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I. Abstract
Genomic DNA extraction from bacteria and whole blood was performed in
this experiment. For bacterial genomic DNA extraction, the method adapted from
Tillett and Neilan was used. Mainly, the method was composed of obtaining the
lysate, salting out and selective precipitation. For genomic DNA extraction from
whole blood, the Wang’s Lysis Method was used. The method consisted of lysis
to remove the erythrocytes which did not contain nuclei, salting out and selective
precipitation, as well. Both methods are rapid, efficient, safe and can serve as
standard laboratory protocols. Analysis using gel electrophoresis in 1x TAE
viewed under UV light is also presented in the paper.
II. Keywords
DNA Extraction, Bacterial Genomic DNA, Blood Genomic DNA, Tillett and
Neilan Method, Wang’s Lysis Method
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Molecular Biology, Biochemistry
and Forensic Analysis. However, In laboratories, there are seven
the process does not start at common protocols used for DNA
extraction or isolation alone. It extraction. Each method has its
actually starts on sample storage advantages and disadvantages, as
before the isolation of genomic will be discussed here.
DNA. Indeed, this is the most
crucial step since it is the quality of The first method is termed as
the starting material which will the preparation of crude lysates.
affect the quality and yield of the Here, the cell lysate is simply
isolated DNA. incubated at high temperatures or
digested with proteinase K. The
For bacteria, sample storage is recovered product will then be an
relatively simple. Cold storage, at a impure and contaminated genomic
temperature range of -20 0C to - 80 DNA. This technique is not
0
C, is sufficient. However, DNA advisable since it only gives rise to
extraction from animal tissues, high failure rates.
especially blood, poses several
challenges. Another technique is the
salting-out method. This method is
In blood DNA extraction, a actually a refinement of the crude
problem encountered is that lysate. Here, the proteins and
mammalian erythrocytes or red contaminants are precipitated from
blood cells do not contain nuclei. the cell lysate using high salt
Consequently, genomic DNA concentrations. Ammonium acetate
cannot be extracted from RBC and and potassium acetate are usually
these must therefore be eliminated. used as salts. However, DNA yield
Upon elimination of erythrocytes and purity are not definitive in this
which comprise majority of the technique.
blood sample, the leukocytes which
contain nuclei remain. Hence, Organic extraction methods are
genomic DNA can be extracted also available for DNA extraction.
from blood. Here, lysis is performed by the use
of a detergent, Afterwards, the
For the isolation proper, DNA lysate is mixed with isoamyl
can be separated from cellular alcohol, polar and non-polar
components using four main steps, reagents. The polar reagent is
namely disruption, lysis, removal usually phenol and the non-polar
of proteins and contaminants, and reagent is usually chloroform.
then recovery of DNA. Upon mixing, the components are
then separated into two phases –
In general, there are several organic and aqueous. Contaminants
methods available for the are in the organic phase and DNA
extraction of DNA. However, molecules are in the aqueous phase.
regardless of the methods used, the However, both phenol and
five main steps which include chloroform may leave residues in
storage, disruption, lysis, removal the DNA sample. More
of contaminants and recovery of importantly, these reagents pose
DNA still hold true in separating health hazards.
DNA from cellular components.
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The principle behind that of the In animal tissues, such as
organic extraction method is the blood, the Wang’s Method can be
same as that of the CTAB method used due to its several advantages.
which was not performed in class
due to the aforementioned The Wang’s Method was first
disadvantages. published in 1994. It was
established in order to have a
In the Cesium Chloride Density standard protocol for rapid and
Gradient Method, the cell lysate is efficient DNA analysis. At that
first precipitated using alcohol. time, extraction of DNA either
Upon doing so, resuspended DNA heavily relied on toxic reagents
is mixed with both CsCl and EtBr, such as phenol and chloroform, or
then centrifuged. The DNA band is on tedious manipulations such as
then collected and then washed literally spooling DNA.
with alcohol to remove EtBr. Not
only is this method tedious and The Wang’s Method is
expensive, it also requires EtBr characterized not only by its
which is a known mutagen. rapidity and efficiency but also by
its reproducibility, high yield and
The sixth method is the anion- high purity.
exchange method. In this method,
the phosphates of the nucleic acids
which have a negative charge
adhere to the positive charged
surface molecules on the substrate.
Using medium-salt washing, the
impurities are washed out and
DNA can be eluted using a high-
salt buffer. The problem with this Figure 1. The figure shows the
method is its high cost. reproducibility of the method with
different sample volumes (Wang,
Lastly, silica-based methods et. al., 1994).
such as kits can be utilized. Here,
nucleic acids selectively adsorb on In the fields of Biochemistry
the silica-gel membrane, in the and Molecular Biology, DNA
presence of high concentrations of recovered from the said method
salts. Several buffers also ensure can be used for electrophoresis
that contaminants do not adsorb on since a high molecular weight is
the membrane. DNA can then be preserved, for restriction
finally eluted out of the membrane. endonuclease digestion and for
As easy as it may seem, this PCR template.
method is expensive to use in
undergraduate laboratory courses.
