Biomedical Engineering Reference
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the larger binding force. This result indicates that the complementary ssDNA chains
exist in the nonequilibrium state. It was believed that when the chain length is larger
than 1,000 bp, the shear force will increase to
70 pN, which is almost the same for
the B-S transition. Thus, it is reasonable to speculate that the shear mode stretching
is actually the process of B-S transition.
In 2008, Gaub et al. found that shear starching force with the 3
0
-3
0
end need
higher force than that with 5
0
-5
0
end. It was believed that dsDNA can form different
conformations with different direction in shear stretching [
54
].
6.5
Binding Force Between a Single DNA Molecule
and Other Matter
In the previous sections, we have introduced the single-molecule mechanics of
DNA itself. In many other situations, DNA is exposed to interact with other
molecules/materials, such as an intercalator or a solid surface. Here we will
introduce some recent progresses in this field. To ensure that the interactions
between DNA and the substrate are measured in the experiments, the single DNA
molecule is often chemically attached to the AFM tip.
6.5.1
Binding Force Between a Single Molecule of dsDNA
and Acridine
Acridine and its derivatives are typical intercalation agents for dsDNA, which can
insert themselves into the neighboring base pairs. In 2007, Zhang and his coworkers
directly measured the binding force between a single molecule of dsDNA and
acridine [
55
]. They found that the binding force was loading rate dependent, which
was 36 pN at a loading rate of 5 nN/s and increased with the increasing loading
rate. Bell-Evans modeling revealed that there were two energy barriers along with
the unbinding trajectory of acridine-dsDNA. One barrier was attributed to the short-
range interactions, such as pi stacking and hydrogen bonding. The other barrier
was attributed to the long-range interactions, such as hydrophobic interaction in the
binding site.
6.5.2
Desorption Force of Single Molecule of ssDNA
from a Solid Substrate
In 2006, Kuehner et al. reported that the desorption force of a single molecule of
ssDNA from the Mg
2C
50 pN [
56
]. More
ions functionalized mica substrate is
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