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Bovine Spleen DNA Isolation Guide

This document summarizes an experiment to isolate DNA from bovine spleen through lysis, precipitation, and purification. Sodium citrate saline buffer, sodium chloride, and cold ethanol were used to extract DNA from the tissue. The extracted DNA and hydrolyzed DNA samples underwent qualitative tests to confirm the presence of deoxyribose, phosphate groups, and purine bases, indicating successful DNA isolation.

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0% found this document useful (0 votes)
469 views7 pages

Bovine Spleen DNA Isolation Guide

This document summarizes an experiment to isolate DNA from bovine spleen through lysis, precipitation, and purification. Sodium citrate saline buffer, sodium chloride, and cold ethanol were used to extract DNA from the tissue. The extracted DNA and hydrolyzed DNA samples underwent qualitative tests to confirm the presence of deoxyribose, phosphate groups, and purine bases, indicating successful DNA isolation.

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© © All Rights Reserved
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ACTIVITY NO.

6
ISOLATION OF DNA FROM BOVINE SPLEEN
CHEM 43 LB1A
Ms. Fatsy Cruz

ABSTRACT

Nucleic acids are polymers of nucleotides, composed of nitrogenous bases, sugar, and phosphate
groups, that carry genetic information and other important cellular processes. There are two kinds of nucleic
acids; deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). In this experiment, extraction of DNA from
bovine spleen was performed. The use of reagents such as sodium citrate saline buffer, sodium chloride, and
cold absolute ethanol was necessary to successfully isolate the DNA from the tissue. An aliquot of the
obtained sample was subjected to hydrolysis cleaving the nucleic acid into individual nucleotides producing
liberated ​purine and pyrimidine bases, oligonucleotides, nucleosides, riboses or deoxyriboses, and
phosphates. DNA and hydrolyzed DNA samples were subjected to ​four qualitative tests to confirm the
presence of specific nucleotide components, such as the deoxy-sugars, purine bases, and phosphate groups.
The Schiff’s test was performed to check for the presence of aldehydes while the diphenylamine test was
done for the confirmation of the presence of deoxyribose. Theoretically, purines form insoluble salts with silver
ions, Murexide test, while a phosphomolybdate yellow complex is formed as the phosphate group reacts with
ammonium molybdate, test for phosphates. Experimental results showed that the extracted DNA and
hydrolyzed DNA contain deoxyribose through the Schiff’s and diphenylamine test, as well as phosphate group
and purine bases through the test for phosphates and test for purines, respectively. This means that the
experiment was successful in isolating the DNA from bovine spleen.

KEYWORDS: isolation of DNA, acid-catalyzed hydrolysis, Schiff’s test, Dische diphenylamine test, Murexide
Test, Test for phosphates

INTRODUCTION

Nucleic acids ​are molecules that allow organisms to


transfer genetic information from one generation to the
next. These macromolecules store the genetic information
that determines traits and makes protein synthesis
​ ​Just as proteins are linear polymers of amino
possible. [1]
acids, nucleic acids are linear polymers of nucleotides. Figure 1. ​Structures of DNA and RNA
Nucleotides are biological molecules that possess a
heterocyclic nitrogenous base, a five-carbon sugar Another apparent difference, which can be noticed through
(pentose), and phosphate as principal components of their their names, is that the 2’-carbon atom of deoxyribose, the
structure. Like the letters in this sentence, the orderly sugar in DNA, lacks the oxygen atom that is linked to the
sequence of nucleotide residues in a nucleic acid can 2’-carbon of ribose, the sugar in RNA.
encode information.​[2]

The two basic kinds of nucleic acids are


deoxyribonucleic acid (DNA​), the repository of genetic
information in cells, and ​ribonucleic acid (RNA)​, which
serves in the expression of the aforementioned information
through the processes of ​transcription and ​translation​.
These long linear polymers differ such that the DNA is a
double-stranded molecule, while the RNA is
single-stranded.
Figure 2. ​Five-carbon sugars of DNA and RNA

