DNA must be tightly packaged to fit inside cells. It is coiled around histone proteins to form nucleosomes, which are connected by linker DNA. Multiple nucleosomes then coil further to form the chromatin fiber. DNA is also supercoiled, winding and twisting upon itself, which allows it to condense even smaller. Supercoiling takes two forms - negative supercoiling unwinds the DNA slightly while positive supercoiling winds it more tightly. In cells, DNA is typically negatively supercoiled to favor processes like transcription and replication.

1. DNA Coiling

2. DNA is a big molecule
• Ruptured viral particle
(bacteriophage)
X95 000
• DNA about 1.7µm
© 2010 Paul Billiet ODWS

3. Supercoiling of topologically
constrained DNA
• Topologically closed DNA can be circular
(covalently closed circles) or loops that are
constrained at the base
• The coiling (or wrapping) of duplex DNA around
its own axis is called supercoiling.

4. Different topological forms of DNA

5. THE NUCLEOSOME
• Uncoiled the DNA of a human would stretch
2m
• The average diameter of a nucleus is 10µm
• The problem: To pack the DNA into the
nucleus and yet have access to the genetic
information.
© 2010 Paul Billiet ODWS

6. THE NUCLEOSOME
• Histones are made of a lot of
basic amino acids
• Combined with acidic DNA
they make a stable
nucleoprotein called
chromatin
Histone core =
an octomer
(8 histone molecules)
Histone molecules
© 2010 Paul Billiet ODWS

7. DNA wraps twice round the core
DNA strand
© 2010 Paul Billiet ODWS

8. DNA held in place by another histone (H1) = the
nucleosome
H1
© 2010 Paul Billiet ODWS

9. Nucleosomes are joined by linker DNA
Linker DNA

10. DNA super coiling
DNA double helix
Nucleosome beads on a
string
30-nm chromatin fibre

11. DNA super coiling
30-nm chromatin fibre
Chromosome in
extended form
Condensed section of
chromosome in
mitosis
© 2010 Paul Billiet ODWS

12. DNA super coiling
Condensed section
of chromosome in
mitosis
Condensed
chromosome
© 2010 Paul Billiet ODWS

13. Negative and positive supercoils
• Negative supercoils twist the DNA about its axis in
the opposite direction from the clockwise turns of
the right-handed (R-H) double helix.
– Underwound (favors unwinding of duplex).
– Has right-handed supercoil turns.
• Positive supercoils twist the DNA in the same
direction as the turns of the R-H double helix.
– Overwound (helix is wound more tightly).
– Has left-handed supercoil turns.

14. Components of DNA Topology : Twist
• The clockwise turns of R-H double helix
generate a positive Twist (T).
• The counterclockwise turns of L-H helix (Z
form) generate a negative T.
• T = Twisting Number
B form DNA: + (# bp/10 bp per twist)
A form NA: + (# bp/11 bp per twist)
Z DNA: - (# bp/12 bp per twist)

15. Components of DNA Topology :
Writhe
• W = Writhing Number
• Refers to the turning of the axis of the
DNA duplex in space
• Number of times the duplex DNA
crosses over itself
Relaxed molecule W=0
Negative supercoils, W is negative
Positive supercoils, W is positive

16. Components of DNA Topology : Linking number
• L = Linking Number = total number of times
one strand of the double helix (of a closed
molecule) encircles (or links) the other.
• L = W + T

17. L cannot change unless one or both strands are
broken and reformed
• A change in the linking number, DL, is
partitioned between T and W, i.e.
• DL=DW+DT
• if DL = 0, then DW= -DT

18. Relationship between supercoiling and twisting

19. DNA in most cells is negatively supercoiled
• The superhelical density is simply the number
of superhelical (S.H.) turns per turn (or twist)
of double helix.
• Superhelical density = s = W/T = -0.05 for
natural bacterial DNA
–i.e., in bacterial DNA, there is 1 negative
S.H. turn per 200 bp
• (calculated from 1 negative S.H. turn per 20
twists = 1 negative S.H. turn per 200 bp)

20. Negatively supercoiled DNA favors
unwinding
• Negative supercoiled DNA has energy stored
that favors unwinding, or a transition from B-
form to Z DNA.
• For s = -0.05, DG=-9 Kcal/mole favoring
unwinding
Thus negative supercoiling could favor initiation
of transcription and initiation of replication.