DNA STRUCTURE AND DNA EXTRACTION ● When a nitrogenous base bonds with a sugar, it is

LECTURER: Mr. John Ryan Quijote, RMT called a nucleoside.

● An N-glycosidic bond is formed between the
COURSE OUTLINE nitrogenous base and the sugar.
● Sugar molecule for DNA: 2-deoxy-D-ribose
I. Nucleotides ● Sugar molecule for RNA: D-ribose
A. Nucleoside
● The sugar is attached to N-1 of a pyrimidine or N-9 of a
B. Nitrogenous Bases
II. DNA Structure purine.
III. RNA Structure
A. 3 Main Types of RNA
B. Protein Synthesis
C. Chemical Structure & Difference with DNA
IV. Chargaff’s Rules (Erwin Chargaff)
V. Central Dogma Of Biology
A. Special Transfers
B. Genetic Codes
VI. Genetic Code
A. Properties of Genetic Code
B. Types of Codons
C.
VII. DNA Extraction
A. DNA Extraction Principles/Steps
VIII. Homemade DNA Extraction

Figure 2. Nucleotide
LEARNING OBJECTIVES
● Memorize the structure of DNA and recognize its functions ● When a phosphate group has already been attached to
● Differentiate between DNA and RNA, the nucleoside, this molecule is now considered to be
● Explain, Chargaff's rules in their own understanding a nucleotide.
● Define the central dogma of Biology ● Nucleotides are the basic structure of a DNA
● Mastery the genetic code along with its properties
● Familiarize the methods and steps of DNA extraction. Functions of a Nucleotide

I. NUCLEOTIDES ● Can be part of coenzymes as donors of phosphoryl

groups, sugars, or lipids.
● DNA is an important component of every living thing ○ Coenzymes are organic molecules that
that contains their genetic material along with the hasten the catalytic activity of enzymes.
codes important for homeostasis and therefore their ○ Since nucleotides contain a phosphoryl group,
survival. they can donate this to coenzymes that might
● DNA along with RNA are polynucleotides. They are need it for some reactions in the body.
made-up of repeating units of nucleotides. ○ Example: ATP can donate a phosphoryl group
● A nucleotide is composed of a nitrogenous base, a to NAD+ in a reaction catalyzed by NAD
sugar molecule, and a phosphate group. kinase. This reaction produces NADP+
● Regulatory nucleotides
A. NUCLEOSIDE ○ Example: cAMP and cGMP
○ cAMP or Cyclic Adenosine Monophosphate is
involved in carbohydrate metabolism.
Catecholamines like epinephrine in the
muscle stimulate Adenyl Cyclase to produce
cAMP which causes glycogenolysis.
○ Glycogenolysis is a process that breaks down
glycogen to form glucose. So this in turn
increases the glucose content of the human
body.
● Control ADP in oxidative phosphorylation.
○ Both ADP and ATP are actually controlled in
the pathway depending on whether a cellular
Figure 1. Nucleoside process needs energy for use or storage of
energy. This just depends.

1
 ● Allosteric regulation
○ Glycolysis involves an enzyme called
phosphofructokinase. When ATP binds to this
enzyme in an allosteric site, its shape is
modified. This causes the enzyme’s activity to
decrease or decline. So this entering causes a
decrease in the production of ATP.
Figure 4. Purines
Other Functions
Purines
● Protein synthesis Adenine & Guanine
● Nucleic acid synthesis
● Regulatory cascades ● Made up of two rings (purine ring + the imidazole ring)
● Signal transduction pathways ○ imidazole ring is a 5-membered ring with two
non-adjacent nitrogen atoms.
Synthetic Nucleotides ● 9 atoms form the actual skeleton of the ring
○ 5 Carbon atoms
● Used in therapy, particularly in cancer through ○ 4 Nitrogen atoms
halogens or AIDS as suppressors ● They function in cell signaling, energy storage as
phosphates and enzyme regulation
B. NITROGENOUS BASES ● Used to make protein and starch since they are
abundant in foods like meat, fish, beans, and grains.
● Ring structures with carbon and nitrogen in the
structure.
● Are also called heterocyclic compounds
● Another term for them would be hetero atoms since
they contain other elements as well like hydrogen
● Can be divided into purines or pyrimidines

