Topic 6: DNA Structure and Function

The journey to understanding the role of DNA in heredity was a long one. A lot of people
contributed to the things we know now. DNA had been underestimated because scientists saw
how simple its basic building blocks were. Its possible importance was overlooked due to its
supposed simplicity. Once the structure was determined, scientists were finally able to see how
such a simple structure could contribute so much to an organism. The first part of this topic
focuses on the events that led to the discovery of the structure of DNA while the second part
delves deeper into the specifics of the DNA structure. DNA contains all the information an
organism needs to grow and survive in its environment. That’s a lot of information that has to
be stored. Organisms have millions and millions of nucleotides that are incorporated into their
DNA. With so much DNA, how can a single cell contain them? The last part of the topic
explains how DNA is packaged in the cell and how it’s able to configure itself into the
chromosomes we all know.

The search for the molecule of heredity

In the history of genetics presented in the first chapter, we stopped the timeline at Gregor
Mendel’s findings. In his papers, Mendel referred to a certain “hereditary factor” that was
passed on from one generation to the next. Although he was able to describe some aspects of
inheritance properly, Mendel was unable to give much information on what exactly this
hereditary factor was. How exactly did scientists determine that DNA was the molecule of
heredity?

Figure 6.1. Scientists who have contributed to the discovery of DNA as the genetic material.
(A) Friedrich Miescher (Source: Mr. Courvoisier, Portrait Sammlung, University of Basel), (B)
Frederick Griffith, (C) Oswald Avery (Source: Encyclopedia Britannica), (D) Maclyn MacCarty
(Source: National Academy of Sciences), (E) Colin Macleod (Source: The Lillian and Clarence de
la Chapelle Medical Archives, NYU).

In 1869, Friedrich Miescher studied the cell nucleus and found that the cell nucleus contained
a mixture of compounds which he collectively called nuclein. The major components of this
nuclein were DNA and proteins. Chemists were already able to identify the structure of DNA
and RNA by the end of the 19th century but not much was known about their function. When
Mendel’s work was rediscovered in 1900, he mentioned the hereditary factor but was unable
to identify what or where in the cell it could be. It was experiments in fruit flies done by Thomas
Hunt Morgan that served as hard evidence to show that genes were found along chromosomes.
Geneticists finally identified the chromosomes as the location for Mendel’s hereditary factor.
The problem was that during that time, the knowledge was that chromosomes were made up of
DNA and proteins. This started a debate that lasted years and years. So which one was the
hereditary factor? DNA or protein? This was the main problem geneticists were trying to solve.

In the protein versus DNA as the hereditary factor debate, more people were actually on the
side of proteins. Very little was known about nucleic acids then. Although their general
structure was known, their function was not well understood. In terms of complexity, proteins
were also above nucleic acids. In humans, there were 20 amino acids that made up proteins and
only 4 nucleotides that made up DNA. So much information was in the hereditary material.
Wouldn’t having 20 monomers be better in storing more information? DNA looked too simple
so they didn’t give it much attention. Looking at what they knew, it was more likely that
proteins were the hereditary material. But in order to make sure, more people made experiments
to find out.

We can actually say that the discovery of the genetic role of DNA started as far back as 1928.
During this time, British medical officer Frederick Griffith was trying to find a vaccine against
pneumonia. He made use of Steptococcus pneumoniae, a bacterium that causes pneumonia in
mammals. He had two strains of the bacterium, a pathogenic strain and a non-pathogenic strain.
The pathogenic strain was designated as the S strain. These microbes were named such because
the colonies they formed on the petri dish when cultured had smooth edges, thus the name S
(smooth) strain. Later research showed that the S strain was pathogenic due to the presence of
a capsule that allows it to escape degradation by the immune system. The non-pathogenic strain
on the other hand, grew in colonies that had rough edges thus the name R (rough) strain. The
R strain did not have the capsule and so was more prone to action by the immune system.

One common way of vaccine making during Griffith’s time required that you make use of parts
of the dead pathogen in order to confer immunity. This was the method Griffith decided to use
to make his vaccine. Figure 6.2 shows a schematic of how the experiment was done.