The sugars in both nucleic acids are linked to one


another by phosphodiester bridges forming a chain which is
referred to as the ​backbone ​of the nucleic acids. Whereas
the backbone is constant in a nucleic acid, the bases vary 10 minutes. The pellets were kept and the supernatants

from one monomer to the next. [3] were discarded. Ten mL of 2.0 M NaCl was added to the
pellets in each falcon tube. Each tube was shaken
vigorously for 1 minute and 250 µL of ​Sodium Dodecyl
Sulfate solution was added. The falcon tubes were
incubated for 10 minutes in a 40°C water bath. After
incubation, the falcon tubes were again centrifuged at 6000
rpm for 10 minutes. This time, pellets were discarded, while
supernatants were collected and pooled in a beaker. Equal
volume of cold absolute ethanol was slowly added to the
supernatant, letting it pass along the sides of the beaker.
Fibrous DNAs were collected by carefully inserting a glass
Figure 3. ​Backbones of DNA and RNA.​ A sugar unit is rod all the way to the bottom and stirring in small circles in a
highlighted in red and a phosphate group in blue. clockwise direction. The collected DNA fibers were washed
with 70% ethanol and were placed in another beaker.
This activity focuses on the isolation of DNA which can These were then resuspended in 10 mL sodium citrate
be found in chromosomes of cells. As already mentioned, saline buffer and stored at 4°C. This solution will serve as
DNA is a long linear polymer of nucleotides, but it is packed the DNA sample.
so tightly into chromosomes and squeezed into a tiny
nucleus with the aid of proteins called ​histones. ​These Hydrolysis of DNA. ​Five mL of the dissolved DNA
proteins provide the energy to fold DNA, compacting it into sample was mixed with an equal amount of 10% H​2​SO​4 in a

microscopic space of the nucleus. [4] test tube. Another setup was prepared using the control 1%
DNA sample. The test tubes were covered with marbles
The ability to extract DNA is of primary importance to and placed in a boiling water bath for 15 minutes. The
studying the genetic causes of disease and for the solutions were cooled and neutralized with concentrated
development of diagnostics and drugs. It is also essential NH​4​OH. These solutions will serve as HDNA samples.
for carrying out forensic science, sequencing genomes,
detecting bacteria and viruses in the environment and for Qualitative Tests. ​Four qualitative tests, namely: (1)
determining paternity.​[5] DNA isolation is a process of Schiff’s test, (2) Dische Diphenylamine test, (3) Murexide
purification of DNA from a sample using a combination of test, and (4) test for phosphates were performed to confirm

physical and chemical methods. [6] the presence of ketones and aldehydes, deoxyribose,
purines, and phosphates, respectively.
The three basic steps of DNA isolation are: (1) ​lysis​, a. Schiff’s test. ​Ten drops each of the DNA sample,
where DNA molecules are freed and cellular proteins are HDNA sample, 1% DNA for the positive control,
dissolved with the aid of detergents such as ​sodium and distilled H​2​O for the negative control were put
dodecyl sulfate​; (2) ​precipitation​, where DNA is being in separate test tubes. Ten drops of Schiff’s reagent
separated from cellular debris using first sodium ions to were added. The test tubes were covered and let
neutralize the negative charges on the DNA molecules, stand for 10 minutes.
making it more stable and less soluble in water, and b. Dische Diphenylamine test. ​Ten drops each of the
alcohol, such as ethanol, to precipitate the DNA out of the DNA sample, HDNA sample, 1% DNA for the
aqueous solution since it is not soluble in alcohol; and (3) positive control, and distilled H​2​O for the negative