Figure 5. Pyrimidines

Pyrimidines
Cytosine, Thymine, Uracil

● A single ring structure

● 6 atoms form the skeleton of the ring:
○ 4 Carbon atoms
○ 2 Nitrogen atoms
● Also function the same way as purines like the cell
signaling, energy storage, and enzyme regulation
Figure 3. Nitrogenous Bases ● The nitrogen atoms are in the first and third positions,
positions 1 and 3.
PURINE PYRIMIDINE Nucleotides may be 3 prime or 5 prime depending on where the
● Cytosine phosphoryl group is attached to the sugar. Most nucleotides
● Adenine have their phosphoryl groups attached to the five prime hydroxyl
● Thymine
● Guanine groups of the sugar.
● Uracil
Double ring structure Single ring structure II. DNA STRUCTURE
(purine ring + imidazole ring) (N atoms at 1 and 3)
9 atoms forming the skeleton 6 atoms forming the skeleton James Watson and Francis Crick
1953, Cambridge University
5C + 4N 4C + 2N
C5H4N4 C4H4N2 ● Made the first correct 3D structure of DNA which was
made of tin sheets and wires.
Sugar attaches to N9 Sugar attaches to N1
They both function in cell signaling, energy storage (as Rosalind Franklin
phosphates), and enzyme regulation. 1952, King’s College, London
Table 1. Difference between Purines and Pyrimidines
● Had a lot of major contributions to the discovery of the
structure of DNA.
● An expert in X-ray crystallography, which she used to
determine the structure of DNA.

2
 ● The structure of DNA was a bit difficult for some ○ The pairing between bases is
scientists to observe or hypothesize, but she was able complementary:
to do this through her expertise in X-ray ■ Adenine & Thymine → 2 hydrogen
Crystallography. bonds
■ Cytosine & Guanine → 3 hydrogen
bonds

Figure 6. (a) Rosalind Franklin, (b) Photo 51; A photograph

showing the DNA’s structure through x-ray crystallography Figure 8. Hydrogen bonds between base pairings

● She took the photo above, called Photo 51, and took Watson-Crick Pairing
notes in her notebook about the structure of DNA
being a double helix. ● Each base along one strand matches with its pair in
● Unfortunately, her photo was shown by her colleague, the opposite strand.
Maurice Wilkins, to the pair James Watson and Francis ● This characteristic does not allow one base to be
Crick. Their model was also based on Franklin’s photo. matched with any other base except only its pair.
The pair, along with Wilkins, were given a Nobel Prize in ● There is no restriction involved in the sequences of
1962. bases. Bases can be arranged into any kind of pattern.
○ Franklin was not given the Nobel Prize This explains how the four bases are able to code for
because she had already died in 1958. The such a big amount of genetic information needed to
Nobel was only given to living people. make an organism
○ Franklin was also not credited for her
contribution. Polarity

● The DNA exhibits polarity, which is determined by the

direction where the nucleotides are pointing towards:
○ Trunk end - 5’ end (5 prime end)
○ Tail end - 3’ end (3 prime end)
● The paired strands are oriented in opposite directions,
where the 5’ end of one strand aligns with the 3’ end of
the other.
● Polarity is directions either 5’ or 3’

Phosphodiester Bridges

● The phosphate group forms two covalent bonds with

Figure 7. DNA Structure two adjacent sugar residues through phosphodiester
bridges.
DNA Structure: Double Helix & Base Pairing ● The phosphate group attaches to two sugar residues
through carbon 5 and 3
● Double Helix structure ○ Carbon 5 → 5’ end
○ Consists of two long chains that consist of ○ Carbon 3 → 3’ end
sub-units, which are nucleotides twisted ● This formation of sugar phosphate forms the sugar
around one another forming a double helix phosphate backbone of DNA.
structure.
○ It is mostly right handed and follows a
clockwise path since its backbone also
follows the same direction.
○ NOTE: DNA can also be left-handed.
● Base Pairings
○ As mentioned, nucleotides and its
nitrogenous bases may either be purines or
pyrimidines.

