DISCOVERY OF THE STRUCTURE OF DNA

THE COMPONENTS OF DNA

From the work of

biochemist Phoebus
Levene and others,
scientists in Watson and
Crick's time knew that DNA
was composed of subunits
called nucleotides . A
nucleotide is made up of a
sugar (deoxyribose), a
phosphate group, and one
of four nitrogenous bases:
adenine (A), thymine (T),
guanine (G) or cytosine (C).

C and T bases, which have

just one ring, are called
pyrimidines, while A and G
bases, which have two
rings, are called purines.
DNA nucleotides assemble in chains linked by covalent bonds,
which form between the deoxyribose sugar of one nucleotide and
the phosphate group of the next. This arrangement makes an
alternating chain of deoxyribose sugar and phosphate groups in
the DNA polymer, a structure known as the sugar-phosphate
backbone

CHARGAFF'S RULES

One other key piece of information related to the structure of DNA came from Austrian
biochemist Erwin Chargaff. Chargaff analyzed the DNA of different species, determining
its composition of A, T, C, and G bases. He made several key observations:

A, T, C, and G were not found in equal quantities (as some models at the time would
have predicted)
The amounts of the bases varied among species, but not between individuals of the
same species
The amount of A always equalled the amount of T, and the amount of C always
equalled the amount of G (A = T and G = C)

These findings, called Chargaff's rules, turned out to be crucial to Watson and Crick's
model of the DNA double helix.
WATSON, CRICK, AND ROSALIND FRANKLIN

In the early 1950s, American biologist James

Franklin’s crystallography gave
Watson and British physicist Francis Crick came
Watson and Crick important clues to
up with their famous model of the DNA double
the structure of DNA. Some of these
helix. They were the first to cross the finish line
came from the famous “image 51,” a
in this scientific "race," with others such as
remarkably clear and striking X-ray
Linus Pauling (who discovered protein
diffraction image of DNA produced by
secondary structure) also trying to find the
Franklin and her graduate student. (A
correct model.
modern example of the diffraction
Rather than carrying out new experiments in
pattern produced by DNA is shown
the lab, Watson and Crick mostly collected and
above.) To Watson, the X-shaped
analyzed existing pieces of data, putting them
diffraction pattern of Franklin's image
together in new and insightful ways . Some of
immediately suggested a helical, two-
their most crucial clues to DNA's structure
stranded structure for DNA .
came from Rosalind Franklin, a chemist working
in the lab of physicist Maurice Wilkins.
Franklin was an expert in a powerful technique Watson and Crick brought together
for determining the structure of molecules, data from a number of researchers
known as X-ray crystallography. When the (including Franklin, Wilkins, Chargaff,
crystallized form of a molecule such as DNA is and others) to assemble their
exposed to X-rays, some of the rays are celebrated model of the 3D structure
deflected by the atoms in the crystal, forming a of DNA. In 1962, James Watson,
diffraction pattern that gives clues about the Francis Crick, and Maurice Wilkins
molecule's structure. were awarded the Nobel Prize in
Medicine. Unfortunately, by then
Franklin had died, and Nobel prizes are
not awarded posthumously.
WATSON AND CRICK'S MODEL OF DNA

The structure of DNA, as represented

in Watson and Crick's model, is a
double-stranded, antiparallel, right-
handed helix. The sugar-phosphate
backbones of the DNA strands make
up the outside of the helix, while the
nitrogenous bases are found on the
inside and form hydrogen-bonded
pairs that hold the DNA strands
together.

The orange and red atoms mark the

phosphates of the sugar-phosphate
backbones, while the blue atoms on
the interior of the helix belong to the
nitrogenous bases.
 ANTIPARALLEL ORIENTATION

Double-stranded DNA is an antiparallel molecule, meaning that it's composed of two

strands that run alongside each other but point in opposite directions. In a double-
stranded DNA molecule, the 5' end (phosphate-bearing end) of one strand aligns with the 3'
end (hydroxyl-bearing end) of its partner, and vice versa.

RIGHT-HANDED HELIX

In Watson and Crick's model, the two

strands of DNA twist around each other to
form a right-handed helix. All helices have a
handedness, which is a property that
describes how their grooves are oriented in
space.