Figure 6.2. Schematic for

Frederick Griffith’s experi-
ment. When cultures of the
non-pathogenic strain were
mixed with heat-killed cells of
the pathogenic strain, the
mixture was able to cause the
disease. He concluded that
there was something in the
pathogenic cells that trans-
formed the non-pathogenic
cells into pathogenic cells.
When the R strain of S. pneumoniae was inoculated into mice, the mouse did not get sick and
lived. When the S strain was inoculated, the mouse got sick and died. This showed that the S
strain was the pathogenic strain. The S strain was then inactivated using heat and inoculated
into mice. The mice did not get sick and lived. The last part was when Griffith killed the S
bacteria using heat and then mixed them with live R strain. He inoculated this resulting mixture
and the mouse got sick and died. When he inoculated samples from these mice, they showed a
combination of both live R and S cells. Some of the living R cells had become pathogenic. In
addition, all the R cells that that became pathogenic remained pathogenic in the following
generation. Griffith concluded that there was some chemical component present in the dead
pathogenic cells that transformed the non-pathogenic cells. He called this the transforming
principle.

This transformation and acquisition of the new trait was also hereditary and could be passed
on. Unfortunately, Griffith had no idea what the transforming principle could be. He called
what he observed as transformation. The modern definition of transformation is the change
in genotype (gene sequence) and phenotype (observed traits) due to assimilation of DNA by a
cell. Back then of course, they still had no idea that DNA was actually the chemical substance
Griffith had been looking for.

Griffith’s findings became the start of a grand treasure hunt. So many of them tried to look for
the chemical substance that caused the transformation that Griffith observed. It was in 1944
that Oswald Avery and his colleagues Maclyn McCarty and Colin Macleod were able to show
that DNA was the transforming molecule people had been searching for.

The experiment Avery did focused on the three main candidates for the transforming substance:
DNA, RNA and proteins. Cultures of S cells were killed using heat. Cell lysates from the heat-
killed S cells were collected. All these three candidate substances were found in the cell lysate
of the heat-killed bacteria. The cell lysates were divided and separately treated with proteases,
RNases and DNases leading to lysates which lacked proteins, RNA and DNA respectively.
The different lysates where added to cultures of non-pathogenic R cells. The cultures with the
lysates treated with proteases and RNases still brought about transformation. Even without
proteins and RNAs, transformation occurred. This means that the transforming principle was
not proteins or RNA. The culture mixed with the cell lysate treated with DNases did not show
transformation. The absence of DNA meant that it was the transforming principle Griffith had
found long ago. There were still some people who doubted these results, however. They argued
that maybe Avery’s experiments were not able to destroy all the RNA and protein in the sample.
This means their results weren’t believable. Because they knew so little about DNA, they had
difficulty believing DNA had such a role.
 Figure 6.3. Avery, McCarty, Macleod experiment. The three candidates for the Griffith’s
transforming principle were DNA, RNA and proteins. In order to fully identify it, Avery’s experiment
made use of cell lysates from cells treated with enzymes. The lysate without DNA was the one that
did not transform the R cells suggesting that DNA was needed for the transformation process.
(Source: O’Connor, 2008. Nature Education)

It was actually research done on bacteriophages that added additional evidence to show DNA’s
role as the genetic material. Bacteriophages are viruses that infect bacteria. Viruses are simple
structures composed of a protein coat enclosing their genetic material (either DNA or RNA).
Bacteriophages reproduce by infecting cells and using the cell machinery to produce the
materials that are needed to make more virus particles.

Figure 6.4. Representative images of bacteriophages. (A) Diagram of a phage

structure. (B) Electron micrograph of T4 phage. Phages have similar structures.
Their genetic material is enclosed in the head while the tail allows it to attach to
outer membranes of microbes. (Source: Hyman et al. (2002). PNAS, 99:8488-93)

In 1952, Alfred Hershey and Martha Chase performed experiments that showed DNA was the
genetic material of a phage known as T2. T2 is one of the bacteriophages that infect Escherichia
coli. T2 was already known to be made up protein and DNA. T2 could infect E. coli and turn
them into factories that made new T2 phages. It was composed of DNA and protein but which
of the two was able to change the normal E. coli into the virus-making factories upon infection?

