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UNIT 2: DNA: The Chemical

(Structural) Basis of Heredity

Deoxyribonucleic acid (DNA)
DNA it is the chemical basis of heredity and is organized into
GENES, the fundamental units of genetic information.
- it contains the genetic information that resides in the sequence
of the monomeric purine and pyrimidine deoxyribonucleotides which
are properly ordered and arranged in a linear chain.
The Chemical Nature of DNA

DNA complex polymers of monomeric deoxyribonucleotide units (dAdenine, dGuanine, dCytosine

and dThymine) that are joined together by 3,5-phosphodiester bridges of a single strand.
A mechanism of reproducing this specific
information with a high degree of fidelity.
Chargaff rules: [A] = [T]; [G] = [C]
Stabilizing forces of the double-stranded
Hydrogen Bonds between the purine &
pyrimidine bases
Van der Waals & Hydrophobic
interactions between stacked adjacent
base pairs
The two strands are antiparallel; one
strand runs in the 5-3 direction and the
other in 3-5 direction.
The DNA double helix
DNA is a two stranded polymer of deoxyribonucleotides linked by phosphodiester
bonds. The biologically most common form of DNA is B-DNA, which has the following
structural features noted by Watson, Crick and Franklin.
1. The two anti-parallel strands wind in a right-handed manner around a common
axis to produce a 20-A- diameter double helix.
2. The planes of the nucleotide bases are perpendicular to the helix axis.
3. Each base pair has the same width which accounts for the near-perfect symmetry
of the DNA regardless of the base composition.
4. The helix has a pitch (rise per turn) of 34 A which contains 10 base pairs.
Watson and Crick Model of DNA double helix
Structural Variants of DNA: Secondary Structures
Comparison of the Structural Variants
Structural features A B Z
Helical sense Right-handed Right-handed Left-handed
Diameter 26 A 20 A 18 A
Base pairs
11.6 10 12 (6 dimers)
per helical turn
Helix pitch 34 A 34 A 44 A
Major groove Narrow and deep Wide and deep Flat
Minor groove Wide and shallow Narrow and deep Narrow and deep
Glycoside bond Anti for pyrimidines, C3
Anti Anti
formation endo for purines
Occupy the core of the Tilted away from the
Base Pairs Orientation Inclined to the helix axis
helix axis core of the helix
Sugar-phosphate C3-endo for purines and
C2-endo conformation C3-endo conformation
backbones orientation C2-endo for pyrimidines
DNA has Limited Flexibility
1. The structurally distinct forms of DNA are
not interconvertible with each other, it
actually deviate from their ideal structures.
The transition from one form to
another requires changes in the physico-
chemical properties of DNA such as
denaturation and interactions with DNA-
binding proteins.
2. The seven torsion angles (degrees of
freedom) of nucleotides are subject to
variety of internal constraints that greatly
prohibit their rotational freedom.
3. The vertex angles of ribose ring is
eclipsed on its planar conformation.
4. The sugar-phosphate chains of the double
helix are stiff due to non-covalent
interactions and steric interferences
between residues.
Sterically hindered
orientations of
nucleotide sugar
DNA can be Supercoiled
Supercoiling aka superhelicity (tertiary structure of DNAs or of Nucleic Acids) is
a phenomenon characterized by peculiar twisted appearance of molecules.
It has important roles in the packaging of DNA in cells and in the unwinding
events that occur as part of DNA replication and RNA transcription.

Increasing degree of supercoiling

Topoisomerases Alter DNA Supercoiling
Topoisomerases group of enzymes that catalyze the alteration of the topological
state of circular DNA but not its covalent structure.
2 Classes:
1. Type I Topoisomerases act by creating transient single-strand breaks in DNA.
a. Type IA Topoisomerases catalyze the relaxation of negatively supercoiled DNA
only by changing the linking number by increments of one. They reversibly
catenate (interlink) single-stranded circles.
b. Type IB Topoisomerases can relax both negative and positive supercoils by
transiently cleaving one strand of a duplex DNA through a nucleophilic attack on
the active site of DNA P yielding a 3-linked phosphor-Tyr intermediate.
Proposed Mechanism for Type IA Topoisomerases
Topoisomerases Alter DNA Supercoiling

2. Type II Topoisomerases -
multimeric enzymes that
require hydrolysis to complete
a reaction cycle in which two
DNA strands are cleaved.
duplex DNA is passed through
the break, and the break is
resealed. Both prokaryotic and
eukaryotic Type II enzymes
relax negative and positive
*DNA Gyrase it can
introduce negative supercoils
Forces Stabilizing Nucleic Acid Structures
A. DNA can undergo Denaturation and Renaturation
- denaturation causes the native structure of DNA to collapse and its two complementary
strands separate and assume random conformations. It also causes the absorbance of DNA to increase
by 40% (Hyperchromic effect)
Agents of DNA denaturation include a characteristic high temperature and chemical that induce
unwinding of duplex DNA.
Forces Stabilizing Nucleic Acid Structures
Denaturation of DNA is a cooperative phenomenon in
which the collapse of one part of the structure
destabilizes the remainder.
Melting Temperature, Tm temperature at its midpoint
in which the duplex DNA optimally collapses and
unwind to single strands. It is affected by nature of the
solvent used, identities and concentrations of the ions
in solutions, and the pH. It increases linearly with the
mole fraction of G.C base pairs.

DNA Can be Renatured by Cooling

- Always occur below the Tm of DNA. Aka Annealing
where the complementary strands of RNA and DNA
hybridize (hybridization) forming RNA-DNA double
helices that are only slightly less stable than the
corresponding DNA double helices.
Forces Stabilizing Nucleic Acid Structures
B. Nucleic Acids are stabilized by Base-Pairing, Stacking and Ionic Interactions
1. Watson-Crick Base Pairs normally occur in DNA and is the most stable mode of base pairing in the
double helix because the bases that participate in this pattern have a higher mutual affinity than those in
non-Watson-Crick pair.
2. Stacking Interactions from Hydrophobic Forces purines and pyrimidines tend to form extended
stacks of planar parallel molecules. These stacking forces are a form of van der Waals interaction.
Forces Stabilizing Nucleic Acid Structures
C. Cations Shield the Negative Charges of Nucleic Acids
Arise from the electrostatic interactions of their charged phosphate groups. Binding of positive
charged ions or ligands to DNA, for example, Na+, increase the melting temperature of duplex DNA
because the ions electrostatically shield the anionic phosphate groups from each other.