3
 Synthesis of RNA:

1. A DNA molecule is split temporarily.

2. One strand is used as a template strand.
3. RNA polymerase moves along the template in 5’ to 3’
direction adding base pairs complementary to the
strand until it reaches the termination point.
4. Codons or complementary code triplets make up the
strand which are then translated into a sequence of
Figure 9. (a) Phosphate group is represented by a blue circle. amino acids that make up a protein synthesized in the
This bonds with two sugar molecules at carbon 3 and carbon 5 cytoplasm.
through a phosphodiester bond. (b) The phosphate group is
represented by the yellow circle that connects with the sugar A. 3 MAIN TYPES OF RNA
molecule.

Antiparallelism

● Orientation of the sugar molecules is in opposing

directions.
○ When 5’ is labeled at the beginning of one
strand, the phosphate group is attached to
carbon 5
○ At its end, the bottom part of the strand is
labeled 3’, meaning the hydroxyl group is
found at carbon #3 mRNA tRNA rRNA
○ The complementary strand starts at 3’ and messenger RNA transfer RNA ribosomal RNA
ends at 5’ (opposite the other strand)
● The strand on the left goes from 5’ to 3’ while its Forms ribosomes
Transports
complementary strand goes the opposite direction, Carries genetic along with about 75
activated amino
from 3’ to 5’ code to the different proteins.
acids to the
○ This follows the antiparallelism quality or cytoplasm to So the physical and
ribosomes to be
characteristic of DNA. control the type of chemical structure
used in the
○ Strands go in opposing direction and their protein to be upon which protein
assembly of the
sugar molecules also face different directions synthesized. molecules are
protein molecule.
actually assembled.
Knowledge of the structure of DNA immediately gave clues to Table 3. Three types of RNA
its function:
B. PROTEIN SYNTHESIS
● The sequence of bases in DNA could be copied by
using each of the separate “partner” strands as a ● RNA molecules particularly function in protein
pattern for the creation. synthesis.
● The DNA could contain genetic information in coded ● Like when the body creates a protein molecule, the
form in the sequence of bases, analogous to letters different types of RNA have their own roles which
printed on a strip of paper. contribute to the process.
● Changes in genetic information (mutations) could ○ mRNA: RNA can serve as templates for
result from errors in copying in which the base protein synthesis
sequence of the DNA becomes altered. ○ rRNA: Structural roles, specifically in
ribosome
III. RNA STRUCTURE ○ tRNA: Adapter molecules for translation
● There is also intrinsic catalytic activity in the form of
DNA RNA ribozymes through the cleavage of nucleic acids.
○ Example: In processing the primary transcript
2-deoxy-D-ribose D-ribose of a gene into a mature mRNA, small nuclear
Thymine Uracil RNA (snRNA) are small molecules that vary
from 90 to 300 nucleotides play a role in RNA
Double stranded Single stranded processing.
shows antiparallelism no antiparallelism
has base pairings no base pairings
Table 2. Difference between DNA and RNA. Further discussed in
“Chemical Structure & Difference with DNA”

