis solution is then transferred
to a spin basket that has a membrane that will bind the DNA in the presence of the chaotropic
salt. (d) The spin basket is centrifuged and the DNA is captured by the membrane as the solution
passes through. (e) Wash buffers are added to the spin basket and (f) pass through the membrane
when centrifuged. (g) Typically 100 µl of elution buffer is added to the membrane; in the absence
of the chaotropic salt the DNA is released from the membrane and (h) is recovered upon a final
centrifugation
To analyse the DNA sample, the first step is to take a small region of the card,
normally a 2 mm diameter circle, place it into a 1.5 ml tube and the non-DNA components are simply washed off, leaving only DNA on the card. The small circle
of FTA paper is then added directly to a PCR (Figure 4.4). The FTA paper extractions are very simple to perform and do not require multiple tube changes,
thus reducing the possibility of sample mixing [13–19]. The technology also provides a simple and relatively inexpensive method for long-term storage of DNA,
removing the requirement for refrigeration.
DNA EXTRACTION FROM CHALLENGING SAMPLES
Figure 4.3 DNA extraction from a buccal swab cells using a salting-out method based on phenolchloroform. (a) Cellular material is added to a lysis buffer and proteinase K and incubated at 56 ◦C
for at least 15 minutes. (b and c) The swab is removed and phenol is added, the solution is then
vortexed and centrifuged. Precipitated protein and carbohydrate form a pellicle at the interface;
this step is repeated until there is no visible material at the interface. Protocols vary – some use
only
phenol, others phenol and chloroform (isoamyl alcohol may be added to the phenol/chloroform
mixture to prevent it separating). (d) In a final step chloroform alone is added; this removes
any residual phenol, which would inhibit downstream processes such as PCR. The aqueous phase
now contains DNA. This can be concentrated by adding sodium acetate and either ethanol or
iso-propanol to precipitate the DNA, followed by centrifugation (the DNA will precipitate and form
a pellet) or by using filter centrifugation, which is similar to the steps in Figure 4.2g– f, except
that the membrane acts as a molecular sieve – allowing small molecules to pass through while
retaining DNA strands.
DNA extraction from challenging samples
The extraction of the many samples encountered in the forensic laboratory, including
blood and shed epithelial cells, can be carried out routinely using any of the above
techniques. There are however some sample types that necessitate variations on the
basic techniques.
Semen
Semen is one of the most commonly encountered types of biological evidence. The
extraction of DNA from the spermatozoa is complicated by the structure of the
spermatozoa (Figure 4.5). DNA is found within the head of the spermatozoa that is capped by the protective acrosome, which is rich in the amino acid cysteine; a
large number of disulfide bridges form between the cysteine residues in the acrosome. Proteinase K, which is a general proteinase, cannot break the disulfide bonds:
however, the addition of dithiothreitol (DTT), a reducing agent that will break the
disulfide bonds, greatly increases the release of spermatozoa DNA [20].
DNA EXTRACTION AND QUANTIFICATION
Figure 4.4 DNA extraction from blood on FTA paper. (a) Sections of the FTA card are removed
with a punch (usually 1.2 mm or 2 mm diameter), added to FTA purification reagent, mixed and
incubated at room temperature for 5 minutes; one or more punched discs can be added to the
extraction. (b) The liquid is removed and replaced with fresh purification reagent; this process
is repeated two or three times. (c) The discs are then washed two or three times in TE (10 mm
Tris-HCl, 0.1 mm EDTA, pH 8.0). (d) Finally, the TE is removed and the FTA discs, containing the
DNA, are left to dry at room temperature or with gentle heat (approximately 50 ◦C). The discs can
now be added directly to a PCR reaction