The brief Note on Structures of DNA

Introduction:

Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the
development and functioning of all known living organisms and many viruses.

Types of structures

 Primary structure of DNA

 Secondary structure of DNA
 Unusual DNA Secondary structure
 Tertiary structure of DNA

Primary structure of DNA

DNA and RNA are called as a nucleic acid (polymer of repeating subunits)

Subunit are comprised of the three parts

 Five carbon sugars: Subunit of RNA contains a pentose sugar called ribose and the
DNA contains deoxyribose sugar. The sugars only differ in the presence or absence of
the oxygen at 2’ position

 A phosphate group : which are negatively charged and give DNA molecules a negative
charge and play it’s a vital role in the phosphodiester bond formation
 A Nitrogenous bases : The nucleobases are classified into two types: the purines, A and
G and the pyrimidine, C , U and T . The uracil is specific for RNA
According to the Chargaff’s rules [A] = [T] and [G] = [C] and [A] + [G] = [T] + [C]

Nucleoside and Nucleotide

When base is chemically linked to a 1’ carbon of the sugar it form nucleoside and when the
phosphate group is attaches to the 5’ carbon of the same sugar it form nucleotide

Nucleotide joins together by condensation reaction forming a DNA strand

Significance of 5' to 3' direction

A phosphate group attached to the 5′-end and hydroxyl group is attached to 3′-end carbon in the
sugar-ring. This naming convention is important because nucleic acids can only be synthesized
in vivo in the 5′-to-3′ direction, as the polymerase that assembles new strands only attaches new
nucleotides to the 3′-hydroxyl (-OH) group, via a phosphodiester bond.

The Length of DNA and RNA

The size of an individual gene or an organism's entire genome is often measured in base pairs
because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the
number of nucleotides in one of the strands A kilo base (kb) is a unit of measurement in
molecular biology equal to 1000 base pairs of DNA or RNA. The haploid human genome (23
chromosomes) is estimated to be about 3.2 billion base pairs long

Secondary Structure of DNA

The secondary structure of a nucleic acid molecule refers to the base pairing interactions
within a single molecule or set of interacting molecules. The secondary structures of biological
DNA's and RNA's tend to be different: biological DNA mostly exists as fully base paired double
helices, while biological RNA is single stranded

 Hydrogen bonds formed between the bases

Two nucleotides on opposite complementary DNA or RNA strands that are connected via
hydrogen bonds are called a base pair. Watson-Crick base pairing, adenine (A) forms a base
pair with thymine (T) by 2 hydrogen bonds and guanine (G) pairs with cytosine (C) by 3
hydrogen bonds in DNA. Hydrogen bonding gives structural stability to the molecules

 Base Stacking provides chemical stability to the DNA double helix

This occurs due to hydrophobic effect of DNA. Stacking eliminates any gapes between
the bases and excludes the maximum amount of h20 from the interior of the double helix

Structure of the Watson –crick DNA double helix

The term double helix refers to the structure formed by

double-stranded molecules of nucleic acids .The double helical
structure of a nucleic acid complex arises as a consequence of its
secondary structure

The two strands of DNA run in opposite directions to each other

and are therefore anti-parallel, one backbone being 3′ (three prime)
and the other 5′ (five prime). This refers to the direction the 3rd
and 5th carbon on the sugar molecule is facing. Attached to each
sugar is one of four types of nucleobases (informally, bases).
It is the sequence of these four nucleobases along the backbone that
encodes biological information.
That sequence is called as a genetic code
Types of DNA

B-DNA A-DNA Z-DNA

 crystallized from water;  Dehydrated form of B-  Found in short stretches

water retained in the inner DNA of native DNA and
structure; predominant  Right handed helix synthetic DNA
form under physiological  11 base pairs/helix  Left handed helix
conditions  Diameter = 26 A  12 base pairs/helix
 10 base pairs/turn of helix  Diameter = 18 A
 Right handed
 Distance bet base pairs
0.34 nm
 Diameter – 2.0 nm or 20 A

Unusual DNA secondary structures

Slipped structures

Present upstream of regulatory sequence , it is a tendem repeat in DNA is two or more adjacent
copies of a pattern of nucleotide arranged in head to tail fashion

Crucifrom structures

These are inverted repeats are base sequence of identical compositions on the complementary
strand .They are some time called as palindromes. The DNA become rearranged so each repeat
pairs with the complementary sequence of its own strand of DNA instead of the complement of
the other strand

Triple-stranded DNA

A triple-stranded DNA is a structure of DNA in which three oligonucleotides wind around each
other and form a triple helix. In this structure, one strand binds to a B-form DNA double helix
through Hoogsteen or reversed Hoogsteen hydrogen bonds.
Tertiary structure of the DNA

 Circular (relaxed) – in E.coli; simian virus 40; bacteriophage; certain animal species

 Supercoiled DNA – extra twisting in the linear duplex; allows DNA to be more
compact in the cell; regulatory role in replication

 Topoisomerase – change topology of the DNA

 Quadruplex DNA – four stranded; in protozoan DNA; occur in G-rich regions;

regulating and stabilizing telomeres and regulation of gene expression