Physical and Chemical

Properties of DNA
Structure of Nucleotides
 “Bases”
A G
•2 purine bases
•Adenine: A
•Guanine: G 6-amino
purine
•Bases
•Pyrimidines
•Purines

2,6-dihydroxy
pyrimidine

C T U
•2 pyrimidine bases (in DNA)
•Cytosine: C
•Thymine: T
•or Uracil: U
(in RNA, instead of Thymine)
 Ribose and phosphate

• β-furanose
pentoses in both
• carbons
numbered:
• 1’,2’,3’,4’,5’
• DNA: 5’
• 2’ Deoxyribose
• or just
deoxyribose 1’

➢ Phosphate 4’
• Gives negative
charge 3’
2’
•Cells can store information for long term & if alterations happens, they
sometimes become significant like mutations
•Carcinogenesis and aging are also slow irreversible accumulation of
alterations in DNA
•Among these alterations → some are non-destructive and important for
function → strand separation for replication & transcription
Structure of Nucleotides
 “Bases”
A G
•2 purine bases
•Adenine: A
•Guanine: G 6-amino
purine
•Bases
•Pyrimidines
•Purines

2,6-dihydroxy
pyrimidine

C T U
•2 pyrimidine bases (in DNA)
•Cytosine: C
•Thymine: T
•or Uracil: U
(in RNA, instead of Thymine)
 Ribose and phosphate

• β-furanose
pentoses in both
• carbons
numbered:
• 1’,2’,3’,4’,5’
• DNA: 5’
• 2’ Deoxyribose
• or just
deoxyribose 1’

➢ Phosphate 4’
• Gives negative
charge 3’
2’
 Nucleic Acid Chemistry → a powerful array of
technologies that have applications in molecular
biology, medicine and forensics

•Cells can store information for long term & if alterations

happens, they sometimes become significant like mutations
•Carcinogenesis and aging are also slow irreversible accumulation
of alterations in DNA
•Among these alterations → some are non-destructive and
important for function → strand separation for replication &
transcription
Solubility

• DNA is polar in nature and thus soluble in water. Its highly

charged phosphate-sugar backbone gives it its polarity.
However, in the presence of salt and alcohol, it is insoluble.
• Salting in and Salting out
Absorption
• At 260 nanometers, the DNA bases can absorb ultraviolet light.
A spectrophotometer can measure this absorption. The amount
of ultraviolet light absorbed increases with the order of the
bases. For example, at 260 nm, a single-stranded DNA absorbs
1.37 units, whereas a double-stranded DNA absorbs 1.00 unit at
260 nm
• All molecules absorb radiant energy at a
specific wavelength, from which it is possible to
extrapolate the concentration of a solute within a
solution.

According to the Beer-Lambert law there is a linear

relationship between the absorbance A (also called
optical density, OD) and the concentration of the
macromolecule given by the following equation:

A=OD=εlc

Where ε is the molar extinction coefficient, c is the

concentration; and l is the pathlength of the cuvette.
Proteins and nucleic acids absorb light in the ultraviolet
range within wavelengths of between 210 and 300 nm. As
previously explained, the maximum absorbance of DNA
and RNA solutions is at 260 nm whereas the maximum
absorbance of protein solutions is at 280 nm.
Denaturation and Renaturation

• On heating, both strands denature, and on cooling, they can

renature. The melting temperature, which varies depending on
the precise DNA sequence, is the temperature at which these
strands are permanently separable.
• In contrast to the region of higher concentration A-T, which is
only bonded with two hydrogen bonds, the region of higher
concentration of C-G has a higher melting temperature because
these bases are bonded with three hydrogen bonds, which
require more energy to break.
DNA/ RNA denaturation

➢DNA/ RNA denaturation: (Reversible, Change in 3-D structure that is

due cleavage of all weak cross linkages inside the molecule except
covalent backbone and can be renatured)
✓E.g. at pH=7, 25oC DNA solutions are viscous but → extreme pH +
temperature above 80 oC decreases viscocity (physical change, solubility)
→ similar to denaturation of proteins → denaturation of DNA
DNA/ RNA denaturation
❖Disruption of the hydrogen bonds between
paired bases and of base stacking cause
unwinding of the double helix to form two
single strand , no covalent bond broken → on
attaining same pH or temp → renaturation or
annealing to intact duplex → partial
denaturation
❖ If completely strands are separated →
complete denaturation → both strands first
find by random collisions each other short
complementary segments and then zipper
themselves fastly to duplex
❖ Hypochromic effect → absorption of UV
light decreases as free strands or nucleotides
are again in duplex form → Hyperchromic
effect when denatured
 When DNA is denatured, the melting point is when half of the DNA is
present as separated single strands → melting temperature tm → different
for different DNA

The greater the G≡C content, the higher the melting point (tm) → tm indicates base
compositions
Electron micrograph showing partially denatured DNA
Red arrows indicate regions of high A-T content, which denature first on careful
increase of temperature

Bubbles

The same happens during replication and transcription which starts from AT rich
sequences
➢ DNA duplexes ↓ stable as compared to DNA-RNA hybrid duplex which is itself ↓
stable to RNA-RNA or RNA duplexes
 Hybridization (DNA or RNA)

❑2 complementary DNA strands can pair with one another → to detect

similar DNA sequences in 2 different species or within the same specie
genome.
❑E.G., human and mouse DNA below tm → Duplex hybrids
❑DNA annealing → temperature, length & conc. of DNA fragments
annealed, concentration of salts of
reaction mixture, and properties of the sequence (GC%)
❑Low temperature → important → too low can anneal even distant
matching parts
❑Common evolutionary heritage → related functional and
structural proteins have same DNAs →
❑applications in
❑modern genetic techniques (Blotting)→ to nitrocellulose
membrane and checking gene sequences by probing
❑unknown genes with known functions can be isolated,
individuals can be identified, diseases before onset can be
detected.