STBP1013 Fundamentals of Molecular Biology DNA helix

• The double helix is a description of the molecular shape

of a double-stranded DNA molecule
DNA Helix • In 1953, Francis Crick and James Watson first
described the molecular structure of DNA, which they
called a "double helix" in the journal Nature
• For this breakthrough discovery, Watson, Crick and
Maurice Wilkins won a Nobel Prize in Physiology or
Medicine, in 1962
• However, a crucial contribution that enabled this
discovery was made by Rosalind Franklin, who was
not acknowledged at that time
• After her death, Crick said that her contribution had
been critical

The double helix DNA and RNA structure and function

• The double helix describes the appearance of double- • The work of Mendel and others provided information
stranded DNA, which is composed of two linear about the nature of deoxyribonucleic acid (DNA)
strands that run opposite to each other, or anti- – genes occur on chromosomes
parallel, and twist together
– mutations in genes caused metabolic errors
• Each DNA strand within the double helix is a long,
– DNA is composed of nucleotides
linear molecule made of smaller units called
nucleotides that form a chain
• The chemical backbones of the double helix are made
up of sugar and phosphate molecules that are
connected by chemical bonds, known as sugar-
phosphate backbones
• The two helical strands are connected through
interactions between pairs of nucleotides, also
called base pairs
• Two types of base pairing occur: nucleotide A pairs
with T, and nucleotide C pairs with G

DNA structure Chargaff’s rules

• The research of several scientists helped determine the • In all organisms, the nucleotide bases are found in
structure of DNA specific proportions
– Erwin Chargaff • Chargaff’s rules are based on two observations
– Rosalind Franklin – The amount of A, C, G, and T varies from species
– Maurice Wilkins to species
– James Watson and Francis Crick – In each species, the amount of A is equal to T and
the amount of G is equal to C
• Equal proportions between two bases indicated that
the bases were paired in the structure of DNA
• The order in which these nucleotides occur differs,
producing great variability in the DNA

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 Franklin’s X-ray diffraction studies
• Rosalind Franklin used X-ray crystallography to study
the structure of DNA
• She took an X-ray of fibers present in a concentrated
solution of DNA
• The X-ray diffraction pattern suggested that DNA had
a helical shape
Wilkins’ X-ray diffraction studies
• Maurice Wilkins began using optical spectroscopy to
study DNA in the late 1940s
• He obtained the first clear crystalline X-ray
diffraction patterns from DNA fibres - the pattern
indicated that DNA was helical in structure
• He checked and verified Crick and Watson’s
hypothetical model
The Watson and Crick model
• Each DNA base (A, C, T or G) is attached to the
backbone and the bases are joined by hydrogen
bonds to form the ‘rungs’
• There are ten 'rungs' for each complete twist in the
DNA helix
• Working out the arrangement of bases in the DNA helix
could also have been assisted by Chargaff's rules
Franklin’s experiment
• One of the most important pieces
of evidence came from Franklin's
experiments of shining X-rays
through crystals of the DNA
molecule, and using
photographic film to record
where the scattered X-rays fall
• The shadows on the film can
be used to work out where the
dense molecules lie
• This technique is known as X-ray
crystallography
The Watson and Crick model
• Watson and Crick developed the definitive model of
DNA structure
• The sugar and phosphate groups are bonded in
alternating sequences to form the sides of a twisted
ladder; each 'upright' pole of the ladder is formed from a
backbone of alternating sugar and phosphate
groups
• Complementary base pairing occurs, meaning A only
bonds with T and G with C
DNA structure
• The function of DNA depends to a large extent on its
structure
• The discovery of the structure of DNA by James
Watson and Francis Crick is one of the most famous
scientific discoveries of all time
• The two scientists used evidence collected by others,
particularly Rosalind Franklin and Maurice Wilkins, to
deduce the shape of DNA
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 From structure to function
• The concept that DNA was made of a sequence of
paired bases along a chemical backbone allowed
Watson and Crick to draw two important conclusions
– First, the two sides or strands of DNA provide a
mechanism for copying - if both strands are copied
then the product is two identical 'daughter'
molecules
– Second, the order (sequence) of bases is the
digital code that carries the instructions for how a
cell should behave
• If we can understand the code, we are closer to
understanding how cells work
The Watson and Crick model
• The two single-strands are anti-parallel to each other
• Going from 5' to 3' of one strand means going from 3'
to 5' of the other strand
• It is the sequence of these four nucleobases along
the backbone that encodes biological information
• Under the genetic code, RNA strands are translated to
specify the sequence of amino acids within proteins
• These RNA strands are initially created using DNA
strands as a template in a process called transcription
Why does a DNA molecule consist of two strands?
• The nucleotide sequence contains the information
found in DNA
• The nucleotides connect the two strands through
hydrogen bonds
• Because each nucleotide has a unique complimentary
nucleotide, each strand contains all the information
required to synthesize a new DNA molecule
• The double stranded structure also makes the
molecule more stable
The Watson and Crick model
• Watson-Crick model of DNA - double helix
• The "double" in the double helix means that DNA is
found in a double-stranded form - two single-
stranded chains of DNA stuck to each other via
hydrogen bonding of the base pairs
• The "helix" in the double helix means that the entire
thing is wound up in a spiral
Why does a DNA molecule consist of two strands?
• The primary function of DNA is to store and transmit
genetic information
• To accomplish this function DNA must have two
properties
– it must be chemically stable so as to reduce the
possibility of damage
– DNA must also be capable of copying the
information it contains
• The two-stranded structure of DNA gives it both of
these properties
Why does a DNA molecule consist of two strands?
• DNA is well-suited for biological information storage
• The DNA backbone is resistant to cleavage, and both
strands of the double-stranded structure store the same
biological information
• Biological information is replicated as the two strands
are separated
• A significant portion of DNA (more than 98% for
humans) is non-coding, meaning that these sections do
not serve a function of encoding proteins (junk DNA)
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 The structure of DNA and RNA
• Nucleotides are joined to each other to form the
polymers known as DNA and RNA
• The nucleic acids are chains of nucleotides whose
phosphates bridge the 3’ and 5’ positions of
neighbouring ribose units