The twisting of the DNA double helix and

the geometry of the bases creates a wider
gap (called the major groove) and a
narrower gap (called the minor groove) that
run along the length of the molecule, as
shown in the figure above. These grooves
are important binding sites for proteins that
maintain DNA and regulate gene activity.
 BASE PAIRING

In Watson and Crick's model, the two

strands of the DNA double helix are held
together by hydrogen bonds between
nitrogenous bases on opposite strands.
Each pair of bases lies flat, forming a "rung"
on the ladder of the DNA molecule.

Base pairs aren't made up of just any

combination of bases. Instead, if there is an
A found on one strand, it must be paired
with a T on the other (and vice versa).
Similarly, an G found on one strand must
always have a C for a partner on the
opposite strand. These A-T and G-C
associations are known as complementary
base pairs.

Base pairing explains Chargaff's rules, that

is, why the composition of A always equals
that of T, and the composition of C equals
that of G . Where there is an A in one strand,
there must be a T in the other, and the same
is true for G and C. Because a large purine
(A or G) is always paired with a small
Although Watson and Crick's original model
pyrimidine (T or C), the diameter of the helix
proposed that there were two hydrogen
is uniform, coming in at about nanometers.
bonds between the bases of each pair, we
know today that G and C form an additional
THE IMPACT OF THE DOUBLE HELIX bond (such that A-T pairs form two
hydrogen bonds total, while G-C pairs form
three) .

The structure of DNA unlocked the door to

understanding many aspects of DNA's
function, such as how it was copied and
how the information it carried was used by
the cell to make proteins.
As we'll see in upcoming articles and
videos, Watson and Crick's model ushered
in a new era of discovery in molecular
biology. The model and the discoveries
that it enabled form the foundations for
much of today's cutting-edge research in
biology and biomedicine.
 DNA
GREGOR MENDEL WATSON & CRICK

the father of genetics, who was starting to In the mid 20th century, structure of
understand the mechanisms or how DNA
inheritance happened, was established by Watson and Crick
and their work was based on the work
of many others, especially folks like
DNA Rosalind Franklin, who essentially
provided the bulk of the data

the molecule that's storing the

information that could be replicated
DNA was discovered in the mid 1800s.
a kind of molecule that was inside of always pair:
nuclei of cells. Adenine & Thymine
Guanine &Cytosine too
molecular basis of inheritance.
1953 wherein this double helix structure
of DNA was established.

Two sides of that twisted ladder and these

rungs (the color coded line). These rungs
are actually where the genetic
information and a sequence of different
bases.
The sequence of these bases essentially in code the
The word deoxyribonucleic acid comes information that make you
from the fact that this backbone is
made up of a combination of sugar
and phosphate. And the sugar that When you see that your smile is
makes up the backbone is similar to your parents it is because
deoxyribose, So that's essentially the that information to a large degree is
D in DNA. And nucleic is, this was encoded genetically. It affects a lot
found in nuclei of cells. of what makes you. This is the basis
And then the phosphate group is by which they are passing down
acidic and that's now where you get their actual traits.
the acid part of it. It is actually mildly
acidic all in total, but for every acid it All living creatures as we know they
actually also has a base, and those have genetic information.
nitrogen bases form the rung of the
ladders and actually each rung is a pair Human genome has ap. 6BILLION
of bases when these complimentary base pairs. 46 chromosomes or 23
nitrogenous bases form these pair of chromosomes. If you divide
hydrogen bonds with each other. 6b by 46 you get a little over on
average 100,000,000 base pairs
per chromosome.
 DNA STRUCTURE
KEY TERMS

DNA (deoxyribonucleic acid) DNA replication

Nucleic acid that transmits genetic Process during which a double-stranded
information from parent to offspring DNA molecule is copied to produce two
and codes for the production of identical DNA molecules
proteins Base pairing
Nucleotide Principle in which the nitrogenous bases
Building block of nucleic acids of the DNA molecules bond with one
Double helix another
Structure of two strands, intertwining
around an axis like a twisted ladder

DNA STRUCTURE

DNA is a nucleic acid, one of the four major

Nucleotides
groups of biological macromolecules. All nucleic acids are made up of
nucleotides. In DNA, each nucleotide is
Chargaff's rules made up of three parts: a 5-carbon sugar
called deoxyribose, a phosphate group, and
In the 1950s, a biochemist named Erwin
a nitrogenous base.
Chargaff discovered that the amounts of
DNA uses four kinds of nitrogenous bases:
the nitrogenous bases (A, T, C, and G) were
adenine (A), guanine (G) cytosine (C), and
not found in equal quantities. However, the
thymine (T).
amount of A always equalled the amount of
RNA nucleotides may also contain adenine,
T, and the amount of C always equalled the
guanine and cytosine bases, but instead of
amount of G.
thymine they have another base called
These findings turned out to be crucial to
uracil (U).
uncovering the model of the DNA double
helix.