C. CHEMICAL STRUCTURE & DIFFERENCE WITH DNA

4
 genetic
● RNA may have a lot of similarities with DNA, but has information.
differences in its chemical structure which allow it to
be distinct from DNA. Single-stranded
Typically a
molecule in most of
double-stranded
PREDOMINANT its biological roles
molecule with a
STRUCTURE and has a shorter
long chain of
chain of
nucleotides
nucleotides
nucleus and
LOCATION nucleus
cytoplasm
SUGARS deoxyribose ribose
A-T A-U
adenine-thymine adenine-uracil
Figure 10. (a) D-ribose. The OH group (encircled) is present in BASES AND PAIRS
C-G C-G
D-ribose, while only Hydrogen is attached to C2 in deoxyribose. cytosine-guanine cytosine-guanine
(a) Thymine contains a methyl group (encircled) which is
lacking in Uracil. Transfer the genetic
code of genetic
1. Both carry a 5 carbon sugar molecule or pentose. But information needed
RNA has D-ribose while DNA has 2-deoxy-D-ribose. for the creation of
● In Fig. (1), D-ribose has an OH group in C2, but proteins from the
in deoxyribose, it only has a hydrogen atom Medium of long nucleus to the
attached to C2, hence the name, deoxyribose. storage and ribosome.
JOB/ROLE
2. Uracil replaces thymine as the pyrimidine in RNA. transmission of
● It does not have a methyl group (CH3) genetic information Prevents DNA from
having to leave the
attached to it, unlike thymine. nucleus, so it stays
3. RNA mostly exists as a single stranded molecule. safe. Without RNA,
● It can exhibit double stranded characteristics proteins could
by folding back on itself like a hairpin, and never be made.
giving a complementary base sequence with
opposite polarity (but usually it's just single Less reactive More reactive
stranded). because of C-H because of C-OH
● This double stranded characteristic happens bonds (hydroxyl) bonds.
only on rare occasions. Stable in alkaline Not stable in
4. Bases are not in equal numbers. conditions. alkaline conditions.
● Being single stranded and complementary to
only one strand of DNA, its number of DNA has smaller
STABILITY RNA has larger
Cytosine is not equal to Guanine. Similarly, grooves where the
grooves which
Adenine residues are not equal to the number damaging enzyme
makes it easier for
of thymine or uracil bases. can attach which
the enzymes to
5. RNA can be hydrolyzed by alkali to 2’ or 3’ cyclic makes it harder for
attack RNA.
diesters of the mononucleotide. the enzyme to
● This is not possible in DNA because it lacks attack DNA.
the 2’ hydroxyl group (DNA only has a The helix geometry
hydrogen atom at C2) The helix geometry
of RNA is of
● This characteristic aids scientists and of DNA is B-form.
A-form.
professionals in the analysis of the molecule
or manipulation. This is important in It is completely
RNA strands are
diagnostic research. protected by the
continually made,
UNIQUE FEATURES body because it
broken down and
destroys enzymes
CHARACTERISTIC DNA RNA reused.
that cleave DNA.
A single stranded
Can be damaged by RNA is more
chain of alternating
exposure to UV resistant to damage
A nucleic acid that phosphate and rays. by UV rays.
contains the ribose units with
Table 4. Characteristics of DNA and RNA
genetic instructions the bases adenine,
used in the guanine, cytosine
DEFINITION and uracil bonded
development and
functioning of all to the ribose.
non living Involved in protein
organisms. synthesis and
sometimes in the
transmission of

5
 ● Slight differences make one animal distinct
from each other. It highlights the difference it
makes in each distinct organism.
3. Rule of DNA Base Pairing: Base pair relation ruling
followed by the Parity Rules.
4. Rule of Molar Equivalence: Molar concentrations of
base pairs are equal.
● This highlights molar concentrations between
complementary base pairs which are equal.
● A direct consequence of DNA base pairings.
● If A is paired with T then A=T. So their molar
Figure 11. Helix Structure concentrations are equal.
● Found in some reference books.