purification​.[7] control were put in separate test tubes. One mL of
diphenylamine reagent was added and the mixtures
The activity was done with the intent of: (1) isolating were vortexed. The test tubes were heated in a
high molecular weight DNA from bovine spleen, (2) boiling water bath for 10 minutes.
identifying the mode of action of each of the c. Murexide test. ​Ten drops each of the DNA sample,
reagents/chemicals used in bovine spleen DNA extraction, HDNA sample, 1% hydrolyzed DNA for the positive
and (3) performing qualitative tests on unhydrolyzed and control, and distilled H​2​O for the negative control
hydrolyzed DNA sample and compare the results. were put in separate test tubes. Ten drops of
concentrated NH​4​OH and two drops of 0.1 M
EXPERIMENTAL AgNO​3​ were added.
d. Test for Phosphates. H ​ alf an mL of the DNA
Isolation of DNA. F​ orty grams of fresh and cleaned sample, HDNA sample, 1% DNA for the positive
bovine spleen was diced and homogenized at high speed control, and distilled H​2​O for the negative control
for 10 minutes with 3.0 mL ice-cold sodium citrate saline were incinerated in separate porcelain crucibles.
buffer for every gram of spleen. Seven falcon tubes were The residues were cooled and 3.0 mL of distilled
each filled with approximately 15 mL of the homogenized water was added to each crucible. The solution was
tissue. The falcon tubes were centrifuged at 6000 rpm for filtered. The residue was discarded and to the
filtrate, 0.5 mL 10% (NH​4​)​2​MoO​4 and two drops of Fibrous DNA molecules were collected through stirring a
concentrated HNO​3 were added. The solutions glass rod in small circles in a clockwise direction. The
were heated for two minutes and were allowed to collected fibers were then washed with 70% ethanol and
stand. resuspended in sodium citrate saline buffer.

RESULTS

For the isolation of the DNA, bovine spleen was


homogenized with ice-cold sodium citrate saline buffer and
transferred into four Falcon tubes.

Figure 7. ​Resuspended DNA fibers in sodium citrate


saline buffer

From the DNA sample, 5 mL undergone hydrolysis, and


DNA and hydrolyzed DNA samples were subjected to four
qualitative tests​, namely: (1) Schiff’s test, (2) Dische
Diphenylamine test, (3) Murexide test, and (4) test for
Figure 4. ​Homogenized tissue in a Falcon tube phosphates to check for the presence of ketones and
aldehydes, deoxyribose, purines, and phosphates,
Seven falcon tubes were then centrifuged at 6000 rpm. respectively. Results obtained are summarized in the
The supernatant of each tube was discarded and to the following tables.
pellets, 2.0 M NaCl was added and shaken vigorously.
a. Schiff’s test
(+) control: 1% DNA
(-) control: distilled H​2​O

Table 1. ​Schiff’s test results


Experimental Observations Results
Results

(+) Light brown Aldehydes


control solution and/or
ketones are
present
Figure 5. ​Homogenized tissue after the addition of
(positive)
2.0 M NaCl solution
(-) Clear, Aldehydes
After a series of procedures, cold absolute ethanol was control colorless, no and/or
added to the pooled supernatant. color change ketones are
was observed not present
(negative)

DNA Clear, colorless Negative


result

HDNA Light brown Positive


solution result

Figure 6. ​Pooled supernatants with cold absolute


ethanol
Based on the experimental results of Schiff’s test, the
DNA Faint turbid Positive
DNA sample for this activity does not contain an aldehyde
yellow solution result
or a ketone group. On the other hand, hydrolyzed DNA
sample tested positive, therefore it has an aldehyde and/or
ketone group in its structure. HDNA Cloudy yellow Positive
to clear result
b. Dische Diphenylamine test or test for deoxyribose solution with
(+) control: 1% DNA small fibrous
(-) control: distilled H​2​O precipitates
Table 2. ​Dische Diphenylamine test results
Similar with the Dische Diphenylamine test, both DNA
Experimental Observations Results
and hydrolyzed DNA samples had a positive result for
Results
Murexide test. This denotes that both samples contain
purines with, again, the DNA sample having a greater
(+) Dark blue Deoxyribose
concentration since it has a stronger color intensity.
control solution is present
(positive)
d. Test for Phosphates
(+) control: 1% DNA
(-) Clear, Deoxyribose (-) control: distilled H​2​O
control colorless, no is not
color change present Table 4. ​Test for Phosphates results
was (negative)
observed Experimental Observations Results
Results
DNA Blue Positive
(+) Yellow solution Phosphates
control are present
(positive)
HDNA Faint blue Positive
(-) White Phosphates
control precipitate are not
present
Although the DNA sample had a darker shade of blue (negative)
for Dische’s test, both DNA and hydrolyzed DNA samples
tested positive. This indicates that deoxyribose is present DNA Yellow solution Positive
for both samples with the DNA sample having a greater result
concentration of the deoxyribose.

