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| Dateline: 5/14/00 | |
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Assembling nanoscale machinery and electronics poses a problem for which we have yet to find an adequate solution, hence nanotechnology has yet to arrive. However, that a solution to the problem exists can be seen in all living systems. Composed of molecular building blocks such as nucleic acids, proteins and phospholipids, biological organisms enter the world equipped with all the necessary means for assembling these components into extremely well organized structures. The purpose of this treatise is to summarize the basic tools that nature has provided for the nanoscientist.
This vast supply of molecular components has been precisely designed not only to function as part of a complex molecular machine, but also with the ability to get themselves to the appropriate locations! Exactly how they find the right place is still under debate. While most agree that they bounce around until they stick somewhere, what exactly allows the speed and precision of most biomolecular self-assembly is still a mystery.
Perhaps the most specific biomolecular self-assembly occurs when two single strands of Deoxyribonucleic Acid (DNA) assemble into the infamous double helix. Based on Watson and Crick base pairing, two complimentary strands of DNA will find each other within an enormously complex mixture. Double helical DNA strands can be separated from one another through simple heating, resulting in single stranded DNA (ssDNA). If the solution is allowed to cool, the two strands will re-assemble into a stable double helix. While the Watson and Crick base pairing then allows the specific assembly of the double helix, which is stabilized by relatively strong hydrophobic interactions between the aromatic bases within the center of the helix also known as pi-stacking.
Nanoscientists can take advantage of the double helix's specific stability in numerous ways. One promising approach is to attach single-stranded DNA to small particles that one wishes to assemble. These components could range from diamondoid manifolds to metallic clusters that function as quantum dots. When DNA is used to create functional surfaces, the technique is called DNA Directed Immobilization (DDI). Such patterned surfaces have applications for both nanoelectronic devices and biosensors. Nanogen, a biosensor manufacturer has a versatile method for that takes advantage of DNA's negative charge. By applying a voltage to various parts of a DNA containing solution, the concentrations of DNA over various parts surfaces can be regulated.
As the primary components of the molecular machinery that makes life possible, proteins have a vast array of resources available to them for biomolecular self-assembly. Take for instance the eukaryotic nucleus of a multicellular organism (such as a human). The organization of the information contained within this tiny compartment is so vast that scientists are only now beginning to attempt to understand it. Containing the compartment is the nuclear membrane, which is filled with proteins that pump nutrients in and messages out. Entwined within what is called the "nuclear matrix" is the entire human genome, containing about 3 meters worth of DNA, packed into an area of only a few cubic micrometers. Keeping it all under control are then histones and thousands of other (non-histone) proteins that carry out processes such as transcription and translation. Each of these proteins has the appropriate information encoded within its peptide sequence for getting it to the location where it can do its job. In order for each of our cells to produce those proteins required for its specific task, only certain genes can be transcribed in certain cells. Thus, a very important amount of information is contained not only in the sequence of the DNA, but in its spatial organization within the nucleus. For instance, when the nucleus divides, all the contents must be unraveled, copied, and then reassembled back into two daughters of the original organized state. All this is accomplished by means of biomolecular self-assembly.
Structural Proteins are generally called "fibrous" because they often have a fiber like nature. With names such as collagen, keratin, elastin, tubulin and fibroin, fibrous proteins self-assemble (often covalently) into large polymers that provide various nano- meso- and even macro-scale structures. Even our most modern synthetic polymers can not compete with fibrous proteins such as fibroin (silk) when it comes to strength, flexibility and overall molecular scale order. Thus, serious efforts are underway to better understand and take advantage of fibrous self-assembly.
Enzymes (biological catalysts) are generally "globular" as opposed to "fibrous" and they often work together in the form of multi-enzyme complexes. This means that both intramolecular self-assembly and intermolecular self-assembly must take place in order for the enzyme to reach the conformation that allows it to do its job. Intramolecular self-assembly means that the newly synthesized protein chain must fold into a functional state. Most often this is accomplished by the aggregation of hydrophobic residues in the center of the protein, thus forcing hydrophilic residues to the surface of the protein. Once a single protein chain is adequately folded, it will often begin intermolecular self-assembly. In order to assemble a molecular machine known as a "multienzyme complex," the numerous subunits (or proteins) contact one another in ways that cause new surfaces to appear, thus allowing further subunit components to bind. Since all the information for this self-assembly is often contained within the protein sequence, it is possible to reproduce this assembly in a test tube. For instance, the molecular machine that builds proteins in E. Coli (the ribosome) can be taken apart into 58 isolated protein chains (as well as a few RNA molecules. If these components are mixed back together with the appropriate timing then functional ribosomes can be reassembled.
Membrane bound proteins are incorporated into the cellular membranes that surround cells and their compartments. In order for these proteins to perform their numerous functions (signal transduction, ion balance maintenance, molecular transport, electron transport, structure, etc.), they must be appropriately oriented and organized within the membrane. Determining their structure within the membrane is not an easy task for biochemists, since the membranes are often destroyed during purification. However, membrane bound proteins often have a common structural characteristic that suggests a mechanism for their assembly. That is, several hydrophobic residues exposed on a certain area of the protein. Since the center of the membrane is hydrophobic, it can be expected that these hydrophobic residues stick to the inside of the membrane. Again, the hydrophobic effect is most effective for this purpose. Finally, once the molecule is incorporated into the membrane, changes in the membranes constitution as well as interactions with neighboring membrane bound proteins govern the organization of these proteins.
Cellular membranes define the boundries between various cellular compartments (such as the nucleus, mitochondria, endoplasmic reticulum, etc.) as well as enclosing the cell from the external environment. Similar to soap bubbles, cellular membranes are made of specific types of surfactants that tend to form bilayers. The primary surfactants are phospholipids, steroids (primarily cholesterol), and glycolipids. Two nanoscale bodies of water can be effectively separated from one by the formation of a bilayer of these molecules. The main barrier is the hydrophobic region in the center of a lipid bilayer membrane. Water and polar molecules dissolved in water can not pass through such a nonpolar barrier without the assistance of ion channels or molecular pumps.
Langmuir-Blodgett (LB) films are formed when synthetic or naturally occurring surfactants are placed at the air-water (or liquid gas) interface where they can organize into a layer that is one molecule thick (a monolayer), two molecules thick (bilayer) or several molecules thick (multi-layer). The polar part of the surfactant molecule tends to be attached to the surface of the water while the nonpolar hydrophobic regions of neighboring molecules will stick together and orient themselves away from the surface. As the lateral pressure (2 dimensional pressure created by compressing the interface area) is changed, the film undergoes phase transitions corresponding to various levels of self-organization.
Thiol self-assembly can be achieved by reacting thiol containing compounds with clean gold surfaces. Sulfhydryl groups on molecules will covalently bind to gold, thus allowing molecules to be arranged two dimensionally over a gold surface. This is extra useful because gold conducts electricity and makes for excellent electrical contacts, thus Scanning Tunneling Microscopy (STM) measurements can be made on such samples. For example, redox proteins can be mutagenically modified with cysteine residues (an amino acid that contains a thiol group). Exposing a gold surface to such engineered molecules results in self-assembled monolayers of protein.