V. CENTRAL DOGMA OF BIOLOGY

The Central Dogma of Biology describes the flow of genetic

information in all living things through 3 general transfers

● Replication: Creating multiple copies (needed for the

synthesis of important biomolecules) of DNA with the
help of DNA polymerase.
● Transcription: The genetic information in DNA is
B-Form DNA A-Form RNA
transferred to RNA
narrow and more elongated shorter and wider ● Translation: mRNA is read as a template by rRNA and
deep and narrow major grove the ribosome with tRNA to create a sequence of amino
wide major grove acids which will become protein. The protein will then
(not easily accessible to
(easily accessible to proteins) go on to perform its cellular function.
proteins)
shallow and wide minor A. SPECIAL TRANSFERS
groove
narrow minor groove
(accessible but has less Extensions to the Central Dogma
information or genetic content)
base pairs are almost base pairs are tilted or ● Reverse transcription
perpendicular to the helix displaced from the helix axis ○ Viruses, like retroviruses, have RNA as their
genetic material and have a special enzyme
NOTE: DNA may also exhibit an A-form, but it is more common called reverse transferase.
to see B-form helix of DNA. ○ his helps catalyze the enzymatic synthesis of
Table 5. Difference between B-form and A-form. a complementary DNA strand to the viral
RNA.
IV. CHARGAFF’S RULE (ERWIN CHARGAFF) ○ Example of virus: HIV
● RNA replication
● Discovered by Erwin Chargaff in 1940. ○ RNA-containing viruses, when present in their
● Species differ in the ratio of bases that they have in host cell, bring about the synthesis of a set of
their DNA. enzymes called RNA replicases.
● It was through chromatographic and quantitative ○ Because of these, duplication of the viral RNA
methods that were performed, that we are able to is possible
separate the four bases from each other and
determine the amount of each base in samples studied B. GENETIC CODES
(1949-1953)
● For a biomolecule to qualify as a genetic material, it
Chargaff’s Parity Rules has to exhibit these 4 requirements:
○ Able to store large amounts of genetic
1. First Parity Rule: The number of purine bases is equal information;
to the number of pyrimidine bases. ○ Transfer the information to daughter cells;
○ Physical and chemical stability and;
A=T;C=G ○ Mutability (ability to change without the major
loss of parental information)
2. Second Parity Rule: The base composition in the DNA ● Large information is stored in the genetic materials
where the ratios of A to T and C to G are roughly the since this contains all expressible and inexpressible
same across different species. traits of the organism. So, through the variation
● The overall percentage of (G+C) does not present in the base sequences, DNA meets these four
necessarily equal the percentage of (A+T). qualifications.
● Base pairing is constantly followed but with ● The highly stable nature of DNA also makes it the
slight difference in percentages of pairs. perfect biomolecule to store information.

6
Its stability is because of these factors inherent to its structure Non Ambiguity

● Sugar phosphate backbone ● One codon cannot specify for more than one amino
○ Extremely stable under all conditions like acid.
extreme temperature and pH. ● Each codon is only specific for one amino acid in the
● Base stacking series.
○ The tendency of the hydrophobic nitrogen ○ Example: CGU will ONLY code for Arginine.
bases to pile on top of each other. ● As opposed to degeneracy where arginine can be
● H bonds coded by different codons, here in non ambiguity, one
○ Weak when they are by themselves, but they codon is specific to only one amino acid.
add tremendous stability when found in
millions between base pairs of a whole DNA.

VI. GENETIC CODE

● The term Genetic Code is given by George Gamow.

● A dictionary corresponding with the sequence of
nucleotides and amino acids.
● This is a set of rules by which information encoded in
genetic material is translated into proteins.
● This collective set of rules is the sequence of
nucleotide bases organized into codons.
Figure 12. (b) Non Ambiguity
● Since 3 nucleotides create a codon specific to an
amino acid, (there are like 20 essential amino acids) so
Non Overlapping
there should be 20 codons. 3 Nucleotides create 64
combinations that are most suited for 20 amino acids.
● The series of nucleotides will only be read as triplets or
every three bases.
● One base cannot participate in the formation of more
than one codon.
● It can be seen in the picture that the genetic code
arranges the bases by three groups and not less than
or more than this.
○ In the example sequence:
■ GUU codes for Val
■ CGC codes for Arg
■ AUC codes for Tyr
○ But if we try to code this sequence into 4
bases like GUUC, this does not correspond to
Figure 12. Codons or code for an amino acid.
○ If we try to translate only 2 bases like AC or
A. PROPERTIES OF GENETIC CODE GU only this does not code for an amino acid.
○ Bases should be read in groups of 3 and
Degeneracy triplets.

● There are 64 combinations possible because each

codon has three nucleotides each.
● Since there are 20 essential amino acids, this means
that a single amino acid can be coded by more than
one codon:
○ Example: Arginine can be coded by 4 different
codons: CGU, CGC, CGA, CGG. Others include
AGA and AGG.

Figure 12. (c) Non Overlapping

Figure 12. (a) Degeneracy

7
Polarity ● Because of these exceptions, we can only consider the
genetic code to be universal.
● There is a definite direction for reading the codons.
● When you read from right to left/ left to right, up to
down/down to up that will affect the kind of amino
acid that will be coded for.
● Let's try to read the sequence from top to bottom:
○ GUU = Val
○ CGC = Arg
○ UAC = Tyr
● Now let's start from bottom to top. This becomes CAU
which will code for a different amino acid, which is His
and then CGC is just the same, Arg, but UUG will now
code for Leu.
● Direction is important. Figure 12. (f) Nearly Universal

B. TYPES OF CODONS

There are two types of codons

● Sense Codons: code for amino acids.

