Deoxyribonucleic acid (DNA) may be regarded as the central molecule of life since it is the carrier of genetic information; it is the chemical constituent of the genes. DNA is a biopolymer composed of deoxyribonucleoside units connected via phosphodiester bridges (Figure 1a). It is the linear order of the nucleobases (A, C, G & T) that contain the genetic information, whereas the deoxyribose phosphate backbone primarily fulfils a structural role.

Two new direct approaches for selective 6-O-acylation of amylose under homogeneous conditions were investigated. In the first method, amylose was initially brominated at C-6 using Nbromosuccinimide and triphenylphosphine in N,N-dimethyfformamide containing lithium bromide. The procedure was found to be highly selective and proceeded with no detectable reaction at the secondary positions. Several 6-bromo-6-deoxyamylose derivatives were prepared with different degrees of substitution by changing the molar equivalence of the reactants. In the second stage these were converted into 6-laurate esters by treatment with cesium laurate in dimethylsulfoxide, which proceeded rapidly under mild conditions. In the second method, the feasibility of 6-O-benzoylation in one step using the Mitsunobu reaction was evaluated. Amylose was treated with diethylazodicarboxylate in the presence of triphenylphosphine and benzoic acid in dimethysulfoxide under ambient conditions. While exclusively 6-O-benzoylation resulted up to degree of substitutions of ca. 0.5, at higher values a small amount of esterification at secondary hydroxyl groups also occurred. Products were characterized by 13C NMR, FTIR and elemental analyses.

A synthetic approach to polyamides containing the tyrosine-leucine linkage is presented. The diphenyl phosphoryl azide, (DPPA), coupling technique was utilized to synthesize the monomers. Solution polymerization of monomer I, tyrosylleucyliminohexamethyleneiminoleucyltyrosine, with adipoyl and sebacoyl chlorides gave polymers with intrinsic viscosities of 0.18 dL/g and 0.13 dL/g respectively in 90% formic acid. Interfacial polymerization of the monomer yielded a fibrous crosslinked material which was found to be a poly(amide-ester) by IR spectroscopic analysis.

Dragline fibers collected at a controlled silking rate from Nephila clavipes spiders were studied by analytical transmission electron microscopy (TEM). The physical microstructure consists of irregularly-shaped ß-sheet crystallites (approx. 70–100 nm in diameter, and comprising approx. 50 volume per cent) in an amorphous matrix. Electron diffraction from single crystallites indicates an orthogonal unit cell with space group P21; the lattice parameters are a = 13.31 Å (inter-sheet repeat), b = 9.44 Å (inter-chain repeat within ß-sheets) and c = 20.88 Å (intra-chain repeat). The crystallites are not truly periodic structures having long range positional order, but are better described as non-periodic layered structures, similar to the ordered structures formed when liquid crystalline random copolymers solidify. Electron energy loss spectroscopy (EELS) reveals chemical microstructure in the fibers. The matrix contains bands (approx. 200 nm wide) of alternately higher and lower nitrogen content. This variation cannot be explained in terms of known protein domains alone, and may reflect the presence of retained small-molecule species from secretory granules. Calcium is localized uniquely to the crystallites (at a concentration of approx. one calcium atom per 120 amino acid residues, as measured by inductively coupled plasma spectroscopy). Varying the calcium content may be one mechanism by which the spider can tailor the evolution of the microstructure, and hence the physical properties of the silk fiber.

rCAS is a recombinant Constant And Subrepeat (rCAS) protein modelled after tandem core repeats found in a 1000-kDa silk protein synthesized by larvae of the midge, Chironomus tentans. rCAS is encoded by a synthetic gene (synCAS) which is expressed in bacteria. Purified rCAS has four cysteine residues that participate in formation of two intramolecular disulfide bonds. Here we report the results of amino acid sequencing and electrospray ionization mass spectroscopic analyses of tryptic fragments of native and reduced rCAS which suggest that these disulfide bonds are heterogeneous. To assist in studying the formation of disulfide bonds in reduced and refolded rCAS, a series of synCAS mutants were constructed with cysteine to alanine substitutions. In comparison to wild-type rCAS and a Cys79→Ala mutant, the refolding of Cys9→Ala appears to be partially inhibited.