At this point, people were really only debating whether proteins or DNA was the genetic
material. Hershey and Chase used a method where only protein and DNA would be present.
They designed their experiment such that a radioactive isotope of sulphur was used to label
proteins and then a radioactive isotope of phosphorus was used to label DNA. Separate samples
of non-radioactive E. coli were infected with the protein-labelled and DNA-labelled phages.

Phages attach themselves to the outer membranes of their host during their infection cycle.
Hershey and Chase used an ordinary blender to process the cultures. The mechanical force
added by the blender forced the phages to separate from the bacteria. Using centrifugation, they
pelleted the bacterial cells while leaving the phage protein coats suspended in the supernatant.
They tested for the radioactive labels and the supernatant showed the marker for the protein
while the marker for DNA was found in the pellet. This suggested that the labelled DNA had
entered the cell and was pelleted along with it. When they cultured these bacterial cells that
took up the labelled DNA molecules, they became virus-producing factories as well. In
addition, some of the DNA in the newly produced viruses were also labelled by radioactive
phosphorous, indicating that the original DNA that had entered the cells was incorporated into
the viral particles that were made by the transformed cells. Their experiments proved that at
least for viruses, DNA was their genetic material.

Figure 6.5. Hershey and Chase blender experiment. (A) Martha Chase and Alfred Hershey
(Source: Cold Spring Harbor Laboratory Archives). (B) Schematic for the Hershey and Chase
blender experiment.

Additional information in support of DNA being the genetic material came from Erwin
Chargaff. Chargaff studied the composition of DNA from several species. In 1950, Chargaff
reported that the base composition of DNA varies from one species to another. One of the
arguments for DNA not being the genetic material was how simple it was compared to proteins.
Chargaff challenged this by showing that different organisms had different amounts of the
nitrogenous bases indicating diversity in the DNA composition of different species. This
display of diversity added a good argument to DNA being the genetic material. Chargaff also
noticed something about the ratios of nitrogenous bases. The number of adenines roughly
equalled the number of thymines while the number of cytosines roughly equalled the number
of guanines. For any given species, A=T and C=G. This eventually became known as
Chargaff’s rules. The reason for this observation was not fully understood until the structure
of the DNA double-helix was discovered just a few years later.

Elucidation of DNA structure

Having shown that DNA was indeed the molecule of heredity, scientists then came about trying
to determine its structure. What structure did DNA form that made it possible to pass on
hereditary information? Although the basic monomers of DNA had been identified in the
1940s, the way they came together and formed higher order structures was still unknown. The
three important scientists trying to discover the three-dimensional structure of DNA were Linus
Pauling at the California Institute of Technology and Maurice Wilkins and Rosalind Franklin
at King’s College in London. Linus Pauling was already quite famous because of the research
he had been doing with proteins. However, it were actually relatively unknown scientists who
were able to solve the puzzle of the DNA structure.
 Figure 6.6. Maurice Wilkins, Rosalind Franklin and their DNA diffraction pattern. One of the
most important pieces of information that Watson and Crick used to construct their DNA model
was from Maurice Wilkin’s (A) laboratory. Rosalind Franklin (B) had been studying x-ray
crystallography of nucleic acids when she had made what is undoubtedly the most recognized x-
ray diffraction pattern to biologists (C). (Source: A,B: Encyclopedia Britannica, C: Rosalind
Franklin, King’s College London)

It all started when an American, James Watson, travelled all the way to Cambridge and met the
Englishman Francis Crick. Crick had been working on identifying protein structure using a
technique known as x-ray crystallography. This was a technique that crystallized proteins and
then bombarded them with x-rays. The x-rays would deflect (the technical term would be
diffract) off of the crystallized structures forming spots and smudges. These spots and smudges
would be analysed by crystallographers. These people use mathematical equations to determine
the structure of the sample. As the technique was improved and developed, it became such that
simple diffraction patterns already represented simple structures. For example, globular
proteins would create a specific kind of diffraction pattern. When these two met, the race to
determine the structure of DNA was well under way. Different laboratories all over the world
were trying to show the structure of DNA and how it is able to pass on hereditary information
through generations. Watson and Crick formed an easy partnership and set out to join the race
to discover the structure of DNA.