● Signal Codons: code for signals, like START or STOP,
during protein synthesis

START codons STOP codons

or Initiation codons or Termination codons
Figure 12. (d) Polarity
AUG UAA, UAG, UGA
Continuous Methionine – eukaryotes
FormylMethionine –
● The genetic code is continuous and does not have a prokaryotes
comma or space between the nucleotides. So it is
continuously read in every 3 bases, in triplets. First amino acid that starts
Can also be called Amber /
● Genes are transcribed and then translated from a fixed the protein synthesis
Ochre / Opal Codon
starting point to a fixed endpoint. process.
● The start codon is usually AUG, which codes for Met. Table 6. Difference between Start Codons and Stop Codons
● Stop codons can be UAA, UAG, or UGA.
● Stop codon may also be called nonsense codon, since Anticodons
it does not code for any amino acid, except that it just
signals in reading the sequences to stop. ● A base sequence of tRNA that pairs with a codon of
mRNA during translation
● Help bring an amino acid to its proper position during
translation

Differences of Anticodons against Codons

● Always present in RNA but never in DNA

● Written in 3’ to 5’ direction
● Some have to pair with more than 1 codon
● Discretely present in cells with or without amino acids
attached, as opposed to codons that are sequentially
arranged in a nucleic acid strand
Figure 12. (e) Continuous
● Codons dictate which anticodon comes next in the
series. Always remember this text so you will not have
Nearly Universal
a hard time differentiating between codon and
anticodon.
● The genetic code is nearly universal since it is almost
the same in humans, bacteria, plants, and other living
VII. DNA EXTRACTION
organisms.
● This is exhibited in which AUG is also the code for Met ● Greatly benefits biotechnology in the production of
in mitochondria, but it also codes for Iso inside the biomedical products and forensics for crime detection.
mitochondria. ● Extraction and purification of DNA allows scientists to:
● There are also exceptions to this rule, like the other ○ detect genetic disorders,
properties in the mitochondrial genome, some ○ produce DNA fingerprints, and
bacteria, and some single-celled eukaryotes. ○ create genetically engineered organisms.

8
DNA Extraction Methods ● Enzymes
○ Generally considered better because
● Silica columns or magnetic bead DNA Extraction they target the bonds between
○ considered to be the best method amino acids.
● Alcohol Precipitation DNA Extraction ○ Considered to be more specific
○ the best method for large samples ○ Under enzymes, we can use:
■ Proteinase K for animal
Physical Methods sample (Tightly suitable
because it still functions in
● Silica columns or magnetic bead DNA Extraction the presence of other
● Paper DNA Extraction chemicals that will be used
in a lysis buffer)
■ Cellulase (plants)
■ Lyticase (yeast)
■ Lysozyme (gram (+)
bacteria)

Some methods apply all of these or both of these processes

● They can first physically destroy the sample through a

blender or mortar and pestle and then they expose the
Figure 13. Physical Methods
lysate to chemicals, either detergents or enzymes
● It’s not choosing between physical or chemical, but you
Chemical Methods
can actually do both to further expose DNA and this
will also make it easier for some to extract and purify
● Organic
the DNA.
○ Phenol Chloroform Method
■ harmful for the environment
Precipitation
● Inorganic
○ Silica Gel-based
● After cell lysis we separate the DNA from
■ Ice-based
contaminants like protein and detergents through
○ Proteinase K
precipitation.
■ produces a high yield by digesting
● Sodium ions or salt
many proteins and nuclei present in
○ Neutralizes DNA
the sample but it needs to be done
○ Which acts by neutralizing the negative
under low temperature
charge in the DNA
○ Salting Out
● Alcohol
■ simple, nontoxic
○ Insolubility of DNA
○ We can use isopropanol or ethanol
○ DNA is insoluble with the solution causing it
to precipitate
● Protease
○ Destroys proteins
○ This degrades proteins associated with DNA

