Biomedical Engineering Reference
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Fig. 6.18 Single-molecule
force curves of dsDNA and
ssDNA in an organic solvent,
diethylbenzene (Reprinted
with permission from Ref.
[ 41 ]. Copyright 2007
American Chemical Society)
the plateau of 65 pN [ 43 , 44 ]. The rest of the experimental results support that the
second transition ( 150 pN) corresponds to the melting process [ 31 , 42 ].
6.4.3
Single-Molecule Mechanics of dsDNA
in Organic Solvents
Normally, the environment of DNA is aqueous solution. It is known that water
molecules have been shown to play an important role in the internal conformation
of DNA strands. But it is difficult to discern effects of water molecules in aqueous
media [ 45 ]. DNA is soluble in some nonaqueous solvents (such as formamide) and
gets denatured into ssDNA, just as treated with high concentration of denaturant
aqueous solution [ 46 ]. Besides these, more organic solvents are poor solvent for
DNA. Recent studies revealed that DNA condensates into toroids in poor solvents
[ 47 - 49 ]. Other detailed information of DNA in poor solvents was still unclear.
In 2007, Cui et al. reported the single-molecule mechanics of dsDNA in organic
solvents. The fingerprint plateaus disappeared in the force curves. The force curves
cannot be distinguished from that of ssDNA (see Fig. 6.18 ). One can speculate that
dsDNA is denatured into ssDNA in the organic solvents [ 41 ].
The results from molecular dynamics simulations show that, if one end of the
dsDNA is dragged from the aqueous phase into the oily phase, dsDNA will be
denatured at the interface (see Fig. 6.19 [ 41 ]). Previous extensive studies showed
that in aqueous environment, the DNA duplex was maintained by several weak
intermolecular interactions, including hydrogen bonding, pi-pi stacking, van der
Waals interactions, and hydrophobic force [ 50 ]. Among others, the hydrophobic
force is very important. In the organic solvents, the hydrophobic force is absent.
Thus, dsDNA is destabilized and tends to be denatured upon external disturbance.
The destabilization effect of organic solvent may be utilized by enzymes, which
helps to unwind dsDNA in the pocket [ 39 , 41 ].
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