• The backbone of the DNA strand is made from alternating phosphate and
sugar residues
• The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar
• The sugars are joined together by phosphate groups that form
phosphodiester bonds between the third and fifth carbon atoms of
adjacent sugar rings
• These asymmetric bonds mean a strand of DNA has a direction
• In a double helix the direction of the nucleotides in one strand is opposite to
their direction in the other strand i.e. the strands are antiparallel

The chemical structure of a nucleotide

Non-covalent hydrogen bonds between base pairs

GC base pair with three hydrogen bonds

A single nucleotide is made up of three components:

1. a nitrogen-containing base (either a purine or a pyrimidine)
2. a five-carbon sugar (either a ribose (in RNA) or a deoxyribose
(in DNA) molecule) AT base pair with two hydrogen bonds
3. a phosphate group

DNA helix DNA helix

• Most important feature of the

DNA structure - two
polynucleotide chains twisted
around each other in the form
of double helix

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 DNA helix
• Nucleotides are attached
together to form two long
strands that spiral to create a
structure called a double
helix
• If you think of the double helix
structure as a ladder, the
phosphate and sugar
molecules would be the
sides, while the bases would
be the rungs
Base stacking
• The bases in DNA are planar and have
a tendency to "stack"
• Major stacking forces
– hydrophobic interaction
– van der Waals forces
Base pairing in DNA
• Two hydrogen bonds connect T to A; three hydrogen bonds
connect G to C
• The sugar-phosphate backbones (grey) run anti-parallel to
each other, so that the 3’ and 5’ ends of the two strands are
aligned
Major and minor grooves
• The narrowness of the minor groove
means that the edges of the bases are
more accessible in the major groove
• As a result, proteins like transcription
factors that can bind to specific
sequences in double-stranded DNA
usually make contacts to the sides of
the bases exposed in the major groove
• This situation varies in unusual
conformations of DNA within the cell,
but the major and minor grooves are
always named to reflect the
differences in size that would be seen
if the DNA is twisted back into the
ordinary B form
Features of DNA structure
1. The DNA double helix is anti-parallel, which means
that the 5' end of one strand is paired with the 3' end of
its complementary strand (and vice versa)
2. Nucleotides are linked to each other by their
phosphate groups, which bind the 3' end of one sugar
to the 5' end of the next sugar
3. Not only are the DNA base pairs connected via
hydrogen bonding, but the outer edges of the
nitrogen-containing bases are exposed and available
for potential hydrogen bonding as well
4. These hydrogen bonds provide easy access to the
DNA for other molecules, including the proteins that
play vital roles in the replication and expression of
DNA
Conformations of the DNA double helix
• One of the ways that scientists have elaborated on
Watson and Crick's model is through the identification of
three different conformations of the DNA double helix
• In other words, the precise geometries and
dimensions of the double helix can vary
• The most common conformation in most living cells
(which is the one depicted in most diagrams of the
double helix, and the one proposed by Watson and
Crick) is known as B-DNA
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 Conformations of the DNA double helix Conformations of the DNA double helix
• Other conformations are A-DNA and Z-DNA • DNA is a double-stranded helix, with the two strands connected
• A-DNA by hydrogen bonds
– a shorter and wider form that has been found in • Most DNA double helices are right-handed; that is, if you were to
dehydrated samples of DNA and rarely under hold your right hand out, with your thumb pointed up and your
normal physiological circumstances fingers curled around your thumb, your thumb would represent
• Z-DNA the axis of the helix and your fingers would represent the sugar-
phosphate backbone
– a left-handed conformation
• Only one type of DNA, called Z-DNA, is left-handed
– a transient form of DNA, only occasionally existing
in response to certain types of biological activity
– was first discovered in 1979, but its existence was
largely ignored until recently
– scientists have since discovered that certain
proteins bind very strongly to Z-DNA, suggesting
that Z-DNA plays an important biological role in
protection against viral disease

Three different conformations of DNA double helix Structural forms of DNA double helix
Property A-DNA B-DNA Z-DNA
Helix handedness Right Right Left

Base pairs per turn 11 10.4 12

Rise per base pair 0.23nm 0.34nm 0.38nm

along axis
Pitch 2.46nm 3.40nm 4.56nm

Diameter 2.55nm 2.37nm 1.84nm

Conformation of anti anti Alternating anti

(a) A-DNA is a short, wide, right-handed helix glycosidic bond and syn
(b) B-DNA, the structure proposed by Watson and Crick, is Major groove Present Present Absent
the most common conformation in most living cells
Minor groove Present Present Deep cleft
(c) Z-DNA is a left-handed helix

Implications of DNA structure

• DNA is (-) charged due to phosphate
– gel electrophoresis, DNA sequencing (Sanger
method)
• H-bonds form between specific bases
– hybridization – replication, transcription, translation
DNA microarrays, hybridization blots, PCR
C-G bound tighter than A-T due to triple H-bond
• DNA-protein interactions (via major & minor
grooves)
– transcriptional regulation
• DNA polymerization
– 5’ to 3’ – phosphodiester bond formed between 5’
phosphate and 3’ OH
– DNA sequencing (Sanger method)