Double helix (1950)

DNA molecules have an antiparallel
structure - that is, the two strands of the
helix run in opposite directions of one
another. Each strand has a 5' end and a 3'
end.
Solving the structure of DNA was one of the
great scientific achievements of the
century.
Knowing the structure of DNA unlocked the
door to understanding many aspects of
DNA's function, such as how it is copied and
how the information it carries can be used
to produce proteins.
 DNA REPLICATION

DNA replication is semi-conservative. This The replication process

means that each of the two strands in double-
stranded DNA acts as a template to produce
two new strands.
Replication relies on complementary base
pairing, that is the principle explained by
Chargaff's rules: adenine (A) always bonds
with thymine (T) and cytosine (C) always
bonds with guanine (G).

DNA replication occurs through the help of

several enzymes. These enzymes "unzip" DNA
molecules by breaking the hydrogen bonds
that hold the two strands together.
Each strand then serves as a template for a
new complementary strand to be created.
Complementary bases attach to one another
(A-T and C-G).

The primary enzyme involved in this is

DNA polymerase which joins nucleotides
to synthesize the new complementary
strand. DNA polymerase also proofreads
each new DNA strand to make sure that
there are no errors.

Leading and lagging strands

DNA is made differently on the two strands at

a replication fork.
One new strand, the leading strand, runs 5' to
3' towards the fork and is made continuously.
The other, the lagging strand, runs 5' to 3'
away from the fork and is made in small
pieces called Okazaki fragments.
 DNA REPLICATION
Example: Determining a
complementary strand
DNA is only synthesized in the 5' to 3'
direction. You can determine the sequence of
a complementary strand if you are given the
sequence of the template strand.
For instance, if you know that the sequence of
one strand is 5’-AATTGGCC-3’, the
complementary strand must have the
sequence 3’-TTAACCGG-5’. This allows each
base to match up with its partner:

Common mistakes and misconceptions

DNA replication is not the same as cell division. Replication occurs before cell division,
during the S phase of the cell cycle. However, replication only concerns the production
of new DNA strands, not of new cells.
Some people think that in the leading strand, DNA is synthesized in the 5’ to 3’ direction,
while in lagging strand, DNA is synthesized in the 3’ to 5’ direction. This is not the case.
DNA polymerase only synthesizes DNA in the 5’ to 3’ direction only. The difference
between the leading and lagging strands is that the leading strand is formed towards
replication fork, while the lagging strand is formed away from replication fork.
 MOLECULAR STRUCTURE OF DNA
Each DNA molecule is made up of a chain
called nucleotides. A nucleotide is an
organic molecule that is the building block
of DNA and RNA. They also have functions
related to cell signaling, metabolism, and
enzyme reactions. A nucleotide is made up
of three parts. The Nucleotide Structure
can form together is complex

The group of dot dot that form 4 nucleotide.

Each nucleotide has phosphate group. The
phosphate groups are actually what make
DNA or actually what make nucleic acid an
acid (the phosphate groups, when they're
protonated (having negative charge), are Deoxyribose doesn't have this oxygen. It
acids) does not have the oxygen on the two prime
carbon.
Something with a negative charge in
phosphate would attract protons, it would When nitrogen is bound to a hydrogen
sap up protons. The reason why its DNA is you're going to have a partially negative
typically drawn with these negative charges charge at the nitrogen and a partially
here is that it's so acidic and that if you put positive charge at the hydrogen.
it in into a neutral solution, it's actually Then oxygen we've always talked about as
going to lose its hydrogens. being electronegative so it has a partial
negative charge. The partial negative charge
of this oxygen is going to be attracted to the
partial positive charge of this hydrogen, and
Nitrogen bases is that these nitrogens are so you're going to have a hydrogen bond.
really electronegative and they can take up That's then going to happen between this
more hydrogen protons because they have hydrogen Its electrons are being hogged by
an extra lone pair. this nitrogen and this nitrogen with who,
which itself hogs electron forms a hydrogen
bond. That's why cytosine and guanine pair
up, and that's why thymine and adenine
pair up.
 Phosphate & sugar & nitrogen base made up
DNA

DNA PROOFREADING AND REPAIR

KEY POINTS:

Cells have a variety of mechanisms to prevent mutations, or permanent changes

in DNA sequence.
During DNA synthesis, most DNA polymerases "check their work," fixing the
majority of mispaired bases in a process called proofreading.
Immediately after DNA synthesis, any remaining mispaired bases can be detected
and replaced in a process called mismatch repair.
If DNA gets damaged, it can be repaired by various mechanisms, including
chemical reversal, excision repair, and double-stranded break repair.

