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Describe different forms of DNA.

Give a note on Watson and


crick model of DNA double helical structure.
1. Introduction:

2. Forms of DNA
A-DNA
A-form DNA was first identified from fibre-diffraction studies of DNA at
low (75%) relative humidity.
In general, A-DNA for any sequence is favoured under dehydrating
conditions, and certain purine stretches will favour an A-conformation,
even in cases of higher hydration levels.
It appears that at least four purines (or pyrimidines) in a row are enough
to set up a local A-DNA helix, although of course certain purine stretches
are more likely to form A-DNA than others. (For example, the sequence
AAAA crystallizes as B-DNA, not in the A-helix.) It is thus possible to have a
DNA sequence that contains some regions in the A-form within the context
of a mainly B-conformation.
Some of the helical parameters of A-DNA are given in Table 2.
The A-DNA helix is a bit wider than B-DNA (and also Z-DNA), and this is
mainly due to the fact that the base pairs stack nearly on top of each
other in B-DNA, but stack a little off-centre in the A-conformation.
Notice in Figure 1b that, if you look down the helix, there is a hole in the Aconformation, which is absent in the two other helical conformations.
As might be expected, this results in the A-DNA helix being less stable
than the B-DNA conformation.
A-DNA is also more rigid than B-DNA, again because the off-centre
stacking of the bases makes them less flexible.
There are about 11 bp per turn for ADNA, compared with about 10 bp per
turn for the B-form.
Finally, the base-pair tilt is higher in A-DNA than in BDNA.
An A-helix is the common form for DNARNA hybrids, as well as doublestranded RNA; this is due to the extra OH group on the ribose sugar, which
cannot fit easily into the tight space allotted to it in B-DNA.
B-DNA

B-DNA is the WatsonCrick form of the double helix that most people are
familiar with (Figure 1). It was first identified in fibres at 92% relative
humidity. Several sequences crystallized to high resolution have been
found to adopt the B-DNA conformation. Although on average the
conformation of B-DNA is the same in crystals as in solution, the local
structure is strongly dependent on its local sequence. Table 1 lists some of
the different structural parameters for B-DNA as a function of dinucleotide
sequence. The table also shows the average parameters, which are very
close to the values obtained in fibre diffraction studies. Of the three
families of DNA helices, B-DNA is the most common, and also the most
variable in structure.
Left-handed Z-helices
One of the first DNA sequences to be crystallized was the oligomer
d(GCGCGC), as shown in Figure 1b. To many peoples surprise, this
structure was a left-handed helix, opposite to that of the
traditionalWatsonCrick helix. The backbone is not a smooth helix, but is
irregular and zigzag in shape, hence its name. At the time, this structure
was quite controversial, but now it is generally accepted that certain DNA
sequences (in particular alternating purine pyrimidine tracts) can form
left-handed Z-DNA, while most other sequences will readily form a righthanded helix. The Z-helix is narrower than the A-and Bconformations, and
it has 12 bp per turn. The nucleotide bases are flipped upside down,
relative to the phosphate backbone, in Z-DNA when compared with A-DNA
and BDNA.
Biology of A-, B-and Z-DNA Biology of A-DNA A-form helices are common
for DNARNA hybrids, as well as for double-stranded RNA; in addition, the
Aconformation is favoured in triplex DNA. A transition from B-DNA to ADNA has been postulated to occur during transcription, where the RNA
DNA hybrid would be more stable in the A-conformation. A-DNA also plays
a role in some processes that do not involve RNA. For example, in
sporulating bacteria, there is a protein which can bind to DNA in the Bconformation and induce a change to the A-DNA helix. Another common
biological occurrence of sequences which can readily form A-DNA is in the
long terminal repeats (LTRs) of transposable elements. These regions often
contain purine stretches which favour the A-DNA conformation. In fact, the
DNA sequence used for the crystal structure sequence of A-DNA shown in
Figure 1b is from an LTR of the human immunodeficiency virus. It is likely
that these regions are involved in recombination. Short stretches of
purines which are likely to form A-DNA conformations exist in genomes in
much greater abundance than would be expected from the
mononucleotide composition, ranging from about a fourth of the genome
in bacteria to close to half the DNA in eukaryotic chromosomes. Biology of
Z-DNA Sequences which can form Z-DNA are essentially not found in
Escherichia coli, and yet they are overrepresented in complex eukaryotes.
A notable example of this is theCpG islands, which could potentially form
Z-DNA, especially when methylated. In a complicated scenario, a protein
which is responsible for mRNA editing is activated upon binding to lefthanded Z-DNA upstream of a gene. In addition, Z-DNA has also been