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IV. Methodology
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To precipitate all cell debris, NaI, 20 mM EDTA and 40 mM
the tubes were centrifuged at Tris-Cl at pH 8.0.
14,000 rpm for 10 minutes. The
supernatant obtained was then Lastly, the TE or Tris-EDTA
transferred to a new buffer was composed of 10 mM
microcentrifuge tube containing Tris at pH 8.0 and 1 mM EDTA.
isopropyl alcohol. Incubation at
room temperature was done for 10 As for the procedure,
minutes. approximately 8 mL of blood was
first extracted. To the sample, 1
After incubation, the samples mg/mL EDTA-Na2 was added. The
were centrifuged at 12,000 rpm for blood solution was then divided
10 minutes. Finally, the DNA into 0.5 mL aliquots in
pellets were washed with 70% microcentrifuge tubes.
ethanol and then were allowed to
air dry. The pellet was then re- Wang’s lysis solution, in an
suspended in 100 uL TE buffer. amount of 0.5 mL, was added next.
The resulting solution was then
B. DNA Extraction from Blood centrifuged at 10, 000 x g for 20
seconds.
The procedure for DNA
extraction from blood used the The supernatant was discarded,
Wang’s Method. But first, a whole 1 mL of lysis solution was added to
blood sample was first extracted. the pellet and then the resulting
solution was mixed by inversion
The main reagent used for this for 30 seconds. Centrifugation at
procedure is the Wang’s Lysis 10, 000 x g for another 20 seconds
solution which is composed of 1% was performed. The addition of 0.5
w/v Triton X-100, 0.32 M Sucrose, mL Wang’s lysis solution and
5mM MgCl2 and 10 mM Tris-Cl at centrifugation was also repeated.
pH 7.5.
After centrifugation, the pellet
There are other reagents aside was re-suspended in 0.2 mL of
from the Wang’s Lysis Solution. enzyme reaction solution.
0
These reagents include the enzyme Incubation at 37 C for 10 minutes
reaction solution, sodium iodide was performed next. Upon doing
solution, Tris-EDTA buffer, 70% so, 10 uL of Proteinase K solution
ethanol, 40% absolute isopropanol was added and incubated at 1 hour
and 20 mg/mL Proteinase K stock for 37 0C, with occasional mixing.
solution stored at -20 0C. 0.3 mL of NaI solution was added,
and then gently inverted to mix. 0.5
The enzyme reaction solution is mL of isopropanol was also added
composed of 1% w/v SDS, 5 mM and then gently inverted.
EDTA and 10 mM Tris-Cl at pH
8.0. Centrifugation was once again
performed, at a rate of 10, 000 x g
The sodium iodide solution, for 10 minutes. Decantation was
stored in the dark at room used to remove the supernatant.
temperature, is composed of 7.6 M
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The pellet remained and to it, 1 experiment because DNA is highly
mL of 40% isopropanol was added. pH-sensitive. The pKa of Tris is
Centrifugation at 10, 000 x g was equal to 8.1, which means that it
performed for 5 minutes. The can prevent drastic pH shifts ad
supernatant was also removed. maintain the pH at a range of 7.0 to
9.0. The second role of Tris is to
The above step was performed interact with the lipopolysaccharide
once again, but 70% ethanol was membrane and make it more
used instead of 40% isopropanol. permeable in order for disruption
and then lysis to occur.
Finally, the resulting pellet was
air-dried for 10 minutes and then Since the membrane has been
re-suspended in 0.1 mL TE buffer, disrupted and lysed, debris such as
maintained at pH 8.0. RNA must be removed. RNAse A
is used to digest contaminating
V. Results and Discussion RNA.
6
Another component of the XS substances, such as alcohol.
buffer is SDS or Sodium Dodecyl Aggregation then occurs, and then
Sulfate. Its main function is to act a white pellet is finally formed.
as anionic surfactant and denature
the proteins that may act as To remove excess alcohol and
contaminants in the DNA sample. those salts which are soluble in
Denaturation occurs because it is alcohol, centrifugation was once
amphiphillic and disrupts the non- again performed. Washing in 70%
covalent bonds of proteins. ethanol was done next, since
ethanol is volatile and easily
Ammonium acetate is also a volatilizes itself from the DNA.
component of the XS buffer. It is
the salt of acetic acid and Finally, the pellet was
ammonia. Approximately, it has a resuspended in TE buffer. A buffer
pKa of 7.0. A salt, in this is needed, and not water, since
experiment, functions to precipitate DNA hydrolyzes in water;
the proteins out of the solution. whereas, its pH is controlled in the
presence of a buffer.
