Single-Molecule Mechanics of DNA - DNA Nanotechnology: From Structure to Function - page 98

350
300
250
200
150
100
50
0

In aqueous solutions

In organic solvents

0.80
Normalized extension,

0.90 1.00

R / L 0

Fig. 6.15 Left : experimental force curves of ssDNA in various aqueous solutions. The dotted line
is the QM-FJC fitting curve. Right : the smoothed force curves obtained in aqueous solutions and
organic solvent (Reprinted with permission from Ref. [ 33 ]. Copyright 2006 American Chemical
Society)

positive result indicates that all the preconditions are tenable: (1) the ab initio results
from the literature are precise enough, (2) the QM - FJC model is appropriate for
ssDNA, (3) the Kuhn length of ssDNA is 0.59 nm, and (4) the ab initio calculation
results obtained in vacuum condition can be applied to the condition in organic
solvents.
We find that for ssDNA, the optimum value of the Kuhn length in QM-FJC is
0.59 nm, which is exactly the length of a repeating unit of ssDNA [ 19 ]. The single-
chain elasticity used in the model fitting was obtained by the ab initio calculations.
The consistence between the real physical parameters and the modeling parameters
suggests that the QM-FJC is a structure relevant model. The reliable inherent single-
chain elasticity of ssDNA can serve as the basis for further studies of dsDNA as well
as the rational design of DNA-based nano-devices in the future.

6.3.3 The Deviation Between the Force Curves of ssDNA

Obtained in Organic Solvent and Aqueous Solutions

By stretching single chain of ssDNA in various aqueous solutions, Cui et al. found
that all the force curves can be superimposed well, despite of the difference in
salt concentration. This result indicates that the aqueous solutions are a class of
environment where ssDNA shows the same single-chain mechanical properties (see
Fig. 6.15 [ 33 ]). It was reported by Dessinges et al. that the single chain of ssDNA
presents a salt concentration-dependent mechanics only when the force is below
10 pN [ 36 ]. Normally, the valid force is higher than 10 pN in AFM. This can explain
why we did not observe the difference in various salt concentrations in Fig. 6.15 .
The force curves obtained in aqueous solutions and organic solvent were
normalized to the same extension and are shown together in Fig. 6.15 . It can be
observed that at the very low and very high force range, the two force curves
superpose well. In the middle force range (about 35 - 250 pN), however, there is
an obvious deviation.