Figure 6.7. Watson, Crick and the structure of DNA. James Watson (A) and Francis Crick (B)
were the first to report the structure of DNA. They developed the structure of DNA and created a
model that is preserved to this day in Cambridge (C). (Source: A,B: Encyclopedia Britannica, C: A.
Barrington Brown)
One would think that Watson and Crick did exhaustive experiments to discover the structure.
They didn’t. Instead what they did was to actually to combine all the scattered clues that have
been reported about DNA by other researchers. They were able to listen in on Rosalind Franklin
presenting the results of her research. Franklin was a part of Maurice Wilkins’ laboratory and
she was doing x-ray crystallography of aqueous DNA molecules. Franklin presented her
diffraction pattern, an image so many molecular biologists and molecular geneticists know by
heart, and it helped Watson and Crick begin visualizing their ideas. Using unpublished data
from Rosalind Franklin, they were able to deduce the structure of DNA that we know today.
With the help of Chargaff’s rules, they were able to further perfect their model. In 1953, they
published their ideas in a 1 page article in the magazine Nature. Once the Watson-Crick model
was proposed, scientists then moved on to study possible modes of replication and information
encoding. The many things DNA can do is due largely in part to how beautifully efficient and
stable its structure is.

The Structure of DNA

DNA is a type of nucleic acid found in the cell. Cells make use of both DNA and RNA during
the gene expression process. A nucleic acid is composed of several repeating units of
nucleotides. An example of a nucleotide is found in Figure 6.8.A. Nucleotides are composed
of a phosphate group, a sugar group and a nitrogenous base. The main difference between RNA
and DNA is in the sugar they contain. They both contain a pentose sugar but RNA uses ribose
while DNA uses deoxyribose (Figure 6.8.B). Another difference between DNA and RNA is in
the nitrogenous bases they use. RNA uses the adenine (A), guanine (G), uracil (U) and cytosine
(C) while DNA uses adenine, guanine, thymine (T) and cytosine (Figure 6.8.C). The
nucleotides are linked together in a chain through the pentose and phosphate groups which
form a backbone of alternating sugar-phosphate-sugar-phosphate for one strand. You can
imagine the sugar-phosphate backbone to be the links in a charm bracelet and the nucleotides
to be the charms attached to them.

RNA is a single stranded polymer while DNA takes up a double-stranded helix form. The
hydrogen bonds that form between the nitrogenous bases keep the two strands of DNA together
in the double-helix. There are three hydrogen bonds that form between an A-T pair and 3
hydrogen bonds that form between a G-C pair. Try to go back to the Chargaff’s rules that was
mentioned before. The amount of A is equal to the amount of T while the amount of G is equal
to the amount of C. This means that in the DNA double-helix, A only binds with T and C only
binds with G.

The way the sugar-phosphate backbone is linked creates a chemical polarity or directionality
in the strands. The bonds between nucleotides are called phosphodiester bonds. The 5’ end has
a free hydroxyl group on the 5’ position of the deoxyribose molecule while the 3’ end has a
free hydroxyl group on the 3’ position of the deoxyribose. This observed directionality, as well
as the observation that synthesis proceeds in a 5’ to 3’ direction, gave rise to the eventual
convention that DNA sequences are written and read in the 5’ to 3’ direction. For example, a
sequence written as TAGAT is automatically understood as (5’)TAGAT(3’). When the
sequence is from 3’ to 5’ then it is a must to label it as so. One characteristic of DNA is that
one strand is in the 5’ to 3’ direction and another strand is in the 3’ to 5’ direction. We call
these antiparallel strands.
 Figure 6.8. Nucleotide structure. (A) Example of a nucleotide showing phosphate group (pink),
pentose sugar (black) and nitrogenous base (blue). (B) Ribose is found in RNA while deoxyribose
is found in DNA. (C) There are five nitrogenous bases associated with nucleic acids, two purines
(A and G) and 3 pyrimidines (U, T and C). (Source: Lodish et al., 2003)

