DISSERTATION

______________________________________________________________________ Introduction
where L is the contour length of DNA. The persistence length is a basic mechanical property of
a polymer and it is a measure of its stiffness. It is defined as a characteristic length over which
the chain maintains a certain direction 37 . When the contour length is smaller than the persistence
length a polymer behaves as a rigid rod, while a flexible coil behavior is observed for contour
lengths much higher than the persistence length. The persistence length of dsDNA is considered
to be around 50 nm 38 , while the persistence length of ssDNA is only 1-2 nm 39,40 . Thus, dsDNA
is expected to behave as a rigid rod and ssDNA as a flexible chain (Figure 1.5).
dsDNA
ssDNA
L = N bp × b = 20 × 0.34 nm
L = 6.8 nm
l p ≈ 50 nm
L ≪ l p (rigid rod)
L = N b × b = 20 × 0.43 nm
L = 8.6 nm
l p ≈ 1 to 2 nm
L > l p (flexible chain)
Figure 1.5. Dependence of the DNA mechanical properties on the persistence length
shown for an example of a 20-mer DNA strand. Nbp and Nb represent the number of base
pairs and number of bases, respectively, while b represents the charge separation.
Nevertheless, the persistence length consists of two contributions:
l p = l 0 + l el (1.10)
where l0 is an intrinsic stiffness due to chain properties and lel is the electrostatic repulsion
within the chain, which depends on the ionic strength:
l el =
l B
(2bκ) 2 (1.11)
Through the Debye length, the ionic strength influences the flexibility of charged polymers,
which should be considered especially while investigating the behavior of ssDNA in solution.
In solutions of increased ionic strength, the Debye length decreases leading to a decrease in the
1.2 DNA 11