After the TER and XS buffer
have been added, the tubes were The above mentioned protocol
incubated at 70 0C for an hour. is for bacterial DNA isolation.
Incubation was done to ensure that Some of its steps are similar to that
complete reaction took place. of DNA isolation from human
tissues, specifically blood;
At this point, it can be inferred whereas, some are not. In this
that RNA, protein and other paper, the method used for DNA
possible contaminants have been extraction from blood is that of
removed from the “cellular soup”. Wang’s.
At the same time, the buffer served
to maintain the pH of the solution DNA isolation from blood
at the physiological level. starts with the proper storage of the
sample. For optimum conditions, it
To further separate the debris must be stored at a temperature of
from DNA, vortexing the DNA at -20 0C to - 80 0C.
10 seconds was done. Care was
observed in vortexing since The first step, upon obtaining
genomic DNA is large and too the stored sample, is the addition of
much agitation can shear the DNA. an anticoagulant. This is needed so
In addition, the solution was as to avoid blood clotting and be
subject to an ice bath to aid in the able to obtain whole blood. In the
precipitation and then centrifuged market, the three main
to finally separate the other cellular anticoagulants used are EDTA-
components from DNA. Disodium, Heparin and Citrate.
Citrate gives poor DNA yields. The
Since the genomic DNA is mode of action of heparin consists
heavier, it remained in the of inhibiting thrombin.
supernatant. Afterwards, it was Consequently, upon inhibition,
treated to isopropanol. This was fibrinogen is not converted to fibrin
done to precipitate the DNA, since and blood does not clot. However,
DNA is insoluble in polar the problem concerning heparin is
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that it interferes with downstream Triton X-100, sucrose, Magnesium
applications of recovered DNA Chloride and Tris-Cl.
(Beautler, et. al., 1990), though the
exact mechanism by which it Before discussing the
interferes has not been elucidated components of the lysis solution, it
yet. is important to note that
mammalian red blood cells or
For this reason, EDTA- erythrocytes do not contain nuclei.
Disodium was chosen to be the Hence, genomic DNA cannot be
anticoagulant for this experiment. extracted from these. Another fact
The said reagent works by is that in whole blood, there are
chelating the calcium ions, which approximately 1000x more
render these inactive to participate erythrocytes than leukocytes which
in coagulation. Moreover, EDTA- contain nuclei. Thus, eliminating
Disodium does not interfere much erythrocytes is needed in order to
with recovered DNA downstream recover DNA that is high in both
applications. yield and purity.
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so as to ensure complete lysis of low temperature can cause it to
the erythrocytes. recrystallize.
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temperature range of -20 0C to - 80
0
C. Such range was not available
and DNA became destabilized.
Lanes 7 to 9 should
theoretically contain blood from
genomic DNA. Such was not the
case. Several mistakes can cause
this. The blood sample might have
not been properly stored, the lysis
solution might have not been
enough to lyse the erythrocytes or
the small pellet might have been
disposed of.
Figure 4. Electrophoresis of
Lastly, Lane 10 served as the
Genomic DNA Purified from
marker for the experiment.
Bacteria (Lanes 1-4) and Blood
(Lanes 7-9). Lanes 5, 6 and 10
Another figure shows the
served as markers.
analysis using electrophoresis, this
time using a kit for bacterial
In Lane 1, no distinct band can
genomic DNA extraction.
be seen. Mishandling of the DNA
might have occurred in the process
of disposing the supernatant. The
pellet, which might have been too
small to settle at the bottom of the
microcentrifuge tube, might have
been disposed of. Thus,
supernatants must be kept until the
analysis of DNA has been
completed since it might contain
valuable DNA.
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experiment protocol can ensue that 2. Wang, et. al., Purification of
DNA is recovered. Genomic DNA from Human
Whole Blood by Isopropanol-
VI. Conclusion and Fractionation with Concentrated
Recommendations NaI and SDS. Japan: Osaka
Research Laboratories, 1994.
At the end of the experiment, it
can be concluded that bacterial DNA 3. Khosravinia, et. al. Influence of
was successfully extracted using the EDTA and Magnesium on DNA
Tillett and Neilan Method. Extraction from Blood Samples
and Specificity of Polymerase
This is supported by the fact Chain Reaction. India: Lorestan
that distinct bands were seen in the gel University, 2006.
electrophoresis.
4. Ty, et. al., Isolation of DNA
Indeed, the protocol used was from Blood Samples and Body
efficient, fast, relatively cheap and Fluids Using E-Z 96 Mag-Bind
safe, when compared to organic Blood System. VWR International,
extraction methods. Issue 21, 2008.
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