DNA is structured such that the nitrogenous bases make up the inside of the double-helix with
the sugar-phosphate backbone making up the outside. The phosphate groups are found at the
outermost areas. When extended, the components of the double-helix resemble a rope ladder.
Again, the basic rule is that purines hydrogen bond with pyrimidine bases, that is, A binds with
T and C binds with G. This rule allows the nitrogenous bases to be packed inside the double-
helix in the most energetically favourable arrangement. The end result is that each base pair is
of similar width inside the double-helix, with the sugar phosphate backbone winding around
the nitrogenous bases in order to form a helical structure (Figure 6.9.A).

The DNA double-helix has distinct features like a major and minor groove. The double-helix
completes one full turn with every ten base pairs. The pitch of the helix is the length it takes
for the helix to complete one full revolution. For DNA, the value is around 3.32 nm (Figure
6.9.B). The base pairs can only fit together perfectly if the strands are antiparallel. This means
that one strand must be in the 5’ to 3’ direction while the other strand must be in the 3’ to 5’
direction. The result of this combination of antiparallel strands is that each strand of DNA is
completely complementary to the nucleotide sequence of the partner strand.

If you are confused with the term ‘complementary’, think back on base pairing rules.
Remember that purines pair only with pyrimidines. A pairs with T and C pairs with G. This
specific pairing is what we call complementary base pairing. A is complementary to T and
C is complementary to G. If we say two sequences are complementary, the other strand is
simply the sequence of first strand but the letters A will be replaced for T and vice versa and
the letter for C will be replaced with G and vice versa. For example, take the sequence TAGC.
If we apply complementary base pairing, the complementary sequence would be ATCG.
Simply replace the base with the base it would normally pair with. This complementary base
pairing allows information to be kept in DNA. Even if one strand of the DNA gets damaged,
the cell uses the complementary strand as a template to regenerate the lost section of DNA. The
complementary strand or the 3’ to 5’ strand, contains the same information as the 5’ to 3’ strand
but simply stated in terms of the sense strand’s complement.

Figure 6.9. Schematic diagram for arrangement of nucleotides in the DNA double-helix. (A)
Antiparallel strands of DNA make up the DNA double-helix. (B) The DNA double-helix contains a
major and minor groove. One turn of the double- helix contains 10 base pairs. (Source: Weaver
2012)

The DNA strand exists in many forms. The form is takes depends on the environment. There
are three main forms of the double-helix: An A form, a B form and a Z form (Figure 6.10). The
B form of the double helix is the form closest to how DNA is found physiologically. It exists
in relatively high humidity (around 92%) and is the hydrated form of DNA. It has a pitch of
3.32 nm and around 10 base pairs per turn. The A form exists at a lower humidity (around 75%)
and is considered the dehydrated form of DNA. It is more compact with a pitch of 2.46 nm and
about 10.7 base pairs per turn. Both A and B forms are right-handed helices. A third form, the
Z form, is not something that occurs naturally in nature. It’s the helix that forms when polyCG
sequences are synthesized. It is longer than the A and B forms. It is a left-handed helix with a
pitch of 4.56 nm and 12 base pairs per turn.
 Figure 6.10. Space filling
models of different DNA
forms. (A) A form, (B) B form,
(C) Z form.
(Source: Weaver 2012)

DNA and its role in heredity

Heredity is the passing of physical or mental characteristics through the genes from one
generation to another. DNA plays an important role in heredity. It contains the genes that carry
all biological information. DNA must also be passed on accurately to the next generation every
time a cell divides to form two daughter cells. The most important function of DNA is to carry
all the genes of an organism.