INTRODUCTION

What does DNA have to do with cancer? Cancer occurs when cells divide in an
uncontrolled way, ignoring normal "stop" signals and producing a tumor. This bad
behavior is caused by accumulated mutations, or permanent sequence changes in
the cells' DNA.
Replication errors and DNA damage are actually happening in the cells of our
bodies all the time. In most cases, however, they don’t cause cancer, or even
mutations. That’s because they are usually detected and fixed by DNA
proofreading and repair mechanisms. Or, if the damage cannot be fixed, the cell
will undergo programmed cell death (apoptosis) to avoid passing on the faulty
DNA.
2.
 Mutations happen, and get passed on to daughter cells, only when these
mechanisms fail. Cancer, in turn, develops only when multiple mutations in
division-related genes accumulate in the same cell.
In this article, we’ll take a closer look at the mechanisms used by cells to correct
replication errors and fix DNA damage, including:
Proofreading, which corrects errors during DNA replication
Mismatch repair, which fixes mispaired bases right after DNA replication
DNA damage repair pathways, which detect and correct damage throughout the
cell cycle

PROOFREADING

DNA polymerases are the enzymes

that build DNA in cells. During DNA
replication (copying), most DNA
polymerases can “check their work”
with each base that they add. This
process is called proofreading. If the
polymerase detects that a wrong
(incorrectly paired) nucleotide has
been added, it will remove and
replace the nucleotide right away,
before continuing with DNA
synthesis .

MISMATCH REPAIR

Many errors are corrected by proofreading, but a few slip through. Mismatch repair
happens right after new DNA has been made, and its job is to remove and replace mis-
paired bases (ones that were not fixed during proofreading). Mismatch repair can also
detect and correct small insertions and deletions that happen when the polymerases
"slips," losing its footing on the template .

How does mismatch repair work? First, a protein complex (group of proteins)
recognizes and binds to the mispaired base. A second complex cuts the DNA near the
mismatch, and more enzymes chop out the incorrect nucleotide and a surrounding
patch of DNA. A DNA polymerase then replaces the missing section with correct
nucleotides, and an enzyme called a DNA ligase seals the gap .
One thing you may wonder is how
the proteins involved in DNA repair
can tell "who's right" during
mismatch repair. That is, when two
bases are mispaired (like the G and
T in the drawing above), which of
the two should be removed and
replaced?

In bacteria, original and newly

made strands of DNA can be told
apart by a feature called
methylation state. An old DNA
strand will have methyl ( ) groups
attached to some of its bases,
while a newly made DNA strand will
not yet have gotten its methyl
group .
DNA DAMAGE REPAIR MECHANISMS

In eukaryotes, the processes that

Bad things can happen to DNA at almost any point
allow the original strand to be
in a cell's lifetime, not just during replication. In
identified in mismatch repair
fact, your DNA is getting damaged all the time by
involve recognition of nicks (single-
outside factors like UV light, chemicals, and X-rays
stranded breaks) that are found
—not to mention spontaneous chemical reactions
only in the newly synthesized DNA .
that happen even without environmental insults!
Fortunately, your cells have repair mechanisms to
REVERSAL OF DAMAGE
detect and correct many types of DNA damage.
Repair processes that help fix damaged DNA
In some cases, a cell can fix DNA include:
damage simply by reversing the Direct reversal: Some DNA-damaging chemical
chemical reaction that caused it. To reactions can be directly "undone" by enzymes
understand this, we need to realize in the cell.
that "DNA damage" often just Excision repair: Damage to one or a few bases
involves an extra group of atoms of DNA is often fixed by removal (excision) and
getting attached to DNA through a replacement of the damaged region. In base
chemical reaction. excision repair, just the damaged base is
For example, guanine (G) can undergo removed. In nucleotide excision repair, as in
a reaction that attaches a methyl ( ) the mismatch repair we saw above, a patch of
group to an oxygen atom in the base. nucleotides is removed.
The methyl-bearing guanine, if not Double-stranded break repair: Two major
fixed, will pair with thymine (T) rather pathways, non-homologous end joining and
than cytosine (C) during DNA homologous recombination, are used to repair
replication. Luckily, humans and double-stranded breaks in DNA (that is, when
many other organisms have an an entire chromosome splits into two pieces).
enzyme that can remove the methyl
group, reversing the reaction and
returning the base to normal .
 BASE EXCISION REPAIR

