NUCLEIC ACID STRUCTURE

DNA/RNA structure
• Structure of DNA can be considered at 3 hierarchical levels:

– the primary structure of DNA is its nucleotide sequence

– the secondary structure is the double-stranded helix

– the tertiary structure refers to higher-order folding that

allows DNA to be packed into the confined space of a cell .
complex packing arrangements of double-stranded DNA in
chromosomes
 NUCLEIC ACID STRUCTURE
DNA structure
• Primary structure
– The primary structure of DNA consists of a string of
nucleotides joined together by
3-5, phosphodiester(COVALENT) linkages not hydrogen bond.
– DNA is typically a very long molecule and is therefore termed
a macromolecule.
• Within 1 chromosome DNA is several cm long, longer than a cell
 NUCLEIC ACID STRUCTURE
DNA structure
• Primary structure
– Polynucleotide
• 5′-phosphate group of one nucleotide join with the 3′-
carbon atom of the next nucleotide. These bonds are
called phosphodiester linkages.
 NUCLEIC ACID STRUCTURE
DNA structure
• Primary structure
– How does a phosphodiester bond form?
 NUCLEIC ACID STRUCTURE
DNA structure
• Primary structure
– Polynucleotide
• An important characteristic of the
polynucleotide strand is its direction, or polarity.
• 5’ end = one end of the strand, a free phosphate
group is attached to the 5′-carbon atom of the
sugar in the nucleotide.
• 3’end = other end of the strand, referred to as
the 3′ end, has a free OH group attached to the
3′-carbon atom of the sugar.
 NUCLEIC ACID STRUCTURE
DNA structure
• Secondary structure
– The double helix
– sugar–phosphate linkages are on the outside of
the helix, and the bases are stacked in the
interior of the molecule.
 NUCLEIC ACID STRUCTURE
DNA structure
• Secondary structure
– The two polynucleotide strands run
in opposite directions—they are
antiparallel, which means that the 5′
end of one strand is opposite the 3′
end of the other strand.
 NUCLEIC ACID STRUCTURE
DNA structure
• Secondary structure
– The strands are held together by two types of molecular
forces:
• Hydrogen bonds link the bases on opposite strands
• Phosphodiester bonds that connect the sugar and phosphate
groups of adjoining nucleotides on the same strand.
 NUCLEIC ACID STRUCTURE
DNA structure
• Secondary structure
– Hydrogen bonds
• The nature of the hydrogen bond imposes a
limitation on the types of bases that can pair.
• Adenine normally pairs only with thymine through two hydrogen
bonds, and cytosine normally pairs only with guanine through three
hydrogen bonds
 NUCLEIC ACID STRUCTURE
DNA structure
• Secondary structure
– Hydrogen bonds
• Because three hydrogen bonds form between C and G and only two
hydrogen bonds form between A and T, C–G pairing is
stronger than A–T pairing.
• .
 NUCLEIC ACID STRUCTURE
DNA structure
• Secondary structure
 NUCLEIC ACID STRUCTURE
DNA structure
• Secondary structure
– The offset pairing of the two strands creates a major groove and
minor groove on the surface of the duplex.
 NUCLEIC ACID STRUCTURE
DNA structure
• DNA has 3 Different secondary
structure
– 3D shape of DNA vary depending
on the condition or the base
sequence itself.
 NUCLEIC ACID STRUCTURE
DNA structure
– B-DNA
• The 3D structure of DNA described by Watson and Crick is the B-
DNA structure.
• B-DNA = alpha helix = right-handed = clockwise spiral
• Condition = plenty of water surrounds the molecule , no unusual
base sequence in the DNA (conditions that are likely to be present
in cells)
• most stable configuration of all three (under physiological
conditions)
• most evidence suggests that it is the predominate structure in the
cell.
 NUCLEIC ACID STRUCTURE
DNA structure
• Different secondary structure
– A-DNA

• Like B-DNA, A-DNA is an alpha (right-handed) helix , but

shorter and wider than B-DNA and its bases are tilted away
from the main axis of the molecule.