c. Murexide test or test for purines HDNA Yellow solution Positive


(+) control: 1% hydrolyzed DNA result
(-) control: distilled H​2​O

Table 3. ​Murexide test results


Experimental Observations Results DNA and hydrolyzed DNA samples tested positive for
Results the test for phosphates, therefore there are phosphates
present in the samples.
(+) Clear Purines are
control yellow-orange present DISCUSSION
solution (positive)
DNA is a long two-stranded molecule that contains each
person's unique genetic code. It holds the instructions for
(-) Clear, Purines are
building the proteins that are essential for our bodies to
control colorless, no not present
function. DNA instructions are passed from parent to child,
color change (negative)
with roughly half of a child's DNA originating from the father
was observed
and half from the mother. [8] ​ ​Each of the two strands is a
long sequence of nucleotides or individual units made of:
(1) a phosphate molecule, (2) a sugar molecule called
deoxyribose, containing five carbons, and (3) a ions creates a temporary attraction between sodium and
nitrogen-containing region which can be any of the the backbone. The DNA is ​temporarily neutralized and then
following: adenine, cytosine, guanine, or thymine. The easily disassociated from the water. At this stage the
order of these four bases forms the genetic code, which is introduction of an ​alcohol forces the DNA and sodium ions

our instructions for life. [9] to become even more tightly bonded, since alcohol is very
nonpolar. Ethanol or isopropyl alcohol can be used. Once
Most DNA can be found in the nuclei of cells and some DNA is disassociated from the water and tightly bound to
is found in mitochondria, which are the powerhouses of the the sodium, it will precipitate out of the solution where it
cells. Because we have so much DNA and our nuclei are can be either concentrated for purification or visualized by
so small, strands of DNA are looped, coiled and wrapped gently spooling it around a smooth glass rod.​[13]
around proteins called histones. In this coiled state, it is
called chromatin. ​Chromatin is further condensed, through To obtain the individual nucleotides, ​acid-catalyzed
a process called supercoiling, and it is then packaged into hydrolysis was performed. The sample was placed in a
structures called chromosomes. These structures allow dilute acid solution and was placed in a boiling water bath.
DNA to be safely stored in the nucleus and prevent Acid-catalyzed hydrolysis can be used to determine the
damage on DNA during cell division.​[10] base composition of nucleic acids which is essential for
certain biological purposes. This mechanism causes
The extraction of DNA is an important preliminary step depurination and phosphodiester bonds cleavage liberating
in which purified DNA is obtained from other cellular purine and pyrimidine bases, oligonucleotides, nucleosides,
components such as proteins, RNA and lipids. DNA ​
riboses or deoxyriboses, and phosphates. [14][15]
isolation refers to the process of extracting DNA from a cell
in a pure form. DNA can be isolated from any nucleated To determine the species present, it is necessary to
cell from diverse sources, both living and dead, such as perform qualitative tests on the products. In this activity,
whole blood, hair, sperm, bones, nails, tissues, faeces, four qualitative tests were done. These are: (1) Schiff’s test
shed feathers, egg shells, saliva, epithelial cells, urine, for aldehydes and ketones, (2) Dische Diphenylamine test
bacteria, animal tissues or plants.​[11] ​The ​spleen or the for deoxyribose, (3) Murexide test for purines, and (4) test
thymus contains a high concentration of DNA, which is for phosphates.
why both are preferred as the main source of the material
in laboratory experiments. Schiff’s test is done for detection of organic aldehydes.
The unknown sample is added to the ​decolorized Schiff
The three basic steps of DNA isolation are: (1) lysis, (2) reagent​; when aldehyde is present a characteristic
