Biomedical Engineering Reference
In-Depth Information
reported [92]. Like the translational capabilities of the ribosome, this method
has interesting potential applications, including designed polymer synthesis.
Recently, Mao and Tian reported a molecular gear based on DNA [93].
The gears are composed of four DNA single strands: one central circular
strand (C) and three peripheral linear strands (Pi,
i
= 1,2,3). By adding the
complementary ssDNA strands of the teeth strands, gears could continu-
ously roll against each other (Fig. 12b). Another variation of the movement
termed “DNA walker” was recently demonstrated by Shin and Pierce [94]. As
described in Fig. 12c, specific DNA strands are used to connect the single-
stranded extensions to the labels on the track. The connector strands are
equipped with single-stranded toehold sections and can be displaced from
the device by their complementary strand via branch migration. This can be
repeated several times with the appropriate connector and removal strands
to move the walker to arbitrary addresses on the track. Besides the spacial
aspects, another report demonstrated that a DNA-based device can con-
trol its movement cycle time. A tunable nanomechanical device, called the
“nanometronome” has been demonstrated by Ha's team [95]. Their device is
made by introducing complementary single-stranded overhangs at the two
arms of the DNA four-way junction. The rate of ticking is controlled either by
Mg
2+
or by additional controlling elements, single-stranded deactivator and
activator.
4
Double Helix Binding
DNA molecules interact reversibly with a broad range of chemicals that in-
cludes water, metal ions and their complexes, small organic molecules, and
proteins. Apart from the binding on the backbone along the exterior of
the helix, which has been discussed already, there are two locations on the
double-helical structure that primarily interact with small molecules: the
edges of base pairs in either the major or minor grooves, and the interspace
between stacked base pairs. The groove binding (Fig. 1) and intercalation
(Fig. 13) are two major modes of interaction between DNA and other com-
pounds. Intercalation results from insertion of a planar aromatic substituent
between DNA base pairs, with concomitant unwinding and lengthening of the
DNA helix. Groove binding, in contrast, does not perturb the duplex structure
to a great extent. Groove-binders are typically crescent-shaped, and fit snugly
into the minor groove with little distortion of the DNA structure.
However, such DNA ligands are often toxic or carcinogenic. Nowadays it is
well known that several pollutants exhibit carcinogenicity through intercala-
tion into DNA. Some examples are: PAHs or aromatic amines, and some en-
docrine disruptors, in coal tar, atmospheric pollutants, automobile exhaust,
and cigarette smoke. PCDDs, PCDFs, and PCBs have especially emerged as
