What is Self-Assembly?

Ever wondered what it takes for an egg to form in an oviparous animal? The process does not only involve creating the ovum; it also involves producing very delicate membranes accompanying nutritive materials like the yoke. Simultaneously, the egg shell is synthesized from extremely low concentrations of calcium atoms and required minerals, in a very limited space. To top it off, this process must yield an ovum against a high ion and molecular concentration gradient[1].

            Mother Nature accomplishes this effortlessly and with great precision, flexibility and error-correction capacity[1] and offers inspiration for “bottom-up” nano-fabrication, that is, the manufacture of new devices and materials starting at the nanoscale[2]. It entails constructing materials atom by atom or molecule by molecule to produce novel supramolecular architectures[3] which are then used as building blocks, also known as “molecular-lego”, for new devices[2]. Self-Assembly of molecules, however, eliminates the tedious process the nano-builder must undertake in arranging every single molecule or atom one at a time. The concept of self-organization is due to the chemical complementarity and structural compatibility of the atoms and molecules both confer weak (example Hydrogen bonding) or covalent bonding interactions that bind building blocks together[1] in the fabrication process. To put it simply, the idea behind self-assembly is that molecules will always seek the lowest energy level available to them, whether this means bonding with an adjacent molecule or reorienting physical positions[4]. The same applies to the force that makes a compass needle always reorient itself in a north-south direction no matter how much you shake it or the directions to which you point it[4]. These are the same techniques self-assembly is based on and so the components of the devices being built can naturally organize themselves the way we want them to[4].

This results in achieving high resolution construction of many novel nanoscale materials with applications in electronics, photonics, mechanics and biotechnology, and serves as a solution to the challenges brought about by the continued shrinking of device features[5]. Before the incorporation of biology into novel synthetics, the full potential of nanotechnological systems was not realized due to difficulty in achieving such high resolution in their synthesis and subsequent assembly into useful structures and nanodevices[6].

Biological Self-Assembly has emerged over times a hybrid methodology that combines nature’s molecular tools with synthetic nanoscale constructs[6]. A process called Biopatterning, a concept for depositing active biomolecules on solid surfaces with submicronic spatial resolution and high reproducibility[7] to aid self-assembly of inorganic constructs on unconventional substrates[8]. It eliminates what used to be the elusive nature control and well-ordered assemblies into two and three dimensions at the nanoscale[6]. One can think of biopatterning as laying a near-perfect foundation aligning it as precisely as possible for a building: if the foundation of say a wall of a building is crooked, the wall to be constructed on this foundation will also be crooked.

Here is an example to illustrate:

Bacterial surface layers (S-layers) have been shown to function as versatile substrates for high precision self-assembly of molecules, metals and semiconductors. S-layers are 2D proteins that make up the outermost cell covering of bacteria and can be isolated from these species to be reassembled on solid supports such as Silicon and even metals. They have high density functional groups in definite locations and orientations. Using bio-patterning, the biomolecules can be controlled spatially to form ordered lateral arrays ranging from the nanoscale to the microscale. This is ensured by using high resolution Micro-contact printing of protein patterns using hard stamps of PDMS obtained by mold assisted lithography[7], micromolding in capillaries (MIMIC), epi-fluorescence to check that the channels have bee aligned correctly and atomic force microscopy, a scanning probe mechanism used to move atoms or molecules around and ensure a uniform topography. Most importantly, while this orderliness is achieved, chemical functionality of the S-layers are preserved as has been proven using covalent attachments between Human IgC antibody and IgC antigens at assembles S-layer substrates[5].

Experiment to Illustrate Inorganic-Specific nature of Proteins:

 Neuron growth on patterned substrates:  It would be useful to be able to direct the growth of neurons spatially. This accomplishes by laying down cell-adherent and cell-repulsive regions.  The substrate is made cell-repulsive, then gold is sputter-coated through a mask and cell-adherent peptides with a thiol end, which have a strong affinity for gold, that are introduced will be the only ones that bond to the gold to begin self-assembling on the gold-coated regions.  Experiments with rat hippocampal cells show that this method indeed works and the neurons grow selectively on the cell-adherent regions.
This process mimics the cell-growth cues found naturally in the brain, only through an artificial method[9].

GEPIs

This concept of inorganic-specific proteins has been extended to an application called GEPIs, Genetically Engineered Proteins for Inorganics. Polypeptides are genetically being engineered to specifically bind to particular inorganic compounds for application in nanotechnology to solve some of the problems that come with manufacturing novel synthetics with full control. GEPIs, as they are known, define a selection of short sequences that have affinity for (noble) metals, semiconducting oxides and other technological compounds. (Bacterial cell surface and Phage display provide the principles for the protocols used for matching specific polypeptides with specific inorganic substrates. This data has been tabulated for reference.)

            GEPIs have been shown to acts as peptide intermediaries in nanostructure assembly. An example is the use of GEPIs, that have strong affinity for gold, to immobilize gold quantum dots from onto a bio-active substrate. One end of the gold-specific GEPI attaches itself to receptors on a substrate while the other end bonds with gold[6].

Applications and Future Prospects

            GEPI’s may find applications in controlling materials’ morphology. They play key roles in performance of implants and 3D cell culture and hard tissue engineering, as they are used to fabricate nanofibers. They are also used for the fabrication for electronics by bacterial phage selection. DNA and proteins bound to inorganic substrates have been used to build microarrays suitable for modern genomics (study and use of genes), pharmogenetics (the study of genetic factors that influence an organism's reaction to a drug )and proteomics (study concerned with structure, function, and interactions of the proteins produced by the genes of a particular cell, tissue, or organism)[10], [6]. Also, a GEPI recognizing and assembling on the surface of a therapeutic device can be fused to a human protein to enhance human compatibility. It could also be used for drug delivery through colloidal inorganic particles. They can also be coupled with molecular motors to make dynamic nanostructures[6]. 

Problems

            GEPIs may have cross-specificity for a diverse number of materials. The chemical and physical basis for GEPI recognition of inorganic surfaces still remains questionable despite the advances made in protocols for determining specific matches between proteins and inorganic compounds[6].