Purification

● Separate DNA from aqueous phase, then store it for

future use. This also stores DNA for future analysis.
Figure 14. Chemical Methods ● DNA is separated from the aqueous phase through
alcohol to remove debris and other materials.
A. DNA EXTRACTION PRINCIPLES/STEPS ● This process differs depending on the type of sample
being isolated, extraction method performed, or its
Cell Lysis application in future experiments.
● You can purify DNA through different methods, but this
● Destroy the cell membrane through physical or entirely depends on the process that you’re doing or
chemical methods to release DNA and RNA your purpose for extracting DNA.
components through the cell lysate.
● Physical: Assessment and Visualization
○ Blender, mortar and pestle
● Chemical ● Evaluate the quality of the sample (PCR, DNA
○ Detergents (sodium dodecyl sulfate/lauryl Fingerprinting, etc.)
sulfate) ● We do this to evaluate the sample of this being
■ Used for rapid disruption isolated through different methods like
Spectrophotometry, gel electrophoresis or more
specific methods (PCR, DNA Fingerprinting, etc.)

9
 VII. HOMEMADE DNA EXTRACTION HOMEMADE DNA EXTRACTION
Pour the mixture into test tubes or other small glass
8
containers, each about ⅓ full.
Add a pinch of enzymes to each test tube and stir gently.
(Use meat tenderizer for enzymes. Pineapple juice or
9
contact lens cleaning solution may be used as an
alternative.)

● We now expose the fruit-cell soup to chemical

methods.

HOMEMADE DNA EXTRACTION

Tilt your test tube and slowly pour rubbing alcohol (70-95%
isopropyl or ethyl alcohol) into the tube down the side so
that it forms a layer on top of the pea mixture. Pour until
you have about the same amount of alcohol in the tube as
10
pea mixture. So we do this slowly so that there's a
separate layer of alcohol above the fruit mixture. We pour
Figure 15. Homemade DNA Extraction Materials until we have about the same amount of alcohol in the
tube as a pea mixture.
● DNA extraction can also be done at home since we can All of the grease and the protein that we broke up in the
follow the same principles that we discussed earlier 11
first two steps move to the bottom, watery layer.
like the cell lysis, precipitation, purification, and
assessment and visualization. DNA will rise into the alcohol layer from the pea layer. You
● When we do this at home, the main ingredients are: 12 can use a glass stirring rod or a wooden stick to draw the
detergent, alcohol, and sources of enzymes (Meat DNA into the alcohol.
tenderizer, contact lens solution , pineapple juice) Slowly turning the stirring rod will spool (wrap) the DNA
● Other materials include the blender, split peas or any 13
around the rod so it can be removed from the liquid.
fruit, salt, water, test tube or containers, strainers and
then measuring cups and spoons.
Main Ingredients in the Homemade Process

HOMEMADE DNA EXTRACTION ● Detergents

First we use a blender. The blender separates the pea cells ○ Help in the removal of fats from the DNA
or the fruit cells from each other. This will create a very source
1 ○ The fats from the cell membrane are broken
thin pea-cell soup or fruit-cell soup depending on what fruit
you’re going to use. apart and DNA is released from the cell.
● Alcohol
And then second is we measure about 100mL or ½ cup of ○ Precipitates the DNA, allowing visualization
2
split peas and then place them in a blender. since it cannot be seen when it’s dissolved in
And then we add a large pinch of salt, less than 1 mL or ⅛ water or detergent.
3 ● Warm water
tsp to the blender.
○ Inactivates DNAse enzymes present to avoid
Add about twice as much as cold water as the DNA source DNA from being cut, which would make it
4
(about 200 mL or 1 cup) to the peas in the blender. more difficult to observe afterward.
5 Blend on high (lid on) for about 15 seconds. ○ Enzymes can be inactivated by heat at 60°C.
However, DNA denatures at 80°C.

● This reflects the principle of physical cell lysis

● We put the sample along with water and salt in the
blender, and then we allow the blades to destroy the
fruit and further expose the fruit cells from each other
or separate the fruit cells from each other.

HOMEMADE DNA EXTRACTION

Pour your thin pea-cell soup through a strainer into another
container like a measuring cup or beaker. Estimate how
much pea soup you have and add about ⅙ of that amount
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of liquid detergent (about 30 ml or 2 tablespoons). Swirl to
mix (carefully, not to break the DNA strands). Let the
mixture sit for 5-10 minutes.
The detergent captures the proteins & lipids of the cell
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membrane.

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