• exists if less water is present.

• There is little evidence that A-DNA exists under physiological

conditions.
 NUCLEIC ACID STRUCTURE
DNA structure
• Different secondary structure
– Z-DNA
• radically different
• left-handed helix.
• sugar–phosphate backbone zigzags back and forth, giving rise to its name.
• It result if the molecule contains particular base sequences, such as
stretches of alternating C and G nucleotides.
• Recently, researchers have found that Z-DNA-specific antibodies bind to
regions of the DNA that are being transcribed into RNA, suggesting that
Z-DNA may play some role in gene expression.
 NUCLEIC ACID STRUCTURE
DNA structure
• Different secondary structure (B-, A- and Z-form )
 NUCLEIC ACID STRUCTURE
• Tertiary structure: Bacterial chromosome:
– Nucleoid
• DNA of a bacterial (such as Escherichia coli), = circular double-
stranded molecule ,also called bacterial chromosome.
• Region where circular DNA packaged = Nucleoid
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
– Nucleoid
• In E. coli, this DNA molecule contains 4.6 million base pairs
(bp).

• A single E. coli, cell contains almost 100 times as much DNA as

a bacteriophage, λ particle.
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:

Circular DNA to Loop DNA to Super coil DNA

 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
– DNA-binding proteins
• looped DNA domains further (supercoiling) using DNA-
binding proteins.

• most abundant of these are protein HU, a small basic

(positively charged) dimeric protein, which binds DNA
nonspecifically by the wrapping of the DNA around the
protein,
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
– DNA-binding proteins
• H-NS (also called H1), a monomeric neutral protein, which
also binds DNA nonspecifically in terms of sequence, but
which seems to have a preference for regions of DNA which
are intrinsically bent region .

• These proteins are sometimes known as histone-like proteins,

and have the effect of compacting the DNA, which is essential
for the packaging of the DNA into the nucleoid, and of
stabilizing and constraining the supercoiling of the
chromosome.
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial plasmid:
– Plasmid DNA
• many bacteria contain one or more small circular DNA
molecules that are free in the cytosol.

• These extrachromosomal self-replicating elements are called

plasmids.

• Most plasmids are only a few thousand base pairs long, but
some contain more than 10,000 bp.
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial plasmid:
– Plasmid DNA
• Plasmids have been found in yeast and other fungi as well as
in bacteria.

• Some plasmids carry genes that are useful to the host

bacterium. For example, plasmid genes make a host bacterium
resistant to antibacterial agents.
 Packaging and tertiary structure
• Eukaryotic DNA can be thousands of times as much as in a
prokaryotic genome, and is made up of a number of discrete bodies
called chromosomes (46 in humans).

• the level of DNA packing changes in the course of cell cycle :

chromosomes progress from a highly packed state to a state of
extreme condensation.

• DNA packing also changes locally in replication and

transcription, when the two nucleotide strands must unwind so
that particular base sequences are exposed.

• packing of eukaryotic DNA (its tertiary chromosomal structure) is

not static but changes regularly in response to cellular processes.
Tertiary structure: Eukaryotic chromosome:
– Chromatin = DNA + Protein in eukaryotic cell

2 Types of chromatin
– Euchromatin –

1. it undergoes the normal process of condensation and decondensation in the

cell cycle.

2. constitutes the majority of the chromosomal material and is where most

transcription takes place.

– Heterochromatin –

1. remains in a highly condensed state throughout the cell cycle, even during
interphase.

2. Found at the centromeres and telomeres.

3. It lacks crossing over, transcription and replication late in S phage

– DNA-binding protein

• Most protein in eukaryotic chromatin consists of histones.

• There are five families: H2A, H2B, H3 and H4, known as the
core histones, and H1.
• The core histones are small proteins, with masses between 10
and 20 kDa, and H1 histones are a little larger at around 23
kDa.