postulated to play a role as a transcription enhancer, and in terminal


differentiation. In some eukaryotic genomes, 10% or more of the genome
contains sequences capable of forming Z-DNA. B-DNA structure and
function As mentioned above, the structure of B-DNA is strongly
dependent on its sequence. Thus, some sequences which can melt readily
(e.g. TATA) can be strategically placed to open the DNA helix for initiation
of transcription. Other sequences that are more rigid (or flexible) can
serve as sites for protein binding and formation of specific complexes. In
bacteria as well as eukaryotes, sequences upstream of transcription start
sites contain regions which are more rigid and will melt more readily. In
addition to the three different helical conformations of DNA, there are
numerous other DNA structures, such as DNA curvature, cruciforms, triplestranded DNA, tetraplex DNA and parallel-stranded DNA, that can be
formed under various conditions. Thus there is much more to DNA
structure than merely the WatsonCrick B-DNA conformation
Summary
Whether a DNA sequence will be in the A-, B-or Z-DNA conformation
depends on at least three conditions. The first is the ionic or hydration
environment, which can facilitate conversion between different helical
forms. ADNA is favoured by low hydration, whereas Z-DNA can be
favoured by high salt. The second condition is the DNA sequence: A-DNA is
favoured by certain stretches of purines (or pyrimidines), whereas Z-DNA
can be most readily formed by alternating purinepyrimidine steps. The
third condition is the presence of proteins that can bind to DNA in one
helical conformation and force the DNA to adopt a different conformation,
such as proteins which bind to B-DNA and can drive it to either A-or
Zforms. In living cells, most of the DNA is in a mixture of Aand B-DNA
conformations, with a few small regions capable of forming Z-DNA.

B-DNA (WatsonCrick DNA)

B-DNA is a right-handed helix; it turns in a clockwise manner when viewed down


its axis. The
bases are stacked almost exactly perpendicular to the main axis with 10.5 bases
per turn. The major
groove is wide and of moderate depth, while the minor groove is of moderate
depth but is much
narrower. B-DNA occurs under conditions of high humidity (95%) and relatively
low salt. Since the
inside of a cell is mostly water with relatively low salt concentration, it follows
that the predominant form in vivo is B-DNA
A-DNA

If the water content is decreased and the salt concentration increased during
crystal formation, the A form of
DNA (A-DNA) will occur. In this right-handed helix the bases are tilted with
respect to the axis and there
are more (11) bases per turn than in B-DNA. The major groove of A-DNA is deep
and narrow, while the

minor groove is shallow and broad. It is unlikely that A-DNA is present in any
lengthy sections in cells.
However, RNA adopts an A-form helix when it forms double-stranded regions.
The 2-hydroxyl group on
the ribose sugar hinders formation of B-form RNA (see Section 4.2).
Z-DNA

In 1979, Alexander Rich and his colleagues at the Massachusetts Institute of


Technology (MIT) made a
novel discovery. They found that oligonucleotides composed of repeating GC
sequences on one strand,
with the complementary CG sequences on the other, formed a left-handed helix.
A left-handed helix turns
counterclockwise away from the viewer when viewed down its axis. Because the
backbone formed a zig-zag
structure, they called the structure Z-DNA. Z-DNA has 12 base pairs per turn. The
minor groove is very
deep and narrow. In contrast, the major groove is shallow to the point of being
virtually nonexistent. ZDNA
was first formed under conditions of high salt or in the presence of alcohol. Later,
it was shown that
this form of double helix can be stabilized in physiologically normal conditions, if
methyl groups are added
to the cytosines (see Section 12.2).
For many years, the biological function, if any, of Z-DNA was debated. However,
the discovery that
certain families of proteins bind to Z-DNA with high affinity and great specificity
provided evidence for
a role in vivo. Z-DNA is now thought to be present transiently in short sections in
cells and to play a role
in regulating gene expression. Recent data show that some Z-DNA-binding
proteins participate in the
pathology of poxviruses, including vaccinia virus and variola (the agent of
smallpox). The crystal structure
of a BZ junction was solved in 2005 (see Fig. 2.8). What came as a surprise is
that design of the BZ
junction is such that it minimizes structural distortion of the helix, by extruding a
base pair at each junction
point. Base extrusion occurs in conjunction with a sharp turn in the sugar
phosphate backbone and a slight
bend (11). Thus, short sections of Z-DNA within a cell are more energetically
favorable and stable than
previously imagined. Insights provided by the crystal structure will likely lead to a
deeper understanding of
the functional role of Z-DNA regulatory elements.