Base excision repair is a mechanism used to To prevent such mutations, a

detect and remove certain types of damaged glycosylase from the base excision
bases. A group of enzymes called glycosylases repair pathway detects and
play a key role in base excision repair. Each removes deaminated cytosines.
glycosylase detects and removes a specific kind Once the base has been removed,
of damaged base. the "empty" piece of DNA
backbone is also removed, and the
For example, a chemical reaction called gap is filled and sealed by other
deamination can convert a cytosine base into enzymes .
uracil, a base typically found only in RNA. During
DNA replication, uracil will pair with adenine
rather than guanine (as it would if the base was NUCLEOTIDE EXCISION REPAIR
still cytosine), so an uncorrected cytosine-to-
uracil change can lead to a mutation . Nucleotide excision repair is another
pathway used to remove and replace
damaged bases. Nucleotide excision
repair detects and corrects types of
damage that distort the DNA double
helix. For instance, this pathway detects
bases that have been modified with
bulky chemical groups, like the ones that
get attached to your DNA when it's
exposed to chemicals in cigarette smoke
.
Nucleotide excision repair is also used to
fix some types of damage caused by UV
radiation, for instance, when you get a
sunburn. UV radiation can make cytosine
and thymine bases react with
neighboring bases that are also Cs or Ts,
forming bonds that distort the double
helix and cause errors in DNA
replication. The most common type of
linkage, a thymine dimer, consists of two
thymine bases that react with each other
and become chemically linked .
 In nucleotide excision repair, the
damaged nucleotide(s) are removed
along with a surrounding patch of DNA.
In this process, a helicase (DNA-opening
enzyme) cranks open the DNA to form a
bubble, and DNA-cutting enzymes chop
out the damaged part of the bubble. A
DNA polymerase replaces the missing
DNA, and a DNA ligase seals the gap in
the backbone of the strand .

DOUBLE-STRANDED BREAK REPAIR

Some types of environmental factors, such as high-energy radiation, can cause double-
stranded breaks in DNA (splitting a chromosome in two). This is the kind of DNA damage
linked with superhero origin stories in comic books, and with disasters like Chernobyl in
real life.

Double-stranded breaks are dangerous because large segments of chromosomes, and

the hundreds of genes they contain, may be lost if the break is not repaired. Two
pathways involved in the repair of double-stranded DNA breaks are the non-
homologous end joining and homologous recombination pathways.

In non-homologous end joining, the two broken ends of the chromosome are simply
glued back together. This repair mechanism is “messy” and typically involves the loss, or
sometimes addition, of a few nucleotides at the cut site. So, non-homologous end
joining tends to produce a mutation, but this is better than the alternative (loss of an
entire chromosome arm) .
In homologous recombination, information
from the homologous chromosome that
matches the damaged one (or from a sister
chromatid, if the DNA has been copied) is
used to repair the break. In this process, the
two homologous chromosomes come
together, and the undamaged region of the
homologue or chromatid is used as a
template to replace the damaged region of
the broken chromosome. Homologous
recombination is “cleaner” than non-
homologous end joining and does not usually
cause mutations .

DNA PROOFREADING AND REPAIR IN HUMAN DISEASE

Evidence for the importance of proofreading and repair mechanisms comes from human
genetic disorders. In many cases, mutations in genes that encode proofreading and
repair proteins are associated with heredity cancers (cancers that run in families). For
example:
Hereditary nonpolyposis colorectal cancer (also called Lynch syndrome) is caused by
mutations in genes encoding certain mismatch repair proteins . Since mismatched
bases are not repaired in the cells of people with this syndrome, mutations
accumulate much more rapidly than in the cells of an unaffected person. This can
lead to the development of tumors in the colon.
People with xeroderma pigmentosum are extremely sensitive to UV light. This
condition is caused by mutations affecting the nucleotide excision repair pathway.
When this pathway doesn't work, thymine dimers and other forms of UV damage
can't be repaired. People with xeroderma pigmentosum develop severe sunburns
from just a few minutes in the sun, and about half will get skin cancer by the age of
unless they avoid the sun .