A human cell has 46 chromosomes found in its nucleus. If you were to collect all the DNA in
the nucleus and place them end to end, the resulting DNA strand would measure approximately
2 meters. Imagine having to store 2 meters worth of DNA into a nucleus that is around 6
micrometers in diameter. This would be similar to fitting 40 km of thread into a tennis ball.
How does the cell do this? The only way DNA can be stored in the nucleus is by packing them
tightly using several coils and loops, eventually forming a highly organized mass of DNA we
see as chromosomes.

In eukaryotes, DNA in the nucleus is split into different chromosomes. Each chromosome
consists of one linear DNA molecule. It associates with different proteins in order to maintain
a highly ordered structure. We call the protein-DNA complex chromatin and we can easily
stain the chromatin in cells and view it under the microscope. Indeed, the word for chromatin
was derived from the Greek word chroma because it could be easily stained. Bacteria have a
single DNA molecule that carries their DNA. It’s often circular unlike the linear DNA
molecules we see in eukaryotes. This is generally referred to as the bacterial chromosome
though they are different from the chromosomes in eukaryotes. This DNA is also associated
with proteins.

All human cells (except germ cells and highly specialized cell like red blood cells) contain 2
sets of chromosomes: 22 pairs of autosomes and 1 pair of sex chromosomes. Each set contains
2 copies of each chromosome except for sex chromosomes where we have an XY for males
and XX for females. We get 1 set of chromosomes from our mother (maternal chromosomes)
and one set from our father (paternal chromosomes). As mentioned before, these similar
chromosomes, of which one is paternal and 1 is maternal, we call homologous chromosomes.
Homologous chromosomes have the same genes in the same loci. The only nonhomologous
chromosome pairs are the sex chromosomes. In males, the Y chromosome is inherited from the
father and an X chromosome from the mother while in females they both inherit one X
chromosome from each parent. Once again, in total human cells contain 46 chromosomes, 22
pairs common to both males and females plus two sex chromosomes which differ based on sex.

Figure 6.11. Karyogram for a somatic cell of a human male. Unduplicated chromosomes are
grouped with their homolog and are arranged from autosome 1 to 22 followed by the pair of sex
chromosomes. Males have an X and a Y chromosome while females have two X chromosomes.
(Source: Cold Spring Harbor Laboratories)

Packing DNA into chromosomes

Given that DNA contains all the information an organisms needs throughout its lifetime, it’s
no surprise that a lot of DNA would be needed by different organisms. In humans, the cell is
able to compress millions of base pairs into different chromosomes by associating with proteins
and then this DNA-protein complex continuously coils and loops. The most condensed form
of the chromosome is the form we see during mitosis/meiosis. Just as with proteins, nucleic
acids also have levels to their structure. The details of the levels of nucleic acids are listed
below. The structure of nucleic acids is very important in order to perform their required
functions.
 Levels of Nucleic Acid Structure

1. Primary structure

- Refers to the nucleotide sequence of the nucleic acid. The nucleotide

sequence is represented using the 4 letters of the 4 nitrogenous bases that
are found in the nucleic acid.

2. Secondary structure

- Refers to structures that form due to hydrogen bonding between nitrogenous

bases. The simplest example is the double-helix of DNA. RNAs also form
different kinds of structures by binding to complementary sections in the
same RNA molecule.

3. Tertiary structure

- Refers to the positions of the atoms in space. Space-filling models which

show all positions of all atoms in the molecule are important things we can
make use of to understand the structure. Here we also note important details
like the handedness of the double-helix (whether right handed or left
handed), the pitch and the presence of the minor and major grooves are also
some features from the DNA double-helix that are covered by this.

4. Quaternary structure

- Refers to the highest, most complex structures that can be formed, usually
by association with other biomolecules. Examples of this are chromatids
which are DNA-protein complexes and ribosomes which are RNA-protein
complexes.

Nucleosomes are the basic unit of chromosome structure

Miescher had demonstrated long ago that the material found in the cell’s nucleus was a complex
of proteins and DNA. There are two classes of proteins that bind to DNA in the chromosomes:
the histone proteins and the nonhistone proteins. Both types of proteins associate with the
nuclear DNA in eukaryotic cells to form chromatin. The amount of histones in the nucleus is
almost equal to the amount of DNA. Histones are responsible for the first level in DNA
packaging. When histones associate with DNA, they form what we know as nucleosomes.

