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210 Biomimetics: Biologically Inspired Technologies

moving nano-scale device. A method for localized element-specific motion control was seen in the
reversible transition between four stranded topoisomeric DNA motifs (PX and JX2) thereby
producing rotary motion (Yan et al., 2002). A very important, though simple DNA machine that
resembles a pair of tweezers has been successfully created, whose actuation (opening and closing)
is also fueled by adding additional DNA fuel strands (Yurke et al., 2000).

7.2.3 Nanosensors

The technology of nanosensing is also under development. For example, silicon probes with
single walled carbon nanotube (CNT) tips are being developed (MIT Media Laboratory Nanoscale
Sensing, http://www.media.mit.edu/nanoscale/). For sensing certain analytes, genetically engi-
neered versions of pore-forming proteins like Staphylococcus aureus a-hemolysin are also being
studied Braha et al., 1997. Light sensors could be made using certain photoreceptive polypeptides
containing azobenzene or spyropyran units as they respond to light or dark environmental condi-
tions by undergoing conformational change, for example, transition from random coil to a a-helix
(Pieroni et al., 2001). An optical DNA biosensor platform has been reported using etched optical
fiber bundles filled with oligonucleotide-functionalized microsphere probes (Ferguson et al., 1996).
Finally, work is in progress to develop sensors for brain implantation, which would foretell the
development of a stroke and be useful for perioperative online monitoring during coronary by-pass
surgery (Manning and McNeil, 2001).
In addition to many of the examples mentioned above which generally correspond to one degree
of freedom (DOF) rotary actuators, there are many other machine elements, the functional capabil-
ities of which have not yet been represented by biomolecular elements. In addition, the assembly of
different molecules in a multi-degree of freedom machine or the formation of hybrid systems
composed of biomolecules and synthetic nonorganic elements has not yet been explored. In this
context, our long term goal is to identify novel biomolecules that can be used as different types of
machine components and to assemble them into controlled multi-degree of freedom systems using
organic and synthetic nonorganic parts.

7.3 DESIGN AND CONTROL PHILOSOPHIES FOR NANOROBOTIC SYSTEMS

The design of nanorobotic systems requires the use of information from a vast variety of sciences
ranging from quantum molecular dynamics to kinematic analysis. In this chapter we assume that
the components of a nanorobot are made of biological components, such as proteins and DNA
strings. So far, no particular guideline or a prescribed manner that details the methodology of
designing a bio-nanorobot exists. There are many complexities that are associated with using
biocomponents (such as protein folding and presence of aqueous medium), but the advantages of
using these are also quite considerable. These biocomponents offer immense variety and function-
ality at a scale where creating a man-made material with such capabilities would be extremely
difficult. These biocomponents have been perfected by nature through millions of years of evolu-
tion and hence these are very accurate and efficient. As noted in the review section on Molecular
Machines, F 1 -ATPase is known to work at efficiencies which are close to 100%. Such efficiencies,
variety, and form are not existent in any other form of material found today. Another significant
advantage in protein-based bio-nano components is the development and refinement over the last
30 years of tools and techniques enabling researchers to mutate proteins in almost any way
imaginable. These mutations can consist of anything from simple amino acid side-chain
swapping, amino acid insertions or deletions, incorporation of nonnatural amino acids, and even
the combination of unrelated peptide domains into whole new structures. An excellent example of