Forces That Stabilize the DNA structure.pptx

1. Forces That Stabilize the DNA
structure

2. PHYSICAL PROPERTIES OF DNA
• DNA base pairs--called complementary base pairing ---- hydrogen bonds
between bases.
• This arrangement of two nucleotides binding together across the double
helix is called a base pair.
• In a double helix, the two strands are also held together via forces
generated by the hydrophobic effect and pi-stacking, which are not
influenced by the sequence of the DNA.

3. Stability of Double Helix: Forces in
duplex DNA
• Since biological processes are regulated, fundamentally, through specific DNA-protein
recognition, and DNA protein recognition is controlled by DNA conformation, the study of
duplex DNA structure and stability is highly significant. Various Weak Forces come together
to stabilize the DNA structure.
• Hydrogen bonding (2-3 kcal/mol per base pair)
• Stacking interactions (4-15 kcal/mol per base pair)
– Hydrophobic interactions
– van der Waals interactions
• Charge-Charge Interactions
• Solvation
• These are cooperative forces; each contributes a little, but adds up because DNA chains can
be millions of nucleotides long.

4. DNA Stability…..?
DNA double stranded helical structure is stabilize by
• Hydrogen bonding
• Base stacking interaction
• Hydrophobic force
• Ionic interaction

5. DNA Stability…..?
Hydrogen bonding-
 hydrogen bond b/w base pairs- G with C, and A
with T.
 It is important to note that three hydrogen bonds
can form between G and C, but only two bonds
can be found in A and T pairs.
 This is why it is more difficult to
separate DNA strands that contain more G-C pairs
than A-T pairs. On the other hand, A-T pairs seem
to destabilize the double helical structures. This
conclusion was made possible by a known fact that
in each species the G content is equal to that of C
content and the T content is equal to that of A
content.
 Although weak energy-wise, is able to stabilize the
helix because of the large number present
in DNA molecule

6. DNA Stability…..?
Base stacking interaction-
• also known as Van der Waals interactions between bases are weak, but the
large amounts of these interactions help to stabilize the overall structure of
the helix.
– Double helix is stabilized by hydrophobic effects by burying the bases
in the interior of the helix increases its stability; having the hydrophobic
bases clustered in the interior of the helix keeps it away from the
surrounding water, whereas the more polar surfaces, hence hydrophilic
heads are exposed and interaction with the exterior water
– Stacked base pairs also attract to one another through Van der Waals
forces the energy associated with a single van der Waals interaction has
small significant to the overall DNA structure however, the net effect
summed over the numerous atom pairs, results in substantial stability.
– Stacking also favors the conformations of rigid five-membered rings of the
sugars of backbone.
– Evidence of Stacking interactions: Compounds that interfere with
Hydrogen bonds (urea, formamide) don’t separate strands by themselves,
still requires heat.

7. DNA Stability…..?
Ionic interaction-
• Ion-ion repulsion of the negatively charged phosphate make DNA duplex
unstable.
• However the presence of Mg2+ and cationic proteins with abundant
Arginine and Lysine residues that stabilizes the double helix.
• Double-stranded helix structure thus, promoted by having phosphates on
outside, interact with H2O and counter ions (K+, Mg2+, etc.).

8. DNA Stability…..?
Hydrophobic force-
• The hydrophobic interactions
between the planar base pairs
stabilize the bases on the inside
of the helix, so these provide
stability to the structure but do
not contribute to the specificity.
• Hydrophobic Interactions are
important for the folding, stability
and biological activity.

9. The absorbance of the solution changes as shown in the graph below. The increase in
absorbance as the strands separate is due to the irregular orientation of the bases in the
SS-DNA compared to the regular planar orientation in the helix.

11. In fact the Tm of a given DNA is linearly dependent on the log of
the monovalent cation concentration..