Spider silks exhibit an unusual combination of strength and toughness that distinguishes them from other natural and synthetic fibers. Silk proteins perform a key natural function as structural fibers, to absorb impact energy from flying insects without breaking. They dissipate energy over a broad area and balance stiffness, strength and extensibility (1,2). In addition to their unusual mechanical properties and visual lustre, silks also exhibit interesting interference patterns within the electromagnetic spectrum (3), unusual viscometric patterns related to processing (4), and piezoelectric properties (3,5,6). These properties suggest they would be good candidates for high performance fiber and composite applications. However, the spider is not capable of producing sufficient quantities of proteins to enable thorough evaluation of their potential. Consequently, we are pursuing recombinant DNA techniques to clone and express adequate quantities of recombinant spider silk for these studies.

The control of structure on the nanoscale relies on intermolecular interactions whose specificity and geometry can be treated on a predictive basis. With this criterion in mind, DNA is an extremely favorable construction medium: The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of double helical DNA, whose structure is well known. The use of stable branched DNA molecules permits one to make stick-figures. We have used this strategy to construct a covalently closed DNA molecule whose helix axes have the connectivity of a cube. The molecule has twelve double helical edges; each edge is two helical turns in length, resulting in a hexacatenane, each of whose strands corresponds to a face of the object. The cube has been fabricated in solution, which is inefficient. We have developed a solid-support-based synthetic methodology that is much more effective. The key features of the technique are control over the formation of each edge of the object, and the topological closure of each intermediate. Each edge results from the restriction of two hairpins, which are then ligated together. The isolation of individual objects on the surface of the support permits one to use both symmetric and asymmetric sites in the formation of edges that close polygons. We have used solid-support-based methodology to construct a molecule whose helix axes have the connectivity of a truncated octahedron. This figure has 14 faces, of which six are ideally square and eight are hexagonal; this Archimedean polyhedron contains 24 vertices and 36 edges. Control of topology is strong in this system, but control of 3-D structure remains elusive. Topological control is enhanced by the use of topological protection techniques. Our key aim is the formation of prespecified 2-D and 3-D periodic structures with defined topologies. Applications envisioned include nanomanipulators and scaffolding for molecular electronic devices.

Molecular recognition is central to the self-assembly of catenanes and rotaxanes. The design criteria for efficient formation of these compounds is gradually becoming clear. Selfassembly of mechanically-interlocked compounds is heading apace towards the nanometre scale.

Complex organized systems evolved from the prebiotic soup approximately three billion years ago, relying on simple molecules which spontaneously and synergistically combine to accomplish certain tasks. As life evolved, the sophistication of these interactions also increased. Organisms evolved by linking the needed functional groups together in proteins to improve the efficiency of the process, and now rely almost exclusively on protein interactions to accomplish needed tasks. It is for this reason that considerable effort has been expended on understanding how such complexes are formed and how the individual components contribute to overall function. The code for these interactions lies buried in the amino acid sequences of the constituent proteins. Biologists are beginning to unravel the secrets of this code, and see how small changes to individual residues can affect the overall stability and function of the complex.

In our continuing efforts towards the design of nonlinear (NLO) optical chromophore containing polypeptides we present an integrated computational approach, in which the design of biomolecular materials with defined secondary and tertiary structures is investigated by means of novel predictive tools, while the effects of the nonlinear optical chromophores are studied with molecular dynamics simulations. A neural network that was trained to predict the spatial proximity of Cα atoms that are less than a given threshold apart, is applied. The double-iterated Kalman filter (DIKF) technique is then employed with a constraints set that includes these pairwise atomic distances, and the distances and angles that define the structure as it is known from the protein's sequence. The results for test cases, particularly Crambin and genetically engineered Eglin-C, demonstrate that this integrated approach is useful for structure prediction at an intermediate resolution. Defined structural motifs of NLO chromophore containing polypeptides are investigated by using molecular dynamics techniques, particularly for the design of coil coiled amphiphatic biopolymers.