Nucleosomes were first described in 1974. When cells in interphase of the cell cycle were
gently broken and their contents analysed using an electron microscope, they found that
chromatin was in the form of a fiber that was around 30 nm in diameter (Figure 6.12.A). When
the cell lysates were further treated, they were able to completely separate the chromosome
into long strands of DNA and protein. The strands they observed using TEM looked like beads
on a string (Figure 6.12.C). The beads were the nucleosomes and the string was the DNA
strand. Each nucleosome is composed of 8 histone proteins. The core of the nucleosome
contains 2 molecules each of the histone H2A, H2B, H3 and H4. The double-stranded DNA
coils around this histone octamer to form the nucleosomes (Figure 6.13). The nucleosome is
separated from the next nucleosome by a linker DNA which varies in length.

Figure 4.12. Chromatin is a made up of a complex of DNA and proteins. (A) Chromatin under
TEM. Scale bar: 200 nm. (B) Chromatin condensed into chromosomes. Scale bar: 100 nm. (C)
Nucleosomes appearing as “beads on a string”. Scale bar: 500 nm. (D) TEM micrograph of
individual nucleosomes without linker DNA. Scale Bar: 500 nm. (Source: Weaver 2012)

The beads-on-a-string fiber consists of one DNA molecule coiling around core histones. Some
refer to this as a 10 nm fiber. In the cell, chromatin rarely looks like this 10 nm fiber. DNA in
this form is easily damaged, either by mechanical stress or by action of enzymes. The chromatin
is actually further coiled to prevent access of otherwise damaging agents to the DNA. The
packaging of DNA starts with the nucleosomes. The nucleosomes are packed on top of each
other forming regular loops of highly condensed DNA. This is actually the 30 nm fiber of
chromatin that was initially seen in the cell lysate of initial experiments. The exact packing
mechanism of DNA is not well understood but there are several models scientists are looking
at. Figure 6.14 shows examples of models that have been proposed for the packing of the 30
nm fiber.

Figure 6.13. Crystal structure of the core particles of nucleosomes. (A) The core is composed
of 2 pairs of H2A (yellow), H2B (red), H3 (blue) and H4 (green). (B) DNA binds itself around the
core histones forming the nucleosomes. (Source: Weaver 2012)
It was suggested that longer strings of nucleosomes form a solenoid structure with intercalated
nucleosomes (Figure 6.14.B). The nucleosomes are able to stack tightly on in each other
because of the presence of another histone, H1. H1 is larger than each of the core histones. A
single H1 molecule binds to DNA and nucleosomes and changes how the DNA exits out of the
nucleosome. The details are not perfectly understood but association of H1 with the
nucleosomes seems vital for compacting nucleosomal DNA. H1 is not evolutionarily conserved
meaning the sequence and structure of the particular protein is not conserved between species.
This means that different species have different versions of the H1 protein. This leads to
differences in how their DNA is packed. A zig-zag model of the 30 nm fiber packing has also
been suggested (Figure 6.14.D). Another model involving the formation of a structure termed
as a boustrophedon was also proposed (Figure 6.14.E).

Figure 6.14. Models of chromatin organization. (A) 10 nm fibre. (B) Side-view of a 30 nm fibre
or solenoid. (C) Top-down view of the solenoid. (D) Zig-zag model of the 30 nm fibre. (E)
Interdigitation of two 10 nm fibres (blue against green) forming a boustrophedon. Numbered circles
are nucleosomes in an array; red arrow follows the path of the DNA; blue arrow represents a gene
promoter. (Source: Quenet et al., 2012)

Figure 6.15. Radial loop models of

chromatin folding. (A) Partial loop model
showing loops attached to a central scaffold.
(B) The loops cover all areas of the central
scaffold allowing them to form a more dense
structure. (Source: Weaver 2012).
After forming into the 30 nm fiber, the DNA is further packaged. One type of folding model is
presented in Figure 6.15. Sedimentation and electron microscopy studies of chromatin have
shown that the 30 nm fiber seems to form radial loops that stretch for around 35-85 kb (kilobase
pairs) of DNA.