Major and minor grooves

The two bonds that attach a base pair to its deoxyribose sugar rings are not
directly opposite. Therefore,
the sugarphosphate backbone is not equally spaced. This results in what are
called the major and minor
grooves of DNA (see Fig. 2.7). The major groove has a significant role in
sequence-specific DNAprotein
interactions. The edges of the base-paired purines and pyrimidines are solvent
accessible. In particular, the
solvent-exposed nitrogen and oxygen atoms of the bases that line the major
grooves of DNA can make
hydrogen bonds with the side chains of the amino acids of a protein. The pattern
of these hydrogen-bonding
groups (whether donors or acceptors) is different for AT, TA, GC, and CG base
pairs. Thus, the major
groove carries a message (the base sequence of the DNA) in a form that can be
read by DNA-binding
proteins. The minor groove of DNA is less informative. In the minor groove, the
hydrogen bonding patterns
are the same regardless of which way the base pair is flipped, and there is only
one difference in the pattern
between AT and GC base pairs. As will be discussed in Chapter 11, most
transcription factors (proteins
involved in regulating gene expression) bind DNA in the major groove.

DNA HISTORY:

1. DNA was first isolated by the Swiss physician Friedrich Miescher who, in 1869,
discovered a microscopic substance in the pus of discarded surgical bandages. As it
resided in the nuclei of cells, he called it "nuclein". [177][178] In 1878, Albrecht Kossel isolated
the non-protein component of "nuclein", nucleic acid, and later isolated its five
primary nucleobases.[179][180]
2. In 1919, Phoebus Levene identified the base, sugar and phosphate nucleotide unit.
[181]

Levene suggested that DNA consisted of a string of nucleotide units linked together

through the phosphate groups.


3. Levene thought the chain was short and the bases repeated in a fixed order. In
1937, William Astburyproduced the first X-ray diffraction patterns that showed that DNA
had a regular structure.[182]
4. In 1927, Nikolai Koltsov proposed that inherited traits would be inherited via a "giant
hereditary molecule" made up of "two mirror strands that would replicate in a semiconservative fashion using each strand as a template".[183][184]
5.

In 1928, Frederick Griffith in his experimentdiscovered that traits of the "smooth" form
of Pneumococcus could be transferred to the "rough" form of the same bacteria by
mixing killed "smooth" bacteria with the live "rough" form. [185][186] This system provided the
first clear suggestion that DNA carries genetic informationthe AveryMacLeod
McCarty experimentwhen Oswald Avery, along with coworkers Colin
MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943.[187]

6. DNA's role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in
theHersheyChase experiment showed that DNA is the genetic material of the T2 phage.
[188]

7. In 1953, James Watson and Francis Crick suggested what is now accepted as the first
correct double-helix model of DNA structure in the journal Nature.[10] Their double-helix,
molecular model of DNA was then based on a single X-ray diffraction image (labeled as
"Photo 51")[189] taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as
the information that the DNA bases are pairedalso obtained through private
communications from Erwin Chargaff in the previous years.
8. Experimental evidence supporting the Watson and Crick model was published in a series
of five articles in the same issue of Nature.[190]Of these, Franklin and Gosling's paper was

the first publication of their own X-ray diffraction data and original analysis method that
partially supported the Watson and Crick model;[49][191] this issue also contained an article
on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and in
vivo B-DNA X-ray patterns also supported the presence in vivo of the double-helical DNA
configurations as proposed by Crick and Watson for their double-helix molecular model of
DNA in the previous two pages of Nature.[50] In 1962, after Franklin's death, Watson,
Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine.[192] Nobel
Prizes are awarded only to living recipients. A debate continues about who should
receive credit for the discovery.[193]
9. In an influential presentation in 1957, Crick laid out the central dogma of molecular
biology, which foretold the relationship between DNA, RNA, and proteins, and articulated
the "adaptor hypothesis".[194] Final confirmation of the replication mechanism that was
implied by the double-helical structure followed in 1958 through the MeselsonStahl
experiment.[195]
10. Further work by Crick and coworkers showed that the genetic code was based on nonoverlapping triplets of bases, called codons, allowing Har Gobind Khorana, Robert W.
Holley and Marshall Warren Nirenberg to decipher the genetic code.[196] These findings
represent the birth of molecular biology.

