Although it seems at first that Nature has provided a limited number of basic building blocks-amino acids, lipids, and nucleic acids-the chemical diversity of these molecules and the different ways they can be polymerized or assembled provide an enormous range of possible structures. Furthermore, advances in chemical synthesis and biotechnology enable one to combine these building blocks, almost at will, to produce new materials and structures that have not yet been made in Nature. These self-assembled materials often have enhanced properties as well as unique applications.

The selected examples below show ways in which clever synthetic methodologies are being harnessed to provide novel biological building blocks for nanotechnology.

The protein polymers produced by Tirrell and coworkers (1994) are examples of this new methodology. In one set of experiments, proteins were

Figure 7.2
Top: a 36-mer protein polymer with the repeat sequence (ulanine-glycine)3 - glutamic acid - glycine. Bottom: idealized folding of this protein polymer, where the glutamic acid sidechains (+) are on the surface of the folds.

designed from first principles to have folds in specific locations and surface-reactive groups in other places (Figure 7.2) (Krejchi et al. 1994; 1997). One of the target sequences was -((AG)3EG)- 36. The hypothesis was that the AG regions would form hydrogen-bonded networks of beta sheets and that the glutamic acid would provide a functional group for surface modification. Synthetic DNAs coding for these proteins were produced, inserted into an E. coli expression system, and the desired proteins were produced and harvested. These biopolymers formed chain-folded lamellar crystals with the anticipated folds. In addition to serving as a source of totally new materials, this type of research also enables us to test our understanding of amino acid interactions and our ability to predict chain folding.

Biopolymers produced via biotechnology are monodisperse; that is, they have precisely defined and controlled chain lengths; on the other hand, it is virtually impossible to produce a monodisperse synthetic polymer. It has recently been shown that polymers with well-defined chain lengths can have unusual liquid crystalline properties. For example, Yu et al. (1997) have shown that bacterial methods for polymer synthesis can be used to produce poly(gamma-benzyl alpha L-glutamate) that exhibits smectic ordering in solution and in films. The distribution in chain length normally found for synthetic polymers makes it unusual to find them in smectic phases. This work is important in that it suggests that we now have a route to new smectic phases whose layer spacings can be controlled on the scale of tens of nanometers.

The biotechnology-based synthetic approaches described above generally require that the final product be made from the natural, or L-amino acids. Progress is now being made so that biological machinery (e.g., E. coli), can be co-opted to incorporate non-natural amino acids such as b -alanine or dehydroproline or fluorotyrosine, or ones with alkene or alkyne functionality (Deming et al. 1997). Research along these lines opens new avenues for producing controlled-length polymers with controllable surface properties, as well as biosynthetic polymers that demonstrate electrical phenomena like conductivity. Such molecules could be used in nanotechnology applications.

Novel chemical synthesis methods are also being developed to produce "chimeric" molecules that contain organic turn units and hydrogen-bonding networks of amino acids (Winningham and Sogah 1997). Another approach includes incorporating all tools of chemistry into the synthesis of proteins, making it possible to produce, for example, mirror-image proteins. These proteins, by virtue of their D-amino acid composition, resist biodegradation and could have important pharmaceutical applications (Muir et al. 1997).

Arnold and coworkers are using a totally different approach to produce proteins with enhanced properties such as catalytic activity or binding affinity. Called "directed evolution," this method uses random mutagenesis and multiple generations to produce new proteins with enhanced properties. Directed evolution, which involves DNA shuffling, has been used to obtain esterases with five- to six-fold enhanced activity against p-nitrobenzyl esters (Moore et al. 1997).


The ability of biological molecules to undergo highly controlled and hierarchical assembly makes them ideal for applications in nanotechnology. The self-assembly hierarchy of biological materials begins with monomer molecules (e.g., nucleotides and nucleosides, amino acids, lipids), which form polymers (e.g., DNA, RNA, proteins, polysaccharides), then assemblies (e.g., membranes, organelles), and finally cells, organs, organisms, and even populations (Rousseau and Jelinski 1991, 571-608). Consequently, biological materials assembly on a very broad range of organizational length scales, and in both hierarchical and nested manners (Aksay et al. 1996; Aksay 1998). Research frontiers that exploit the capacity of biomolecules and cellular systems to undergo self-assembly have been identified in two recent National Research Council reports (NRC 1994 and 1996). Examples of self-assembled systems include monolayers and multilayers, biocompatible layers, decorated membranes, organized structures such as microtubules and biomineralization, and the intracellular assembly of CdSe semiconductors and chains of magnetite.

A number of researchers have been exploiting the predictable base-pairing of DNA to build molecular-sized, complex, three-dimensional objects. For example, Seeman and coworkers (Seeman 1998) have been investigating these properties of DNA molecules with the goal of forming complex 2-D and 3-D periodic structures with defined topologies. DNA is ideal for building molecular nanotechnology objects, as it offers synthetic control, predictability of interactions, and well-controlled "sticky ends" that assemble in highly specific fashion. Furthermore, the existence of stable branched DNA molecules permits complex and interlocking shapes to be formed. Using such technology, a number of topologies have been prepared, including cubes (Chen and Seeman 1991), truncated octahedra (Figure 7.3) (Zhang and Seeman 1994), and Borromean rings (Mao et al. 1997).

Other researchers are using the capacity of DNA to self-organize to develop photonic array devices and other molecular photonic components (Sosnowski et al. 1997). This approach uses DNA-derived structures and a microelectronic template device that produces controlled electric fields. The electric fields regulate transport, hybridization, and denaturation of oligonucleotides. Because these electric fields direct the assembly and transport of the devices on the template surface, this method offers a versatile way to control assembly.

There is a large body of literature on the self-assembly on monolayers of lipid and lipid-like molecules (Allara 1996, 97-102; Bishop and Nuzzo 1996). Devices using self-assembled monolayers are now available for analyzing the binding of biological molecules, as well as for spatially tailoring the

Figure 7.3.
Idealized truncated octahedron assembled from DNA. This view is down the four-fold axis of the squares. Each edge of the octahedron contains two double-helical turns of DNA.

surface activity. The technology to make self-assembled monolayers (SAMs) is now so well developed that it should be possible to use them for complex electronic structures and molecular-scale devices.

Research stemming from the study of SAMs (e.g., alkylthiols and other biomembrane mimics on gold) led to the discovery of "stamping" (Figure 7.4) (Kumar and Whitesides 1993). This method, in which an elastomeric stamp is used for rapid pattern transfer, has now been driven to < 50 nanometer scales and extended to nonflat surfaces. It is also called "soft lithography" and offers exciting possibilities for producing devices with unusual shapes or geometries.

Self-assembled organic materials such as proteins and/or lipids can be used to form the scaffolding for the deposition of inorganic material to form ceramics such as hydroxyapatite, calcium carbonate, silicon dioxide, and iron oxide. Although the formation of special ceramics is bio-inspired, the organic material need not be of biological origin. An example is production of template-assisted nanostructured ceramic thin films (Aksay et al. 1996).

A particularly interesting example of bio-inspired self-assembly has been described in a recent article by Stupp and coworkers (Stupp et al. 1997). This work, in which organic "rod-coil" molecules were induced to self-assemble, is significant in that the molecules orient themselves and self-assemble over a wide range of length scales, including mushroom-shaped clusters (Figure 7.5); sheets of the clusters packed side-by-side; and thick films, where the sheets pack in a head-to-tail fashion. The interplay between hydrophobic and hydrophilic forces is thought to be partially responsible for the controlled assembly.

Published: September 1999; WTEC Hyper-Librarian