Mineralized biological tissues form by growth of inorganic phases in or on polymers and membranes. This paper discusses the mechanisms for these processes from a bio-mimetic point of view. Mineralization within a polymer or gel can lead to very fine precipitates because particle agglomeration is prevented and solute diffusion rates are low.

Localization of mineralization appears to occur in biology by activation of particular surfaces. The possibility is discussed that this may be due to a close lattice match between the spacing of groups on the polymer and the spacing of ions in the mineral. It is shown that this mechanism is unlikely and other possibilities are discussed.

The nacreous (mother-of-pearl) sections of molluscan shells are natural laminates of aragonitic calcium carbonate platelets and an organic matrix. The multi-edged platelets are sub-micrometer thick and surrounded on all sides by 10–20 nm-thick organic matrix that contains several proteins and polysaccharides. Our goal is to identify the components and structure of the organic matrix and determine their function in shell formation and organization. We have extracted organic material from red abalone-Haliotis rufescens, and chambered nautilus-Nautilus pompilius. From the soluble portion, we have partially purified two proteins and determined their amino acid compositions.

Two fiber forms can be obtained from cells of the rod-shaped bacterium, Bacillus subtilis, one called macrofibers, the other bacterial thread. Macrofibers are highly organized, multicellular structures, millimeters in length that selfassemble in a unique way. Each fiber is essentially a single chain of cells linked end-to-end that has repeatedly folded upon itself and twisted into helical form. The growth of individual cells yields both the material of the macrofiber and the forces required for its assembly. The forces involved stem from twisting motions caused by cell growth geometry. The folding process is akin to negative supercoiling. New approaches have been used to estimate the magnitude of forces. Torque generated by single filaments has been estimated from snapopening motions resulting from aborted attempts at folding to be in the range of 10−10 to 10−8 dyne-cm. In contrast, multifilament fibers carrying small wires in their loops must have generated a torque of at least 10−5 dyne-cm and a supercoiling force of at least 10−5 dyne in order to have moved the wires in viscous solutions at the rates observed. The second bacterial fiber form, bacterial thread, and its mineralized derivatives, called bionites, are man-made materials. They are produced by the drawing and drying of bacterial cell filaments from cultures grown in the form of a textile-like web. The material properties of bacterial thread reflect primarily those of the strength-bearing cell wall polymer, peptidoglycan. A variety of new fiber-like materials have been produced by mineralizing the cell walls in situ in web cultures and drawing the products. Iron, copper, calcium, and potassium phosphate-containing bionites have been obtained in this manner. We are currently searching for order in the bionite crystal forms that may reflect the electrostatic nature of the wall polymer structural templates.

A total of 20 biogenic carboxylic acids, which contain one to three negatively charged -COO− group(s), were investigated as dispersion additives in the processing of ceramic particles. Only carboxylic acids containing one or more hydroxyl groups were able to disperse α-A12O3 particles in aqueous suspensions. Detailed studies of two carboxylic acids, citric acid and tricarballylic acid were undertaken: measurements of zeta potential, particle packing, and dispersant adsorption characeristics indicated that carboxylic acid groups and hydroxyl groups are both important for dispersion of the ceramic particles. Hydroxyl groups increased the adsorption of the molecules to the particles.

In recent experiments we have patterned smooth HOPG surfaces with periodic arrays of nanometer dimension holes on a 20nm lattice using two-dimensional (2-D) protein crystals as templates. The bacterial cell wall crystals were deposited on HOPG substrate and overcoated at oblique incidence with an ultrathin (3.5 nmn) TiO2 film. Fast atom beam (FAB) milling patterns the TiO2 film into a screen having the protein lattice periodicity and the screen then acts as a mask for the pattern transfer to the HOPG substrate. This method provides an inexpensive, “benchtop,” intrinsically parallel technique for the periodic nanostructuring of surfaces. Here we extend it to the patterning of silicon single crystal surfaces. We will describe the use of silane coupling agents to enable protein adhesion with the cytoplasmic side up, as is preferable for the patterning. We will show AFM images of the T1O2 -protein-silicon composite surface at various stages of the fabrication process.