precipitation, and (3) purification. In ​lysis​, the cell and the magenta color develops. This qualitative test utilizes the
nucleus are broken open to release the DNA inside and Schiff’s reagent which is made from basic fuchsin, a
there are two steps to do this. First, mechanical disruption magenta dye, that is decolorized when reacted with
breaks open the cells. This can be done with a tissue sulfurous acid or sodium bisulfite due to the sulfonation of
homogenizer, with a mortar and pestle, or by cutting the fuchsin’s central atom which then disrupts the favored
tissue into small pieces. The bovine spleen in this delocalized extended pi-electron system and resonance in
experiment was homogenized with ​sodium citrate saline the parent molecule.​[16] The Schiff reagent itself has a
buffer to maintain the osmotic pressure inside the cell limited system of conjugation, the adduct with an aldehyde
preventing it from bursting during homogenization. has an extended system of conjugation, resulting in a
Mechanical disruption is particularly important when using highly colored compound.​[17] ​The Schiff reagent acts as a
plant cells because they have a tough cell wall. Second, nucleophile that adds to the carbonyl group of an aldehyde.
lysis uses detergents and enzymes to free the DNA and With the addition of aldehydes, this reagent will return the
dissolve cellular proteins.​[7] ​Sodium dodecyl sulfate is a pink color of the compound.​[16]
strong anionic detergent that can solubilize the proteins
and lipids that form the membranes. It removes the
negative ions from the protein and destroys its
conformation. Because of loss of conformation the protein
loses its structure. The proteins from the cell membrane
get damaged and cell gets broken. This will help the cell
membranes and nuclear envelopes to break down and
expose the chromosomes that contain DNA. In addition to
removing the membrane barriers, SDS helps release the
DNA from histones and other DNA binding proteins by
denaturing them.​[12]

Once DNA has been removed from the nucleus of a cell


and allowed to mix with water, the introduction of ​sodium Figure 8. ​ Schiff’s Test for Aldehydes
Although Schiff's reagent is used to detect In this test, the DNA acid-hydrolysis cleaved the
aldehydes, these are not usually found free in tissues and predisposed purine N-glycosyl bonds. If the nucleic acids
must be produced in some fashion [18]​​ . Theoretically, the are placed in a dilute acid solution, coupled with heating,
DNA would show a color change in the Schiff’s test adenine and guanine residues are liberated, thus it will
because of the reaction of the deoxyribose with the acid in exhibit positive results​[19]​. Theoretically, the positive result
the reagent to form an aldehyde. However, the should have white precipitate in the solution, the turbid
experimental results stated otherwise, and affirmed a solution is not a highly conclusive qualitative result for the
negative result from the test, a reason for this may be the confirmation of purines in the solution. It is possible,
reagent used in the experiment may not have been an however, that the formation of white precipitate produced
active reagent and also some inconsistencies encountered the turbid solution, indicating the presence of purines from
for the duration of hydrolysis of DNA, which is needed to the positive controls.
produce aldehydes from the deoxyribose.
Lastly, ​test for phosphates confirms the presence
On the other hand, hydrolyzed DNA tested positive of phosphates. Phosphate ions react readily with
for Schiff’s test. The reason for this is that acid hydrolysis ammonium molybdate to produce a yellow precipitate. This
removes purine bases from the DNA, thereby unmasking is due to the formation of a phosphomolybdate complex.​[20]
free aldehyde groups. The aldehyde groups then react with Both the extracted DNA and HDNA also agreed with the
Schiff's reagent, which results in the, theoretically, purple positive results, which was expected due to the phosphate
staining.​[19] backbone of nucleic acids.

