In 1959 Richard Feynman delivered what many consider the first lecture on
nanotechnology. This lecture, presented to the American Physical Society at the California
Institute of Technology, prompted intense discussion about the possibilities, or
impossibilities, of manipulating materials at the molecular level. Although at the time of
his presentation, the manipulation of single molecules and single atoms seemed improbable,
if not impossible, Feynman challenged his audience to consider a new field of physics, one
in which individual molecules and atoms would be manipulated and controlled at the
molecular level (Feynman 1960).
As an example of highly successful machines at the “small scale,” Feynman prompted his
audience to consider the inherent properties of biological cells. He colorfully noted that
although cells are “very tiny,” they are “very active, they manufacture various substances,
they walk around, they wiggle, and they do all kinds of wonderful things on a very small
scale” (Feynman 1960). Of course, many of these “wonderful things” that he was referring to
are a result of the activities of proteins and protein complexes within each cell.
The field of nanotechnology has indeed emerged and blossomed since Feynman's 1959
lecture, and scientists from many disciplines are now taking a careful look at the protein
“machines” that power biological cells (Drexler 1986). These “machines” are inherently
nanoscale, ranging in width from a few nanometers (nm) to over 20 nm, and have been
carefully refined by millions of years of evolution.
As a graduate student in molecular biology, I have been especially interested in
creative approaches to bridging the fields of biology and nanotechnology. Both DNA and
protein molecules possess a number of intrinsic characteristics that make them excellent
candidates for the assembly of dynamic nanostructures and nanodevices. Properties such as
the site-specific molecular recognition among interacting protein molecules, the
template-directed self assembly of complementary DNA strands, and the mechanical properties
of certain protein complexes have enabled bionanotechnologists to envision a molecular
world built “from the bottom up” using biological-based starting materials.
In my own research, I have been very interested in investigating protein interactions
and protein pathways on a genome-wide scale. In many ways, protein pathways are analogous
to nanoscale “assembly lines,” since protein pathways often involve a series of proteins
that act in successive order to yield a particular molecular “product” or perform a
particular molecular function. While these protein-based “assembly lines” are commonplace
within biological cells, they prompt two interesting questions with respect to the field of
nanotechnology. First, can we mimic these multicomponent protein-based “assembly lines” on
nanofabricated surfaces? And, second, can we tailor these “nanoscale assembly lines” to
perform new and unique tasks?
Nanomechanical protein complexes, such as the rotary ATP synthase complex, have also
generated much interest from a nanotechnology standpoint (Soong et al. 2000). These protein
complexes enable highly controlled mechanical motion at the nanoscale and may some day lead
to novel rotary machines that function as molecular motors for a variety of nanoscale
applications.
In order to fully exploit these nanoscale protein machines, it is of prime importance to
be able to position individual proteins and protein complexes at the nanoscale.
Progress in this area has recently been reported by Yan et al. (2003), who developed a
method to construct two-dimensional protein arrays using DNA-directed templates. Building
on work pioneered by Nadrian Seeman (Seeman 2003), Yan et al. constructed two-dimensional
DNA “nanogrids” by exploiting the pairing that occurs between complementary DNA strands
(Figure 1). The two-dimensional DNA nanogrid exhibits a repeating periodic structure
(Figure 1B) due to the inherent qualities of the individual DNA tiles that make up the
nanogrid (Figure 1A). The distance between adjacent tile centers is approximately 19 nm
(approximately 4.5 turns of the DNA double helix plus the diameter of two DNA helices).
Yan et al. utilized these DNA nanogrids to assemble periodic protein nanoarrays. The DNA
nanogrid, in this case, served as a molecular scaffold for the self assembly of protein
molecules into ordered arrays. In order to control the location of protein assembly, Yan et
al. first tethered a covalently linked biotin moiety to the central region of each DNA
tile. The biotin was covalently linked to one of the DNA strands at the position
corresponding to the center of the tile. This design resulted in a uniform array of
biotinylated tiles, with each biotin moiety separated by about 19 nm. The authors then
added streptavidin, a protein that has a strong binding affinity for biotin, to form a
periodic streptavidin protein array on top of the biotinylated DNA lattice. The resulting
array represents the first periodic, self-assembled DNA lattice in which individual protein
molecules are precisely positioned into a periodic array with nanometer dimensions.
It is interesting to consider some of the applications of self-assembled protein arrays.
Soong et al. (2000) demonstrated that the ATP synthase protein complex could be used to
power the rotation of an inorganic nickel “nanopropeller.” ATP synthase is a multisubunit
protein complex with a domain that rotates about its membrane-bound axis during the natural
hydrolysis of ATP within a cell. Soong et al. attached a nanoscale inorganic “propeller” to
the rotary stalk of ATP synthase, creating a “rotary biomolecular motor.” It is intriguing
to consider the construction of an ordered array of ATP synthase driven nanomachines, each
positioned precisely along a DNA scaffold, similar to that described by Yan et al. Such an
assembly, combined with proposed “nanogears” (Han et al. 1997), may one day enable the
construction of nanoscale variations of the traditional “gear-train” and “rack-and-pinion”
gearing systems. Construction of such systems may facilitate the design of machines that
can transmit and transform rotary motion at the nanoscale.
In addition to rotary biomolecular motors, proteins that undergo substantial
conformational changes in response to external stimuli might also find some interesting
uses in nanoarrays. Dubey et al. (2003) are working on methods to exploit the pH dependent
conformational changes of the hemagglutinin (HA) viral protein to construct what they term
viral protein linear (VPL) motors. Proteins that undergo substantial conformational changes
in response to environmental stimuli may facilitate the design of nanoscale machines that
produce linear motion (Drexler 1981), as opposed to rotary motion. At neutral pH, the HA
2 polypeptide forms a compact structure composed of two α-helices folded
back onto each other. At low pH, HA
2 undergoes a substantial conformational change, which results in a
single “extended” helix. This conformational change results in a linear mechanical motion,
with a linear movement of approximately 10 nm (Dubey et al. 2003). It would be interesting
to investigate the applications of ordered arrays of dynamic VPL motors, since an array of
such “hinge” structures may enable the coordinated linear movement of hundreds of tethered
macromolecules in a synchronous manner.
The work of Yan et al. (2003) has opened up exciting new avenues in the field of
nanotechnology and has provided the molecular framework for the construction of dynamic
protein-based assemblies. It is foreseeable that variations of these same DNA scaffolds
will eventually be used for the design and construction of more complex protein-based
assemblies, such as nanoscale “assembly lines” or periodic arrays of dynamic motor
proteins. This work is important to me because it demonstrates not only that it is possible
to create uniform arrays of protein biomolecules using biomolecular scaffolds, but the
study also emphasizes the important role that molecular biology will undoubtedly play as
the field of nanotechnology matures.
As the field of nanotechnology continues to evolve, it is likely that we will see many
more nanotechnology applications utilizing biological macromolecules. Toward the end of
Richard Feynman's 1959 lecture, he quipped, “What are the possibilities of small but
movable machines? They may or may not be useful, but they surely would be fun to make.”