Figure 6.16. Overview of DNA packaging. (Source: David Sadava, Nature)

A summary of DNA packaging is seen in Figure 6.16. The DNA double-helix is first coiled
around core histone proteins forming nucleosomes. The resulting 10 nm fiber is further coiled,
whether is a solenoid form or zig-zag form, in order to form the 30 nm fiber. The 30 nm fiber
forms radial loops further creating condensed DNA complexes. These loops get looped even
further eventually forming the chromosomes that we see during cell division.
Why is DNA the ideal molecule for heredity?
There are three points we can consider when we think of DNA and its role as the molecule of
heredity.

1. DNA is a very stable molecule.

Compared to other polymers, DNA is very stable. Proteins denature and break down
easily from heat, acid, pH, etcetera. DNA’s structure is such that the nitrogen bases
are safely tucked inside the sugar-phosphate backbone. The nitrogenous bases are
held together by hydrogen bonds. When exposed to heat, usually around 95oC or
higher, instead of breaking apart, the hydrogen bonds between the bases are broken
apart leading to the strands separating in a process we call melting. When DNA is
denatured, it separates into 2 strands with each strand still in perfect condition. If
you bring the temperature down, around 60oC to 70oC, the hydrogen bonds reform
between the bases and the DNA strands join together to reform the double-helix.
This process we call annealing of the two strands. This does not damage the
information contained in the DNA molecule. When proteins denature, covalent
bonds are broken and the structure of the protein is changed. Going back to their
original state before denaturation is energetically unfavorable. If we think of how
the genetic material has to be passed on continuously through generations, it would
be best if we had a stable, hard to damage molecule. DNA fits that description
perfectly.

2. DNA is able to store a lot of information.

Before anything was known about how DNA was able to code for proteins, proteins
were originally thought to be able to store more information. DNA had four
nucleotides compared to the 20 amino acids that made up proteins. When we think
of all the possible permutations, you get more possible molecules with 20
monomers compared to 4 monomers. The moment it was shown that DNA could
code for all possible amino acids, it changed everything. It no longer mattered that
there were 20 amino acids and only 4 deoxyribonucleotides. The 4
deoxyribonucleotides were enough to produce all the 20 amino acids needed for
proteins.

Another extra feature DNA had was that if one strand contained biological
information, the other strand was the same as the first strand but simply its
complement. This means that the first strand contained the same information as the
second strand albeit stated differently. When one part of the DNA is damaged, DNA
repair mechanisms make use of the other strand in order to fill in the information
that was removed or damaged. Should you lose a section of the chromosome, to
some extent, a cell can still fix the problem because you have another copy of that
segment in the chromosome’s homologous pair. This means that while DNA stored
information, it also had the means to protect ensure that the sequence in DNA
remains intact.
 If we apply this to how a genetic material works, all we have to do is think about
how many processes DNA has to go through during cell division or during
development. The DNA is mechanically moved around during cell division, DNA
is constantly wound and unwound during cell division as well. When cells are
growing, DNA is opened up in order for enzymes to enter and allow expression of
genes. With all these things that DNA has to go through, there is a chance for it to
get damaged as it is used and passed down through generations. Fortunately, DNA
has a means of protecting sequences as well as resynthesizing DNA sequences in
case they were damaged or lost.

3. DNA is able to replicate itself with very high fidelity.

As we have seen, DNA is doubled during the S phase of the cell cycle. This ensures
that the daughter cells all get a complete copy of all the nuclear DNA during cell
division. No other molecule is capable of replicating itself to the degree that DNA
does. The replication occurs with high fidelity and very minimal errors. There are
even systems in place that double check if the correct nucleotides are incorporated
or if there are unwanted covalent bonds that formed within the strand. These errors
are corrected before the cell even goes into the mitotic phase of the cell cycle. If we
talk of being passed down to the next generation of cells, DNA truly exhibits the
best characteristics for this.