The ​Dische diphenylamine test is a test for


deoxyribose. It will detect the deoxyribose of DNA and will
not interact with the ribose in RNA. Acidic conditions
convert deoxyribose to a molecule that binds with
diphenylamine to form a blue complex. The intensity of the
blue color is proportional to the concentration of DNA.​[20] In
the experiment, the extracted DNA and HDNA were proved
to contain deoxyribose based on the positive control. Figure 11. ​Reaction involved in the Test for phosphates
However, the intensity of both samples were different. The
amount of blue color observed in the DNA sample was The aforementioned qualitative tests confirmed that
more pronounced because the hydrolyzed DNA contains there is DNA from the present samples. Theoretically, the
lesser DNA after hydrolysis. Schiff’s test and diphenylamine test are highly conclusive
tests for detecting the presence of DNA. These tests can
easily detect the presence of DNA through its deoxyribose
that is converted to aldehyde and giving specific,
observable results.

CONCLUSIONS
Figure 9. ​Dische’s Diphenylamine Test
The extraction of DNA from spleen was confirmed
Murexide Test is a test confirming the presence of through a series of qualitative tests. Both the Schiff and test
purine bases in a sample. Nucleotide bases are relatively for deoxyribose involves the opening up of the pentose
insoluble in water. Depending on the pH, they may exist in sugar to an aldehyde, forming the necessary complexes for
two or more tautomeric forms (Figure 10). They can be a positive result. Test for purines follow the principle of
precipitated by as their silver salts by the addition of insoluble salt formation with silver ions, forming white
ammoniacal silver nitrate. A positive result is indicated by precipitate. Test for phosphates is due to the formation of a
the presence of a white precipitate. phosphomolybdate yellow complex. The experiment
showed that the extracted DNA and hydrolyzed DNA are
consistent with the positive controls. This confirms the
successful extraction of the molecule from spleen.

It is recommended to use fresh bovine spleen and


monitor the duration time for the hydrolysis as it is crucial
for the next tests to follow. Also, make sure to use active
and incontaminated Schiff’s reagent to ensure the positive
result displayed or as an alternative use a different dye. It is
also advisable to use other qualitative methods in
Figure 10. ​Tautomerism in nucleotide bases confirming the presence of DNA in samples, such as the
Feulgen staining and Killer- killani test. Different sources for the mechanism of the Schiff reaction as determined by
extraction can also be used to determine and compare the nuclear magnetic resonance spectroscopy," Canadian
presence of DNA. Journal of Chemistry, 58 (4) : 339–347.
[17] N.A., ‘Identification of an Unknown - Alcohols,
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[2] Reginald Garrett and Charles Grisham, http://stainsfile.info/stain/schiff/schiffwhatis.htm
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[7] AlaskaBioPREP, ‘The Basics of DNA extraction’, 20
October 2019, ​https://bioprep.community.uaf.edu/lear CERTIFICATION OF CONTRIBUTION
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ction/. I hereby certify that I have given substantial contribution
[8] Tim Newman, ‘What is DNA and how does it work?’, to this report:
11 January 2018, ​https://www.medicalnewstoday.com/
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[9] Biocyclopedia, ‘Chemical Nature of DNA’, 21 October Isabela N. Fami
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[10] Biocyclopedia, “Physical Nature of DNA’, 21
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[11] VLAB AMRITA, ‘Extraction of DNA from Fish Fins’,
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[12] Prachi Bhatia. ‘What are the functions of SDS in
DNA extraction?’, 18 April 2017, ​https://www.quora.com/
What-are-the-functions-of-SDS-in-DNA-extraction.
[13] Stacy Taylor, ‘Why is Sodium used in DNA
extraction?’, Sciencing, 26 April 2018,
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