Small quantities of acidic macromolecules were added to crystallizing calcium carbonate in an attempt to engineer crystal growth. The additives are simple analogs to those molecules found in close association with the mineral phase in biological ceramics. When 5 or 10 ppm of the four additives (poly-L-glutamate, poly-L-aspartate, polyacrylate and polymaleate) were added to aqueous suspensions of metastable vaterite, the transformation to calcite was markedly retarded, and the morphology of the final crystal product was altered. The two polypeptides were most effective in inhibiting calcite nucleation and growth; they also promoted vaterite aggregation, and caused the formation of large calcite crystals.

Biological materials such as shells possess a useful combination of mechanical properties. For instance, good fracture toughness combined with a relatively high hardness has been reported. The response of these properties to a tribological performance could presumably be very beneficial. Unfortunately no such research has been reported, although this kind of information is invaluable in possible utilization of biomimetic or biological processes in producing of materials.

In this work chemical composition of Unio Crassus shells were characterized using secondary ion mass spectroscopy (SIMS) and Rutherford backscattering spectroscopy (RBS) and the microstructure was determined with X-ray diffraction (XRD) and scanning electron microscopy (SEM). Specimens of 20×10 mm in size with a thickness of a few millimetres were cut and mechanically polished followed by ultrasonic cleaning in deionized water. Wear and friction measurements were performed in a pin-on-disc tester with a hardened steel pin 6 mm in diameter as a counter face. Tests were carried out in a relative humidity of 50 % at room temperature with a sliding speed of 15 mm/s. The measurements indicate a friction coefficient of 0.3 – 0.4 which is reasonable low. Moreover, wear resistance was found to be excellent. The wear resistance of the material was similar to those of the best synthetic diamond-like carbon films. The storage of the specimen at room temperature for 150 days deteriorated the material resulting in much worse tribological properties.

Heterogeneous nucleation and crystal growth on protein substrates are critical steps in biological hard tissue formation. Self assembled monolayers can be derivatized with various organic functional groups to mimic the “nucleation proteins” for induction of mineral growth. Studies of nucleation and growth on SAMs can provide a better understanding of biomineralization and can also form the basis of a superior thin film deposition process. We demonstrate that micron-scale, electron and ion beam, lithographic techniques can be used to pattern SAMs with functional organic groups that either inhibit or promote mineral deposition. Patterned films of iron oxyhydroxide were deposited on the areas patterned with nucleation sites. Studies of the deposition kinetic of these films show that the surface indeed induces heterogeneous nucleation and that film formation does not occur via absorption of polymers or colloidal material formed homogeneously in solution. The nucleus interfacial free energy was calculated to be 88 mJ/m2 on a SAM surface composed entirely of sulfonate groups.

The technology to manufacture rigid, highly porous materials of very low density that are suitable for use in a wide range of industrial applications has recently been developed in this laboratory. These materials, derived from naturally occurring polymers, have many useful physical characteristics including very large pore volume, pore size distribution in a useful range, and high surface area. These characteristicsw, hen combinedw ith their robust mechanicals trength, make them potentially useful as support matrices for various complexing agents. One demonstrated application of this material is as a polymeric carrierfo r selective liquid metal extractants in hydrometallurgicalp rocesses. We have successfully impregnated our porous matrix with several selective metal extractants, and demonstrated retention of the basic metal binding properties of the immobilized agent. Results of bench scale pilot studies using a copper selective impregnated resin indicate excellent capacity, and good selectivity and extraction/elution kinetics.

ProNectin®F is a recombinant engineered protein polymer of de novo design which incorporates the RGD epitope recognized by mammalian cell integrins. It is biologically active as a cell attachment protein, manifests properties of a planar polymeric surfactant, and is extremely resistant to thermal degradation. ProNectin®F was dispersed onto polystyrene powder, fabricated into plastic ware through injection molding, and the plastic ware was shown to have cell attachment activity. This technology represents a new paradigm for the production of plastic ware useful for mammalian cell culture under serum free conditions; and more generally, for the production of molded devices for use in contact with cells in vitro or in vivo.