Page 123 - Nanotechnology an introduction

Chapter Contents

11.1 The Structural Nature of Biomolecules215
11.2 Some General Characteristics of Biological Molecules216
11.3 The Mechanism of Biological Machines216
11.3.1 Biological Motors 218
11.3.2 Microtubule Assembly and Disassembly 219
11.3.3 The Cost of Control 220
11.4 DNA as Construction Material221
11.5 Biosensors222
11.6 Biophotonic Devices222
11.7 Summary224
11.8 Further Reading224
Bionanotechnology is defined as the incorporation of biological molecules into nano-artifacts. The highly-refined molecular binding specificity of biological molecules is particularly valued and used to facilitate the assembly of unique
structures from a solution of precursors, and for capturing chemicals from the environment prior to registering their presence via a transducer (biosensors). A further application involves using the widely encountered ability of biomolecules
to easily accomplish actions associated with difficult and extreme conditions in the artificial realm, such as the catalysis of many chemical reactions, and optical nonlinearity with single photons, a feature which can be exploited to construct
optical computers. The kidneys provide an excellent example of biological nanoengineering that functions to extract certain substances from highly dilute solutions, an operation that may become of increasing importance as conventionally
processable ores become depleted.
Keywords: structure, mechanism, motors, microtubules, biosensors, biophotonics
Bionanotechnology is defined as the application of biology to nanotechnology (note that biotechnology is the directed use of organisms to make
useful products, typically achieved by genetically modifying organisms); that is, the use of biological molecules in nanomaterials, nanoscale devices
or nanscale systems. It should be contrasted with nanobiotechnology (Chapter 4); if the bionanotechnology is then applied to human health
(nanomedicine or nanobiotechnology), consistency in terminology would demand that we call it bionanobiotechnology.
The discovery of some of the mechanistic details of complicated biological machinery such as the ribosome, which encodes the sequence of
nucleic acids as a sequence of amino acids (called “translation” in molecular biology), was happening around the time that Eric Drexler was
promoting his assembler-based view of nanotechnology, and these biological machines provided a kind of living proof of principle that elaborate
and functionally sophisticated mechanisms could operate at the nanoscale. Some of these biological machines are listed in Table 11.1. There are
many others, such as the mechanism that packs viral DNA ultracompactly in the head of bacteriophage viruses.
Table 11.1 Examples of biological nanosized machines
Name Natural function State of knowledgea
Muscle (myosin) Pulling C, S, T
Kinesin Linear motion C, S, T
Nerve Information transmission T
ATPase Synthesis of ATP from proton e.p.g. b C, S, T
Bacteriorhodopsin Generation of proton e.p.g. from light C,T
Transmembrane ion pump Moving selected ions against an adverse e.p.g. C,T
Hemoglobin Oxygen uptake and release C,T
a
C, crystal structure determned; S, single-molecule observation of operation; T, theoretical mechanism(s) available.
i
b Electrochemical potential gradient.
The machines listed in Table 11.1 are proteins (polypeptides); some are considered to be enzymes (e.g., ATPase). Enzymes (and possibly other
machines as well) can also be constructed from RNA, and some known machines, such as the ribosome, are constructed from both polypeptides
and RNA. RNA and polypeptides are synthesized (naturally or artificially) as linear polymers, most of which can adopt their functional three-
dimensional structure via a self-assembly process (Section 8.2.11) that occurs spontaneously (and often reversibly).
Some of these machines show consummate scaling out to the macroscopic realm. Muscle is a good example: although the actin–myosin pair that
is the molecular heart of muscular action develops a force of a few piconewtons, by arranging many “molecular muscles” in parallel, large animals
such as elephants can sustainably develop kilowatts of power, as humans have known and made use of for millennia.
These natural nanomachines are inspiring in their own right; their existence and the detailed study of their mode of operation have driven efforts to
mimic them using artifically designed and constructed systems—this is called bio-inspired nanotechnology or biomimetic nanotechnology. Many
structures and especially devices produced in living systems are constituted from biopolymers designed to fit to congeners with exquisite
specificity and precise stoicheiometry. One of the challenges of biomimetic nanotechnology is to recreate these attributes with simpler artificial
systems—without much success until now. Could one, for example, create a synthetic oxygen carrier working like hemoglobin but with a tenth or
fewer the number of atoms? Possibly, although one wonders whether such a “lean” carrier would be as resilient to fluctuations in its working
environment.
Returning to our definition of bionanotechnology (the incorporation of biological molecules into nanoartifacts), after recalling the basics of biological
structure and biomolecular mechanism, we shall survey three example areas in which biological molecules have been used structurally or
incorporated in nanoscale devices: DNA as a self-assembling construction material; biosensors; and biophotonic memory and logic gates.
Although a rather exotic system of a motile bacterium harnessed to push a tiny rotor has been reported [75], the main current areas of
nanotechnological significance are biosensors and biophotonics.
11.1. The Structural Nature of Biomolecules
Polypeptides (PP) (Proteins)
These are linear polymers of amino acids (H N–CHR–COOH, where R (bonded to the central C) is a variable side chain (“residue”)—there are 20
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different natural ones. To polymerize them, water is eliminated between –COOH and H N– to form the peptide bond, hence there is a common
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