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Bio-Nanorobotics 209

into the external medium. In addition to rotary engines and propellers, E. coli’s standard accessories
include particle counters, rate meters, and gearboxes and thus have been described as a nanotech-
nologist’s dream (Berg, 2000). Berg developed one of the earliest models for the rotary motor
(Berg, 1974). Improved models came in 1992 (Ueno et al., 1992, 1994). Flagella motor analysis
coupled to real-time computer assisted analysis of motion has also been performed (Khan et al.,
1998). Researchers in Japan have applied crystallographic studies in order to understand the
molecular structure of flagella motors as well as that of kinesin (Namba and Vonderviszt, 1997).
Finally, Hess’ group is attempting to build a nano-scale train system, complete with tracks, loading
docks and a control system. Since motor proteins are a thousand times smaller than any man-made
motor, they aim to utilize them in a synthetic environment as engines powering the nanotrains (Hess
and Vogel, 2001).

7.2.2.4 Other Motors and Mechanisms

In addition to work on naturally existing motors, considerable effort is also being applied to
develop synthetic molecular motors. The structure of the ATP synthase, a rod rotating inside a
static wheel, suggests the use of rotaxanes as potential artificial models for natural motors (Harada,
2001). Rotaxanes are organic compounds consisting of a dumbbell-shaped component that incorp-
orates one or more recognition sites in its rod section and is terminated by bulky ‘‘stoppers,’’
encircled by one or more ring components. The possibility of manufacturing specific forms of
rotaxane and creating molecular motors capable of guided rotary motion and the possibility of
fueling such a motor by light, electrons, and chemical energy have been proposed (Schalley
et al., 2001).
Schemes for using pseudorotaxanes, rotaxanes, and catenanes as molecular switches to perform
chemical, electrochemical, and photochemical switching and controllable molecular shuttles have
also been proposed recently (Balzani et al., 1998). Molecular shuttles have been reported using
a-cyclodextrin — a parent of rotaxanes and catenanes (Harada, 2001). A light-driven monodirec-
tional rotor made of helical alkene, with rotation around a central carbon–carbon covalent bond due
to chirality has been reported (Koumura et al., 1999). Another simple way to convert chemical
energy into mechanical motion in a controlled fashion is by using a metal ion which can be
translocated reversibly between two organic compartments with the change of its ionization state,
controllable by redox reaction or pH change (Amendola et al., 2001). Motility of unicellular
organisms like vortecellids reminds us of energy storage and release by mechanical springs on a
macromolecular scale. Spring-like action has been observed in sperm cells of certain marine
invertebrates during fertilization. Springs and supramolecular ratchets by actin polymerization
have yet to be built in vitro, but they theoretically can be generalized, as recently demonstrated
(Mahadevan and Matsudaira, 2000).

7.2.2.5 DNA-Based Molecular Nanomachines, Joints, and Actuators

Several researchers are exploring the use of DNA in nano-scale mechanisms. DNA is small,
relatively simple, and homogeneous and its structure and function is well understood. The predict-
able self-assembling nature of the double helix makes it an attractive candidate for engineered
nanostructures. This property has been exploited to build several complex geometric structures,
including knots, cubes, and various polyhedra (Seeman, 1998). Mathematical analyses of the elastic
structure of DNA using energy minimization methods have been performed to examine its
molecular stability, wherein short DNA strands were treated as an elastic rod (Tobias et al.,
2000). Initial experiments on DNA visualization and manipulation using mechanical, electrical,
and chemical means have been underway for a decade (Yuqiu et al., 1992; Hu et al., 2002).
A dynamic device providing atomic displacements of 2–6 nm was proposed in Mao et al. (1999),
wherein the chemically induced transition between the B and Z DNA morphologies acts as a