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Molecular Combinatory Computing and its Applications in Nanotechnology
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Intelligent matter is any material in which individual molecules or supra-molecular clusters function as agents to accomplish some purpose. Intelligent matter may be solid, liquid or gaseous, although liquids and membranes are perhaps most typical. Universally programmable intelligent matter (UPIM) is made from a small set of molecular building blocks that are universal in the sense that they can be rearranged to accomplish any purpose that can be described by a computer program. In effect, a computer program controls the behavior of the material at the molecular level. In some applications the molecules self-assemble a desired nanostructure by "computing" the structure and then becoming inactive. In other applications the material remains active so that it can respond, at the molecular level, to its environment or to other external conditions. An extreme case is when programmable supra-molecular clusters act as autonomous agents to achieve some end. This report outlines a one-year exploratory research project to investigate the feasibility of UPIM.
We demonstrate how combinatory molecular computation allows parallel self- assembly of several kinds of nanomembranes and nanotubes. One such nanomem- brane is a square grid constructed of cross-linked horizont al and vertical chains. We show that a relatively minor change causes it to self-assemble into a nanotube with the same cross-linked structure. A second nanomembrane is a monolayer arranged in a hexagonal grid.
Summary This paper presents an overview of recent experimental progress by the Duke DNA NanoTech Group in our efforts to utilize novel DNA nanostructures for computational self-assembly as well as for templates in the fabrication of functional nano-patterned materials. We have prototyped a new DNA tile type known as the 4x4 (a cross-like structure composed of four four-arm junctions) upon which we have deposited metal to form highly conductive nanowires and also are adapting multi-tile 4x4 sets for a variety of computational applications. We have recently described a DNA barcode lattice composed of DX tiles assembled on a long scaffold strand; the system propagates 1-dimensional (1D) information encoded on the scaffold strand into a specific and reprogrammable barcode pattern which is visible in 2D by atomic force microscopy. We have succeeded in demonstrating the first highly parallel computation via DNA tile self-assembly by using a single- layer superstructure made of DX tiles which computes the entire lookup table of pairwise XOR calculations up to a modest size input string length. We have prototyped a 2-state DNA lattice assembly containing actuator components and demonstrated its ability to be controllably switched between the two states. We are currently working on a molecular robotics experiment aimed at demonstrating unidirectional motion of a small DNA fragment along a track constructed of DNA. We have demonstrated a diverse set of novel structures and applications which extend the inherent information carrying capacity of DNA in a variety of novel directions.
Hydrogen bond-mediated self-assembly is a powerful strategy for generating large structures from smaller subunits. The synthesis of molecules containing two isophthalic acid units covalently attached to a rigid aromatic spacer is described. By normal pairing of carboxylic acids into hydrogen-bonded dimers, these molecules self-assemble in organic solvents to form either a series of linear aggregates or a cyclic hexamer. These molecules were linked to the core of a family of polyether dendrimers, which caused the hexamer to be formed preferentially. The stability of the hexamer depended on the generation number of the dendrimer. The largest of these hydrogen-bonded macromolecular assemblies is roughly disk-shaped with a 9-nanometer diameter and a 2-nanometer thickness. Its size and molecular mass (34,000 daltons) are comparable to that of small proteins.
MBBs are, therefore, the structural intermediates between atoms, the most basic of all building units, and macromolecules or extended arrays, of which the MBBs are the common structural element. While many MBB approaches are not directed toward the design of nanostructures or nanoscale materials, all share the same design considerations and are consistent with the criteria used to distinguish the MBB approaches considered here from other nanoscale fabrication techniques.
Attempts to fabricate mechanical devices on the molecular level have yielded analogues of rotors, gears, switches, shuttles, turnstiles and ratchets. Molecular motors, however, have not yet been made, even though they are common in biological systems. Rotary motion as such has been induced in interlocked systems and directly visualized for single molecules, but the controlled conversion of energy into unidirectional rotary motion has remained difficult to achieve. Here we report repetitive, monodirectional rotation around a central carbon-carbon double bond in a chiral, helical alkene, with each 360 degrees rotation involving four discrete isomerization steps activated by ultraviolet light or a change in the temperature of the system. We find that axial chirality and the presence of two chiral centres are essential for the observed monodirectional behaviour of the molecular motor. Two light-induced cis-trans isomerizations are each associated with a 180 degrees rotation around the carbon-carbon double bond and are each followed by thermally controlled helicity inversions, which effectively block reverse rotation and thus ensure that the four individual steps add up to one full rotation in one direction only. As the energy barriers of the helicity inversion steps can be adjusted by structural modifications, chiral alkenes based on our system may find use as basic components for 'molecular machinery' driven by light.
Molecular recognition between complementary strands of DNA allows construction on a nanometre length scale. For example, DNA tags may be used to organize the assembly of colloidal particles, and DNA templates can direct the growth of semiconductor nanocrystals and metal wires. As a structural material in its own right, DNA can be used to make ordered static arrays of tiles, linked rings and polyhedra. The construction of active devices is also possible--for example, a nanomechanical switch, whose conformation is changed by inducing a transition in the chirality of the DNA double helix. Melting of chemically modified DNA has been induced by optical absorption, and conformational changes caused by the binding of oligonucleotides or other small groups have been shown to change the enzymatic activity of ribozymes. Here we report the construction of a DNA machine in which the DNA is used not only as a structural material, but also as 'fuel'. The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of 'fuel' DNA; each cycle produces a duplex DNA waste product.