DNA STRUCTURE

DNA Stabilization--H-bonding &

Base pair stacking
.
Advantages to Double Helix

Stability---protects bases from attack by H2O soluble compounds and H2O it self.

Base stacking interactions (hydrophobic and electrostatic in nature, and depend on

the aromaticity of the bases) in DNA and RNA are due to attraction, short-range
exchange repulsion, and electrostatic interactions, which contribute to stability
Base stacking
in a DNA
double helix
 The nucleotide sequence of a nucleic acid molecule encodes the amino acid
sequence of a protein. The entire nucleotide sequence of an organism; transmitted
to off spring during reproduction is the genome.

Deoxyribo nucleicacid (DNA): It serve as the genome for the proteins of all
cellular organisms, both eukaryotic and prokaryotic. DNA also serves as the genome
for certain viral groups.

Ribonucleic acid(RNA): It serve as an inter mediate in gene expression in

eukaryotic and prokaryotic organisms, as well as some viruses. RNA serves as the
genome for certain viral groups.
The Structure of DNA Provides
an Explanation for Heredity
Each strand contains a nucleotide sequence that is exactly complementary to the
nucleotide sequence of its partner strand, both strands actually carry the same
genetic information

If we designate the two strands A and A', strand A can serve as a mold or template
form a king a new strand A', while strand A can serve in the same way to make a
new strand A.

Thus genetic information can be copied by a process in which strand A separates

from strand A and each separated strand then serves as a template for the
production of a new complementary nucleic acids partner strand.
The Nucleotide Sequence of a Gene Determines
the Amino Acid Sequence of a Protein

DNA is relatively inert chemically.

The information it containsis expressed in directly via other molecules: DNA directs
the synthesis of specific RNA and protein molecules , which in turn determine the
cell's chemical and physical properties.

At about the time that bio physicists were analyzing the three-dimensional structure
of DNA by x-ray diffraction, biochemists were intensively studying the chemical
structure of proteins.
 It was already known that proteins are chains of amino acids joined to gether by sequential
peptide linkages; but it was only in the early 1950s, when the small protein insulin was
sequenced.
It was discovered that each type of protein consists of a unique sequence of amino acids.

Sequencing insulin provided a key to understanding the structure and function of proteins.

If insulin had a definite, genetically determined sequence, then presumably so did every
other protein. It seemed reasonable to suppose, more over, that the properties of a protein
would depend on the precise order in which its constituent amino acids are arranged.
 Both DNA and protein are composed of a linear sequence of sub units; eventually,
the analysis of the proteins made by mutant genes demonstrated that the two
sequences are co-linear- that is, the nucleotides in DNA are arranged in an order
corresponding to the order of the amino acid sin the protein they specify.
 The strand back bones are closer together on one side of the helix than on the
other.
The major groove occurs where the back bones are far apart.
The minor groove occurs where they are close together.
FORMS OF DNA
 Forms of DNA
Properties A-form B-form Z-form

Helical sense Right handed Right handed Left handed

Diameter ~2.6 nm ~2.0 nm ~1.8 nm

Base-pairs per 11 10.5 12

helical turn(n)

Helix rise per bp 0.26 nm 0.34 nm 0.37 nm

Helix pitch 2.8 nm 3.4 nm 4.5 nm

Major groove Narrow Wide Flat

Minor groove Wide Narrow Narrow

 Denaturation of DNA
How observed A260 ?
Denaturation by heating.
For dsDNA,
A260=1.0 for 50 g/ml

For ssDNA and RNA

A260=1.0 for 38 g/ml

The T at which the DNA sample is denatured is

called the melting temperature (Tm)
Importance of Tm
Critica limportance in any technique that relies on complementary base pairing
Designing PCR primers
Southern blots
Northern blots
Southern Blot
Chemical & Physical Properties
of Nucleic Acids
Effectofacid

At strong acid e.g. per chloric acid(HClO4) & at elevated temperature (100C),
nucleic acids are hydrolyzed (bases, sugar & phosphate)

In diluted acid (pH3-4) , hydrolyzed selectively (glycosydic bonds are broken) and
nucleic acid becomes apurinic/apyridimic.
Effect of alkali

At increasing pH in RNA phosphodi ester bond is broken down because of 2 OH

group is not present in DNA.
At neutral pH RNA is hydrolyzed
Chemical Denaturation

Chemical agents e.g. Urea and form amide cause denaturation of DNA/RNA at
neutral pH.
These chemicals disrupt the hydrogen bond