H1 histones differs from other due to (larger size, more

variation in sequences both between and within species
than in the other classes).
• Tertiary structure: Eukaryotic chromosome:
– DNA-binding protein
• nonhistone proteins (NHP) are also found but in less
abundance
• One molecule of histone H1 binds to the nucleosome, and acts
to stabilize the point at which the DNA enters and leaves the
nucleosome core.
• Tertiary structure: Eukaryotic chromosome:
– Nucleosomes
• The first level of packaging involves the binding of the
chromosomal DNA to histones.
• When chromosomes are gently ‘decondensed’, they have the
appearance under the electron microscope of ‘beads on a
string’.

= DNA found btn 2 nucleosome

• Tertiary structure: Eukaryotic chromosome:
– Nucleosomes
• nucleosomes consist of DNA complexed with histones.
• The ‘string’ is linear double-stranded DNA between adjacent
nucleosomes and is called linker DNA.
• Tertiary structure: Eukaryotic chromosome:
– Nucleosomes
• Each nucleosome core particle contains:
• a double-stranded DNA fragment 146 bp long, and that bound to a
complex of eight histones, the histone octamer.
• The histone octamer is consists of two molecules each of histones H2A,
H2B, H3 and H4.
• Tertiary structure: Eukaryotic chromosome:
– Nucleosomes

Nucleosomes showing core histone proteins Nucleosomes showing linker histones

and nonhistone proteins

Octomer (H2A H2B H3 H4 x 2) …. H1…. Non-histone proteins

– Chromatosomes

• A nucleosome core plus H1 is known

as a chromatosome.
 DNA structure

• Tertiary structure: Eukaryotic chromosome:

– Higher order chromatin structure: 30 nm fiber

• When chromatin is in a condensed form, adjacent

nucleosomes are not separated by space equal to the length of
the linker DNA;

• rather, nucleosomes fold on themselves to form a dense,

tightly packed structure that makes up a fiber with a diameter
of about 30 nm[=
– Higher order chromatin structure: 30 nm fiber

 2 different models have been proposed for the 30-nm fiber:

1. a solenoid model, in which a linear array of nucleosomes are coiled,

and

2. a helix model, in which nucleosomes are arranged in a zigzag ribbon

that twists or supercoils. Recent evidence supports the helix model
• Tertiary structure: Eukaryotic chromosome:

– Higher order chromatin structure: 30 nm fiber

• next-higher level of chromatin structure is a series of

loops(loop DNA) of 30-nm fibers, each anchored at its base by
proteins in the nuclear scaffold.

• On average, each loop encompasses some 20,000 to 100,000

bp of DNA and is about 300 nm in length, but the individual
loops vary considerably.
 Selonoid => loop => 250nm fibre => helical coiling =>chromatid

• Tertiary structure: Eukaryotic chromosome:

– Higher order chromatin structure: 30 nm fiber

• The 300-nm loops are packed and folded to produce a 250-nm-

wide fiber.

• Tight helical coiling of the 250-nm fiber, in turn,

produces the structure that appears in metaphase—
individual chromatids approximately 700 nm in width.
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Eukaryotic chromosome:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Eukaryotic chromosome:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Eukaryotic chromosome:
 properties of a geometric object that are preserved under
DNA topology: continuous deformations, such as stretching, twisting, crumpling
and bending

• Tertiary structure: DNA topology:

– In the simplest case of a linear DNA in
solution, untangling is possible due to
the free rotation of the ends of the DNA.

– However, for all natural DNAs, free end

rotation is either restricted or forbidden
altogether.
Illustrates this for the
– Consequently, untangling the two DNA imaginary case of a circular
strands becomes topologically DNA molecule where the
impossible. two strands are
tangled only once.
• Tertiary structure: DNA topology:
– A DNA segment constrained so that the free rotation of its ends is
impossible is called a topological domain.

– A canonical example of a topological domain is circular DNA, which is

typical of bacteria, mitochondria, chloroplasts, many viruses, etc.

