Recollection of well known

theories, chemistry and

biology
Rajalakshmi

DNA detective
DNA is too small to see, but under a
microscope it looks like a twisted up
ladder!

DNA stands for:

D: Deoxyribose
N: Nucleic RN A stands for:
A: Acid R: Ribose
N: Nucleic
A: Acid
 Nucleic acids
• In most living organisms (except for
viruses), genetic information is stored 36 base pairs
Backbone - blue;
in the molecule deoxyribonucleic acid,
Bases- gray
or DNA. DNA is made and resides in
the nucleus of living cells. DNA gets its
name from the sugar molecule
contained in its
backbone(deoxyribose);
 Major bases in nucleic acids

• The bases are

abbreviated by their first
letters (A, G, C, T, U).
• The purines (A, G) occur
in both RNA and DNA

• Among the pyrimidines, C

occurs in both RNA and
DNA, but
• T occurs in DNA, and
• U occurs in RNA
 Structure of nucleosides

Remove the phosphate group, and you have a nucleoside.

H
 Structure of nucleotides

Nucleotides have three characteristic components:

A nitrogenous base
A phosphate group (pyrimidines or purine)

A pentose sugar
 Chemical composition
 DNA is a polymer of nucleotides. Nucleotides
consist of:
 deoxyribose (5-carbon) sugar
 nitrogenous base
 phosphate group(s)

There are four nitrogenous bases used to make the four

types of nucleotides found in a DNA molecule:
Adenine, Thymine, Cytosine and Guanine.
 Nucleotides and nucleic acids

Nucleotides are the building blocks of nucleic acids

Nucleotide
RNA DNA
 Base + sugar = Nucleoside
 Base + sugar + phosphate = Nucleotide

Nucleotides are stronger because of the

phosphate linkage

Sugar is Ribose its RNA whereas if it is

Deoxy ribose then DNA
Interstrand H-bonding between DNA bases

Watson-Crick base pairing

 Pyrimidine and purine

Nucleotide bases in nucleic acids are pyrimidines or purines.

 Deoxyribonucleotides
2'-deoxyribose sugar
with a base (here, a purine,
adenine or guanine)
attached to the C-1'
position is a
deoxyribonucleoside
(here deoxyadenosine and
deoxyguanosine).

Phosphorylate the 5' position

and a nucleotide(here,
deoxyadenylate or
deoxyguanylate)

Deoxyribonucleotides are abbreviated (for example) A, or

dA (deoxyA).
 There are four nitrogenous bases that are
found in DNA: adenine, thymine, guanine
and cytosine.
 Adenine and thymine are purine bases (2-
ring structure)
 Cytosine and guanine are pyrimidines
(single-ring structure)
 Backbone of DNA is
 The phosphodiester bond of the nucleotide
chain is formed between the phosphate
attached to the 5´ carbon of one sugar and
the 3´ carbon of the next.

 The5´ end of the strand bears a phosphate

group; the 3´ end bears a hydroxyl (OH)
group.

 Thetwo strands of DNA in a helical molecule

are antiparallel to each other.
 Chargaff’srules
Base composition varies among species.
Base composition is constant for all cells
of an organism and within a species.
The amount of adenine equals the amount
of thymine. (A = T)
The amount of cytosine equals the
amount of guanine. (C = G)
The amount of purine bases equals the
amount of pyrimidine bases.
 Within cells the standard structure of DNA is the
B form.
 The B form structure consists of two antiparallel
polynucleotide chains twisted around one
another to form a double helix.
 The nitrogenous bases form the “rungs” in the
center of the helix, with
adenine forming hydrogen bonds with thymine and g
 The helix is right-handed, and each chain
makes one complete turn every 34 angstroms.
 Base pairing was worked out by trial and
error. The distance between the sugar-
phosphate backbone groups is constant
Therefore pu rin e-pu rin e or pyr imidin e-
pyr imidi ne were not allowed because spacing
would be in inconsistent with data
 Purines = A and G (two organic rings)
 Pyrimidines – C and T ( one organic ring)

Pu rin e- pyr imid inebase pairing would be

consistent with X-ray data
Hydrogen bonding between purines and
pyrimidines established the appropriate pairs and
reinforced Chargaff’s Rules
2 hydrogen bonds between
A and T
 3 hydrogen bonds between

G and C
 Area of Research

 Construction of a small molecule which

binds this DNA, if it is a organic molecules
called as ligands, intercalators.
 Metal ions, present along with the
intercalators are called as
metallointercalator.
 The ligands which recognizes the specific
 The earliest work on the DNA-binding of
metal centers focused on
tris(phenanthroline) complexes of Ru, Cr,
Zn, Ni, and Co. Photo physical and NMR
studies suggested that these complexes
bind to DNA via
hydrophobic interaction in the minor
groove and intercalation of a
phenanthroline ligand into the helix in the
major groove.
 Intercalators are small organic molecules
or metal complexes that unwind DNA in
order to pi-stack between the two base
pairs.
 Eg. Two well known intercalating ligands
are phi(9,10-phenanthrenequinone
diammine) and dppz.
 Ru and dppz- based metallo-intercalators
have proven to be molecular light
switches for the detection of DNA.
 Rh intercalators have been shown to be
efficient agents for photoactivated DNA
strand cleavage.
 Metallo intercalator and insertor

 Metallo-intercalatorsenter the double helix via

the major groove, with the intercalating ligand
acting as a new base pair. Intercalation results in
a doubling of the rise and a widening of the
major groove at the binding site.
 Metallo insertors unwind the DNA and insert
their planar ligand between two intact base pairs,
it ejects the bases of a single base-pair with the
incoming ligand acting as a pi- stacking
replacement in the DNA base stack.
Th e “ Best is ye t to Co me”

By,
S. Rajalak sh mi.