Kinematic Self-Replicating Machines
© 2004 Robert A. Freitas Jr. and Ralph C. Merkle. All Rights Reserved.
Robert A. Freitas Jr., Ralph C. Merkle, Kinematic Self-Replicating Machines, Landes Bioscience, Georgetown, TX, 2004.
4.5.3 Positional Assembly Using Microbes and Viruses
Artificial microbes (Section 4.4) might also be employed in molecular construction. A variety of biological molecular machines are already known which display linear motions, movements related to opening, closing and translocation functions, rotary movements, and threading-dethreading movements . Gerald J. Sussman at MIT claims that when computer parts are reduced to the size of single molecules, engineered microbes could be directed to lay down complex electronic circuits . “Bacteria are like little workhorses for nanotechnology; they’re wonderful at manipulating things in the chemical and ultramicroscopic worlds,” he says. “You could train them to become electricians and plumbers, hire them with sugar and harness them to build structures for you.”
Regarding microbe-directed parts fabrication, one strain of bacteria (Pseudomonas stutzeri AG259) is known to fabricate single crystals of pure silver in specific geometric shapes such as equilateral triangles and hexagons, up to 200 nm in size [2102, 2103]. Several anaerobic bacteria grow 300-nm nanosphere shells outside their cell envelopes , and microorganisms can accumulate materials and synthesize inorganic structures composed of bismuth , CdS [2106, 2107], gold , magnetite [2107, 2110], selenium , silica , and silver [2107, 2108].
As for microbe-directed parts assembly, Kondo et al  used a grooved film (created by chemically precipitating cellulose tracks less than 1 nm apart onto a copper base) to induce the bacterium Acetobacter xylinum to exude neat ribbons of cellulose  along the prepared track at a rate of 4 microns/minute. The group is attempting to genetically modify the organism to secrete alternative sugar molecules that might better resist natural degradation. Natural fibroblasts in human tissue construct complex 3-dimensional collagenous fiber networks of extracellular matrix (ECM) during wound healing , fibrillogenesis  and fibroplasia . Although ECM strand positioning is stochastic in natural fibroblasts , cell functionality and ECM network characteristics can be altered by chemotactic factors [2117, 2118], contact guidance and orientation , hypoxia , and local mechanical stress . Fibroblasts can be genetically engineered , are capable of crosslinking collagen fibers  (a “covalent parts joining” type of operation), and can apply ~100 pN forces while embedded in a 3-dimensional collagen lattice .
To establish digital control over microorganisms, genetic circuits that can function as switches  or computational logic elements such as AND, NAND, and NOR gates (Nanomedicine , Section 10.2.3.1) are under active investigation [2126-2141]. For example, in 2000 Gardner et al  added a memory device to an E. coli bacterium using two inverters for which the output protein of each is the input protein of the other. Elowitz and Leibler [2129, 2133] made an oscillator with three inverters connected in a loop – in one test of their “Repressilator” system, “a fluorescent protein became active whenever one of the proteins was in its low state....the result was a population of gently twinkling cells like flashing holiday lights.”  By 2002, Weiss [2139-2143] had created a five-gene circuit in E. coli that could detect a specific chemical in its surroundings and turn on a fluorescent protein when the chemical concentration enters within preselected bounds .
The Synthetic Biology Lab at MIT is similarly trying to create cells that are “engineered genetic blinkers”  and which use light as a faster means of cellular I/O than chemical-mediated signals .) They are also creating a set of “BioBricks” [1883, 2145] which are “a [standardized] set of [building block] components that have been designed for use as logic functions within a cell. The members of this family are designed to be compatible, composable, interchangeable, and independent so that logic circuits may be constructed with little knowledge or concern for the origins, construction, or biological activities of the components.” These components are being accumulated in M.I.T.’s Registry of Standard Biological Parts , an online database that by June 2004 listed distinct 517 parts or devices, with the number growing by the month. Boston University bioengineer and Cellicon Inc. founder and Senior Scientist Timothy Gardner explains  that the eventual goal “is to produce genetic ‘applets’, little programs you could download into a cell simply by sticking DNA into it, the way you download Java applets from the Internet.” Bacterial memory has also been demonstrated: 150-base-long messages encoded as artificial DNA have been stored within the genomes of multiplying E. coli and Deinococcus radiodurans bacteria and then accurately retrieved . Unfortunately, notes Weiss : “Replication is far from perfect. We’ve built circuits and seen them mutate in half the cells within five hours. The larger the circuit is, the faster it tends to mutate.”
External control has been shown experimentally. Jacobson’s team  has demonstrated remote electronic control over the hybridization behavior of DNA molecules by inductive coupling of a GHz radio-frequency magnetic field to a 1.4 nm gold nanocrystal covalently linked to DNA , offering the prospect of remote-controlled enzymes and “radio-controlled bacteria” . Single-molecule heating of bioconjugable gold nanowires, nanocircles and nanocoils is also being investigated by the von Kiedrowski group .
Bacteria can also be used as physical system components. For example, Tung et al [2150, 2151] are attempting to incorporate living bacteria into microelectromechanical systems (MEMS) to form living cell motors for pumps and valves. The bacteria will be completely sealed inside the bioMEMS device. “When its flagellum is attached to a surface, the bacterium moves in a circular fashion, and always in the same direction,’ explains Tung . “A single bacterium can become a flagellar motor or pump, but a number of bacteria, all rotating in the same direction, could become a conveyor belt.” However, Tung  notes that unlike ATPase which can potentially be assembled from proteins, flagellar motors cannot yet be artificially manufactured so the replication techniques developed for ATPase may not be applicable to flagellar motors. Smith  also notes that it is presently unknown how to synchronize the rotational directions of multiple flagella in the lab.
Similarly, Linda Turner and colleagues at the Rowland Institute at Harvard have affixed a film of Serratia marcescens bacteria onto tiny beads, allowing the microbes’ rotating appendages to carry the beads along. When the film is applied inside tiny tubes, the gyrating bacterial arms blend fluids twice as fast as diffusion alone . Carlo Montemagno at UCLA has combined living cells with isolated MEMS structures to create cell-powered mechanical motors. In one experiment in 2003, a lithographically-produced U-shaped structure 230 microns wide is attached to a cardiac muscle cell like a tiny prosthesis. When presented with glucose solution, the muscle cell contracts repeatedly, causing the mechanical structure to “walk” at a speed of ~46 microns/min with a repetition rate controlled by the spring constant of the MEMS structure . Sequeira and Copik [2156, 2157] once proposed using bacteria as power units for microscale mechanical systems.
Viral shells also can provide useful templates for nanoscale assembly. Belcher [1435, 2158-2163] employs virus capsid shells as temporary scaffolds for the directed nanoassembly of nanoparticles such as quantum dots , CoPt and FePt nanowires , and ~30 other inorganic semiconducting or magnetic materials in a process she describes  as the “biomimetic synthesis of nonbiological inorganic phases with novel electronic and magnetic properties directed by proteins and synthetic analogs.” In one experiment , a genetically engineered M13 bacteriophage with a specific recognition moiety for zinc sulfide nanocrystals was used to assemble a ZnS-containing film having nanoscale ordering and 72-micron-sized domains. Belcher and Hu have formed a company, Senzyme, to commercialize this process. Viral coat proteins can be engineered by various techniques  and have been used by others as scaffolds for nanomaterials synthesis [2170, 2171], in self-assembly  (e.g., of viral capsid monolayers on gold surfaces ), and for encapsulation of reactants or polymers inside viral capsid cage structures .
Last updated on 1 August 2005