– In this case, there are obviously no DNA ends at all, since both DNA
strands are covalently closed.

– Although eukaryotic chromosomes are linear overall, they consist of large

DNA loops firmly attached to the nuclear matrix.

– These loops represent topological domains, i.e. they are equivalent to

circular DNA topologically.
• Tertiary structure: DNA topology:
– The ends of linear DNA can also be affixed to the membrane, as has been
shown for some viruses, making this DNA topologically closed.

– Finally, a stretch of DNA situated between the two massive protein bodies
can also be considered a topological domain.

– For simplicity, the features of topological domains will be considered

below for circular DNAs, but the principles can be applied for all other
cases.
• Tertiary structure: DNA topology:
Examples of topological domains

Circular DNA,
chromosomal DNA loops,

linear DNA attached to the membrane,

linear DNA attached to protein aggregates.

• Tertiary structure: Supercoiling:
– Many DNA molecules in cells consist of closed-circular CCCdouble-
stranded DNA molecules, for example bacterial plasmids and
chromosomes and many viral DNA molecules.

– This means that the two complementary single strands are each joined
into circles, 5΄ to 3΄, and are twisted around one another by the helical
path of the DNA.

– The molecule has no free ends, and the two single strands are linked
together a number of times corresponding to the number of double-
helical turns in the molecule.

– This number is known as the linking number (Lk).

• Tertiary structure: Supercoiling:
– "Supercoiling“ means the coiling of a coil.

– DNA is coiled in the form of a double helix, with both strands of the DNA
coiling around an axis.

– The further coiling of that axis upon itself produces DNA supercoiling.

– When there is no net bending of the DNA axis upon itself, the DNA is said
to be in a relaxed state.
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Supercoiling:
• Tertiary structure: Supercoiling:
• Tertiary structure: Supercoiling:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Supercoiling:
Schematic representation of DNA
supercoiling. In this example, the
DNA in (a) is anchored between
two plates and given a twist as
noted by the arrows. A left-
handed twist (underwinding)
could produce either (b) fewer
turns or (c) a negative supercoil.
A right-handed twist
(overwinding) produces (d) more
turns or (e) a positive supercoil.
The structures shown in (b) and
(d) are unstable.
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Supercoiling:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Supercoiling:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Supercoiling:
 NUCLEIC ACID STRUCTURE
DNA structure
• Tertiary structure: Bacterial chromosome:
 NUCLEIC ACID STRUCTURE
DNA structure
• Viral Genome:

– Viruses - infectious particles – has nucleic acid surrounded

by a capsid of proteins

– For replication, viruses rely on their host cells i.e. the cells
they infect

– Most viruses exhibit a limited host range

– They typically infect only specific types of cells of one host

species
 DNA structure
• Viral Genome:
• Viral Genome:
– genetic material of virus= viral genome = viral
chromosome
– The genome can be of
• DNA or RNA
• – Single-stranded or double-stranded
• – Circular or linear
– Viral genomes vary in size from a few thousand to more
than a hundred thousand nucleotides
 NUCLEIC ACID STRUCTURE
DNA structure
• Viral Genome:
• Viral Genome:
– Complex viruses, such as T2 bacteriophages, undergo a
process called directed assembly
• Virus assembly requires proteins that are not part of the
mature virus itself
– The noncapsid proteins usually have two main functions:
– (1) Carry out the assembly process
• Scaffolding proteins that are not part of the mature virus
– (2) Act as proteases that cleave/split viral capsid proteins
• This yields smaller capsid proteins that assemble correctly
 RNA structure
• RNA is also a long polymer consisting of nucleotides
structure joined by 3,5-phosphodiester bonds.

• As with DNA, the nucleotide sequence of RNA is also

written as a base sequence in the 5→3 direction.

• The RNA serves as the template for protein synthesis.

• three major types of RNA participate in protein synthesis:

– ribosomal RNA (rRNA)

– transfer RNA (tRNA)

– messenger RNA (mRNA).