410 9.3  Synthetic Biology, Biomimicry, and Bionanotechnology

sample aggregation at the high concentrations typically used, and the random orientation of

particles means that analysis is limited to small groups at a time with limited potential for

high-​throughput analysis, though PCA has to somewhat tackled many of these issues (see

Chapter 8). If instead one attaches the target protein to specifically engineered binding sites

on a self-​assembled 2D DNA template, this minimizes many of these issues. It also opens

the possibility for 2D crystallography if proteins can be bound to the template in consistent

orientations, for example, using multiple binding sites.

DNA origami can also be utilized to make dynamic as opposed to just static nanostructures

can be made from DNA. These are examples of artificial molecular motors. A motiv­

ation to develop artificial molecular motors is for the transporting of specific biomedical

cargo molecules for use in lab-​on-​a-​chip devices (see later text). Several such devices have

been constructed from DNA, inspired by the mechanisms of natural molecular motors

(see Chapter 8). The key process in all DNA-​based artificial molecular motors is known as

toehold-​mediated strand displacement (Figure 9.3c). Here, a single-​stranded DNA toehold

(also known as an overhang or sticky end) is created at the end of a double-​stranded (i.e.,

duplex) segment of DNA called a “toehold.” This single-​stranded toehold can bind to an

invading DNA strand that competes with the bound strand. Since unpaired bases have a

higher effective Gibbs free energy than paired bases, then the system reaches steady state

when the minimum number of unpaired bases is reached, which results in displacement

of the originally bound strand. This strand displacement imparts a force on the remaining

duplex structure, thus equivalent to the power stroke of natural molecular machines (see

Chapter 8), with the equivalent “fuel” being the invading DNA strand. Such developments

currently show promise at the point of writing this book. However, issues include artificial

motors being slow and inefficient compared to native molecular motors, and DNA logic

circuits are not currently as reliable as conventional electronic ones.

One interesting further application of DNA origami lies in computationally complicated

optimization–​minimization problems. These are exemplified by the so-​called traveling

salesman problem:

Given a finite number of cities and the distances between them what is the shortest route to

take such that each city is visited just once prior to returning to the starting city?

This turns out to be precisely the same problem as a single strand of DNA exploring the most

optimal annealing routes for a self-​assembly duplex formation process. Thus, biophysical

observations of the kinetics of annealing can potentially be used as a biomolecular computa­

tional metric to complex optimization–​minimization problems.

9.3.4  BIOFUELS, BIOPLASTICS, AND A GREENER ENVIRONMENT

Synthetic biology approaches have been used to engineer modified cells to generate “green”

biofuels, to manufacture biodegradable plastics, and even to clean our environment (a pro­

cess known as bioremediation). Advanced biofuels may end up being crucial to building a

cleaner energy economy. With depletion of fossil fuels and decommissioning of many nuclear

power stations coupled with safety and environmental concerns of those remaining, biofuel

development has an appeal.

Although at an early stage of development, there are emerging signs of promising pro­

gress. For example, certain nanoparticles can increase the efficiency of biofuel production,

which employ enzyme catalysis to convert cellulose from plants into smaller sugars high in

their fuel value. There are also developments in biobatteries. These are miniaturized elec­

trical charge storage devices that utilize biological materials. Examples are oil-​stabilized

nanodroplet arrays, discussed previously (see Chapter 6), though currently are low power

and inefficient.

Other interesting designs include nanowire microelectrodes that can be energized

by a fuel of only a few molecules of natural redox enzymes (Pan et al., 2008). A key

challenge here is that for conventional electrical conductors, the electrical resistance

varies inversely with the cross-​sectional area, so that a material that obeys Ohm’s law of