Structure of DNA

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other
organisms. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the
cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in
the mitochondria (where it is called mitochondrial DNA or mtDNA). DNA is found in the
nucleus of eukaryotes and the cytoplasm or nucleoid of prokaryotes and functions as the
molecule of heredity.

In DNA there are four bases: adenine (abbreviated A), guanine (G), thymine (T) and cytosine
(C). Adenine and guanine are purines; thymine and cytosine are pyrimidines.

A nucleoside is a pyrimidine or purine base covalently bonded to a sugar. In DNA, the sugar is
deoxyribose and so this is a deoxynucleoside. There are four types of deoxynucleoside in DNA;
deoxyadenosine, deoxyguanosine, deoxythymidine and deoxycytidine.

A nucleotide is base + sugar + phosphate covalently bonded together. In DNA, where the sugar
is deoxyribose, this unit is a deoxynucleotide.

In DNA the nucleotides are covalently joined together by 3’-- 5’ phosphodiester bonds to form a
repetitive sugar–phosphate chain which is the backbone to which the bases are attached.

The DNA sequence is the sequence of A, C, G and T along the DNA molecule which carries the
genetic information.

In a DNA double helix, the two strands of DNA are wound round each other with the bases on
the inside and the sugar–phosphate backbones on the outside. The two DNA chains are held
together by hydrogen bonds between pairs of bases; adenine (A) always pairs with thymine (T)
and guanine (G) always pairs with cytosine (C).

Each nucleotide consists of three major parts: (1) a five-carbon sugar (pentose); (2) a flat,
heterocyclic, nitrogen-containing organic base; and (3) a negatively charged phosphate group,
which gives the polymer its acidic property. The nitrogenous base in each nucleotide is
covalently attached to the sugar by a glycosidic bond. The phosphate group is also covalently
linked to the sugar.

Bases in the nucleotides spontaneously form hydrogen bonds in a highly specific manner.
Adenine normally forms two hydrogen bonds with thymine in a complementary strand of the
DNA double helix like, Guanine forms three
hydrogen bonds with cytosine.

Human DNA consists of about 3 billion bases, and

more than 99 percent of those bases are the same in
all people.

Nucleotides are arranged in two long strands that form

a spiral called a double helix. The structure of the
double helix is somewhat like a ladder, with the base
pairs forming the ladder’s rungs and the sugar and
phosphate molecules forming the vertical sidepieces
of the ladder.

An important property of DNA is that it can replicate,

or make copies of itself. Each strand of DNA in the
double helix can serve as a pattern for duplicating the
sequence of bases. This is critical when cells divide because each new cell needs to have an exact
copy of the DNA present in the old cell.

Watson and Crick model of DNA

DNA is a double stranded helix, with the two strands connected by hydrogen bonds. Adenine
bases are always paired with thymine, and cytosine is always paired with guanine, which is
consistent with and accounts for Chargaff's rule. This is called complementary base pairing.
Watson and Crick discovered that DNA had two sides, or strands, and that these strands were
twisted together like a twisted ladder the double helix.

Most DNA double helices are right handed, only one type of DNA, called ZDNA, is left handed.
The G:C and A:T base pairing also maximizes the number of effective hydrogen bonds that can
form between the bases; there are three hydrogen bonds between each G:C base pair and two
hydrogen bonds between each A:T base pair. Thus A:T and G:C base pairs form the most stable
conformation both from steric considerations and from the point of view of maximizing
hydrogen bond formation.

The sides of the ladder comprise the sugar phosphate portions of adjacent nucleotides bonded
together. The phosphate of one nucleotide is covalently bound to the sugar of the next
nucleotide.

The hydrogen bonds between phosphates cause the DNA strand to twist.
The DNA double helix is antiparallel, which means that the 5' end of
one strand is paired with the 3' end of its complementary strand (and
vice versa). As shown in Figure, 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.

Along the whole length of the DNA molecule, there are two
depressions—referred to as the ―minor groove‖ and the ―major
groove‖—that lie between the strands.

In a DNA molecule, the different nucleotides are covalently joined to

form a long polymer chain by covalent bonding between the phosphates
and sugars.
For any one nucleotide, the phosphate attached to the hydroxyl group at the 5’ position of the
sugar is in turn bonded to the hydroxyl group on the 3’ carbon of the sugar of the next
nucleotide. Since each phosphate–hydroxyl bond is an ester bond, the linkage between the two
deoxynucleotides is a 3’5’ phosphodiester bond. Thus, in a DNA chain, all of the 3’ and 5’
hydroxyl groups are involved in phosphodiester bonds except for the first and the last nucleotide
in the chain. The first nucleotide has a 5’ phosphate not bonded to any other nucleotide and the
last nucleotide has a free 3’ hydroxyl. Thus each DNA chain has polarity; it has a 5’ end and a
3’ end.

Erwin Chargaff was one of a handful of scientists who expanded on Levene's work by
uncovering additional details of the structure of DNA, thus further paving the way for Watson
and Crick.
A, B and Z forms of DNA

The Watson-Crick structure is also referred to as B form DNA, or B-DNA. The B form is the
most stable structure for a random-sequence DNA molecule under physiological conditions and
is therefore the standard point of reference in any study of the properties of DNA. Two structural
variants that have been well characterized in crystal structures are the A and Z forms. These
three DNA conformations are shown in Figure, with a summary of their properties.

The A form is favored in many solutions that are relatively devoid of water. The DNA is still
arranged in a right-handed double helix, but the helix is wider and the number of base pairs per
helical turn is 11, rather than 10.5 as in B-DNA.
The plane of the base pairs in A-DNA is tilted
about 20with respect to the helix axis. These
structural changes deepen the major groove while
making the minor groove shallower. The reagents
used to promote crystallization of DNA tend to
dehydrate it, and thus most short DNA molecules
tend to crystallize in the A form.
Z-form DNA is a more radical departure from the B structure; the most obvious distinction is the
left handed helical rotation. There are 12 base pairs per helical turn, and the structure appears
more slender and elongated. The DNA backbone takes on a zigzag appearance. Certain
nucleotide sequences fold into left handed Z helices much more readily than others. Prominent
examples are sequences in which pyrimidines alternate with purines, especially alternating C and
G or 5-methyl-C and G residues. To form the left-handed helix in Z-DNA, the purine residues
flip to the syn conformation, alternating with pyrimidines in the anti-conformation. The major
groove is barely apparent inZ-DNA, and the minor groove is narrow and deep. Whether A-DNA
occurs in cells is uncertain, but there is evidence for some short stretches (tracts) of Z-DNA in
both prokaryotes and eukaryotes. These Z-DNA tracts may play a role (as yet undefined) in
regulating the expression of some genes or in genetic recombination.

Chargaff Rules

 The nucleotide composition of DNA varies among

species
 The amount of adenine (A) is usually similar to the
amount of thymine (T), and the amount of guanine (G)
usually approximates the amount of cytosine (C).
 The total amount of purines (A + G) and the total
amount of pyrimidines (C + T) are usually nearly equal.