Structure of DNA
LIZABETH A. ALISON

Secondary structure of DNA


The primary structures of DNA and RNA are generally quite similar, however their
conformations are quite
different. RNA commonly exists as a single polynucleotide chain, or strand. In
contrast, as Watson and
Crick deduced, the biologically active structure of DNA is more complex than a
single string of nucleotides
linked by phosphodiester bonds. DNA generally exists as two interwound strands.
This structural difference
is critical to the different functions of the two types of nucleic acids. The
secondary and tertiary structure of
RNA will be discussed along with the versatility of its function in Chapter 4. The
remainder of this chapter

will focus on DNA. Various chemical forces drive the formation of the DNA double
helix. These include
hydrogen bonds between the bases and base stacking by hydrophobic
interactions.

Hydrogen bonds form between the bases

Thermodynamically stable hydrogen bonds form between the nitrogenous bases


on opposite strands of the
interwound DNA chains (Fig. 2.4). Hydrogen bonds are very weak bonds that
involve the sharing of a
hydrogen between two electronegative atoms, such as oxygen and nitrogen. The
hydrogen bonds provide
one type of force holding the strands together. Although individually very weak,
hydrogen bonds give
structural stability to a molecule with large numbers of them. The hydrogen
bonding between bases is
referred to as WatsonCrick or complementary base pairing. It occurs in such
a way that adenine (A)
normally pairs with thymine (T) by two hydrogen bonds, and guanine (C) pairs
with cytosine (C) by three
hydrogen bonds. WatsonCrick base pairing allows the 1-carbons on the two
strands to be exactly the same
distance apart (1.08 nm). This results in the regular, symmetric framework of the
DNA double helix. The
WatsonCrick structure of paired complementary strands explains Chargaff s
rules the relationships among
the molar concentrations of the different bases.
Why arent there other stable base pairs present in DNA, such as G with A, or C
with T? Some of these
are ruled out by the difficulty of making two or more hydrogen bonds. But others,
such as G with T, are
not excluded for that reason (Fig. 2.5). The hydrogen bonding between G and T
produces a pair with a
similar overall shape to WatsonCrick base pairs (see Fig. 2.4). Likewise, GU base
pairing is stable, and is of
importance in RNA structure and RNAprotein interactions (see Section 4.2).
However, if G-C to G-T
changes were to occur in DNA, the sequence of bases in the DNA could change
drastically with each cell
division. In fact, there are proofreading mechanisms and DNA repair mechanisms
that recognize nonWatsonCrick base pairs and correct the majority of mistakes (see Section 6.6
and 7.6).

Base stacking provides chemical stability to the DNA double helix

The molecular processes of cellular life generally take place in a watery solution,
and intracellular components
are largely molecules that are easily dissolved in water. The nitrogenous bases
are an exception as they are nonpolar and thus hydrophobic (water hating). On
their own they are practically insoluble in the aqueous
environment of cells. The asymmetric distribution of charge across a polar water
molecule thus has important
consequences for the structure of DNA. Once the bases are attached to a sugar
and a phosphate to form a
nucleotide, they become soluble in water, but even so their insolubility still
places strong constraints on the

Structure of the WatsonCrick DNA double helix

Alternating deoxyribose sugars and phosphate groups form the backbone of


DNA. The bases are attached
to the sugars and are located between the backbones of the DNA strands, lying
perpendicular to the long
axis of the strands. As the backbones of the two strands wind around each other,
they form a double helix

KARP
The Watson-Crick Proposal
When protein structure was discussed in Chapter 2, the importance
of secondary and tertiary structure as determinants
of the proteins activity was stressed. Similarly, information
about the three-dimensional organization of DNA was
needed if its biological activity was to be understood. Using
X-ray diffraction data (obtained by Rosalind Franklin and
Maurice Wilkins at Kings College London) and models constructed
from cutouts of the four types of nucleotides,Watson
and Crick proposed a structure of DNA that included the
following elements (Figure 10.10):
1. The molecule is composed of two chains of nucleotides.
This conclusion followed on the heels of an erroneous
proposal by Linus Pauling, who had suggested that DNA
was composed of three nucleotide strands.
2. The two chains spiral around each other to form a pair of
right-handed helices. In a right-handed helix, an observer
looking down the central axis of the molecule would see
that each strand follows a clockwise path, as it moves
away from the observer. The helical nature of DNA was
revealed in the pattern of spots produced by Franklins
X-ray diffraction image (seen on page 386), which was
shown to Watson during a visit to Kings College 3. The two chains comprising one
double helix run in opposite
directions; that is, they are antiparallel. Thus, if one
chain is aligned in the direction, its partner
must be aligned in the direction.
4. The sugarphosphatesugarphosphate backbone of
each strand is located on the outside of the molecule with
the two sets of bases projecting toward the center. The
phosphate groups give the molecule a large negative charge.
5. The bases occupy planes that are approximately perpendicular
to the long axis of the molecule and are, therefore,
stacked one on top of another like a pile of plates. Hydrophobic
interactions and van der Waals forces (page 36)
between the stacked, planar bases provide stability for the
entire DNA molecule.Together, the helical turns and planar
base pairs cause the molecule to resemble a spiral

staircase. This manner of construction is evident in the


chapter-opening photograph, which shows the original
Watson-Crick model.
6. The two strands are held together by hydrogen bonds
between each base of one strand and an associated base
on the other strand. Because individual hydrogen bonds
are weak and easily broken, the DNA strands can
become separated during various activities. But the
strengths of hydrogen bonds are additive, and the large
numbers of hydrogen bonds holding the strands
together make the double helix a stable structure.
7. The distance from the phosphorus atom of the backbone
to the center of the axis is 1 nm (thus the width of the
double helix is 2 nm).
8. A pyrimidine in one chain is always paired with a purine
in the other chain. This arrangement produces a molecule
that is 2 nm wide along its entire length.
9. The nitrogen atoms linked to carbon 4 of cytosine and
carbon 6 of adenine are predominantly in the amino
(NH2) configuration (Figure 10.9c) rather than the
imino (NH) form. Similarly, the oxygen atoms linked to
carbon 6 of guanine and carbon 4 of thymine are predominantly
in a keto (C O) configuration rather than
the enol (C OH) form. These structural restrictions
on the configurations of the bases suggested that adenine
was the only purine structurally capable of bonding
to thymine and that guanine was the only purine capable
of bonding to cytosine. Therefore, the only possible pairs
were A-T and G-C (Figure 10.10c). This fit perfectly
with the base composition analysis carried out by Chargaff
whose results were communicated to Watson and Crick
during a meeting of the three scientists in Cambridge in
1952. Because an A-T and G-C base pair had the same
geometry (Figure 10.10c), there were no restrictions on
the sequence of bases; a DNA molecule could have any
one of an unlimited variety of nucleotide sequences.
10. The spaces between adjacent turns of the helix form two
grooves of different widtha wider major groove and a
more narrow minor groovethat spiral around the outer
surface of the double helix. Proteins that bind to DNA
often contain domains that fit into these grooves. In
many cases, a protein bound in a groove is able to read

3 S5
5 S3
the sequence of nucleotides along the DNA without
having to separate the strands.
11. The double helix makes one complete turn every 10
residues (3.4 nm), or 150 turns per million daltons of
molecular mass.
12. Because an A on one strand is always bonded to a T on
the other strand, and a G is always bonded to a C, the
nucleotide sequences of the two strands are always fixed
relative to one another. Because of this relationship, the
two chains of the double helix are said to be complementary

to one another. For example, A is complementary


to T, 5_-AGC-3_ is complementary to 3_-TCG-5_,
and one entire chain is complementary to the other. As
we shall see, complementarity is of overriding importance
in nearly all the activities and mechanisms in
which nucleic acids are involved.
The Importance of the Watson-Crick Proposal From the
time biologists first considered DNA as the genetic material, it
was expected to fulfill three primary functions (Figure 10.11):
1. Storage of genetic information. As genetic material, DNA
must contain a stored record of instructions that determine
all the inheritable characteristics that an organism
exhibits. In molecular terms, DNA must contain the information
for the specific order of amino acids in all the
proteins that are synthesized by an organism.
2. Replication and inheritance. DNA must contain the information
for synthesis of new DNA strands (replication).
DNA replication allows genetic instructions to be
transmitted from one cell to its daughter cells and from
one individual to its offspring.
3. Expression of the genetic message. DNA is more than a
storage center; it is also a director of cellular activity.
Consequently, the information encoded in DNA has to
be expressed in some form that can take part in events
that are taking place within the cell. More specifically,
the information in DNA must be used to direct the order
by which specific amino acids are incorporated into a
polypeptide chain.
The Watson-Crick model