A non-SPM-based approach to molecular mechanoassembly

(c) 2000 Robert A. Freitas Jr.

21 February 2000
(The following brief note extends the discussion of a preliminary draft paper [1] on molecular assembly that was privately circulated in November 1998.)The overall problem of molecular manufacturing is to deterministically construct vast numbers of almost exactly similar congeries of atomically-specified parts, e.g. molecular machines.

Although it would reduce the problem of parts fidelity and orientation during assembly, it will be very hard to build molecular structures atom at a time because individual atoms are more difficult to mechanically grasp and release, and have less-easily controlled covalent reactivities than molecules. Thus early molecular manufacturing systems should probably build using molecular parts rather than atomic parts. Molecular parts having 10-100 atoms placed in precise relative positions are already accessible to current chemical synthetic techniques, and can in theory be produced in mole quantities, so there would be an abundance of selfsame parts with which to work.

But molecular manufacturing also requires that one be able to assemble large numbers of parts deterministically to make molecular-featured useful (e.g. marketable) product. It is quite possible to imagine that an SPM could be used to manually assemble a simple nanoreplicator device. The replicator device could be free-floating or wall-anchored in design. The initial one-off replicator would then operate on nanoparts presented to it and build more replicators. When enough replicators had been built, a signal would be sent to the fleet of replicators that tells them to change their mode of operation, and the replicators now begin assembling useful product from the sea of parts, rather than more replicators.

The practical problem here is that the design for the replicator must be known in advance and completely specified. The replicator must be sophisticated enough to preclude all alternative assembly pathways except the one or more pathways which are desired. The replicator also must be capable to at least two (or more) distinct modes of operation – as the structure of the useful product object differs more and more from the structure of the replicator, the replicator will need increasing complexity of structure and sophistication of design to properly execute its two (or more) distinct output modes. Also, at least from the viewpoint of simple early systems, such a replicator will be very functionally brittle. It will be able to assemble only a very limited range of output products, and slight changes in the design of those output products may necessitate a complete redesign of the replicator structure, with systemwide alterations possibly needed.

A less-brittle approach to mass-production molecular assembly would be a technique that would allow alteration of each parts-assembly step without necessitating a redesign of the entire system; which would allow new assembly pathways to be inserted without redesigning the entire system; which would isolate each step of the parts assembly process, thus reducing or eliminating unwanted assembled-nanopart congeries.

Let's assume that we have some nanometer-scale parts that we wish to assemble into useful product nanomachines in a deterministic fashion. At least three different near-term ways to get them to assemble are readily apparent:

  1. Self-assembly in solution phase. Each part is manufactured so as to incorporate complementary surface features or handles on one face, and noncomplementary or nonattractive surfaces on all other faces, with the result that parts which meet in random orientations or positions will join only in one specific position and orientation. A collection of parts will thus spontaneously assemble into the desired congeries or finished product nanomachines. The principle difficulty here is that at each step, all alternative assembly pathways must be known, well-characterized, and excluded in advance; as the number of assembly steps increases, the total number of such pathways may become very large, even if the self-assembly steps are performed strictly sequentially allowing isolation of each assembly cycle.
  2. SPM-based assembly in vacuum or solution phase. Each part is grabbed by a separately maneuverable functionalized SPM tip, brought into contact in the proper relative orientation under the view of an SEM or similar viewing facility, and the parts then bond (a) covalently if chemically active handles have been included on the parts’ surfaces, (b) electrostatically if the parts contained charged handles, or (c) by simple van der Waals forces if the parts contain complementary surface features. The SPM tips then must detach from the assembled unit, releasing the assembled unit for further assembly downstream. One major difficulty here is that even with a large number of of parallelized tips working in unison, the output count is still going to be relatively low. This is certainly not fatal to the concept. Many useful nanomachines can be conceived for which only one (or some small number) will suffice in a particular application -- for example, sensors (at the low-complexity end of the spectrum) and replicators (at the high-complexity end).
  3. Mechanoenzymes [2-4] in solution phase. A mole quantity of parts "A" and "B" are suspended in working fluid. Parts "A" and "B" have no natural complementarity and will not spontaneously self-assemble. Some number of identical "mAB" mechanoenzyme molecules are next introduced. The mechanoenzyme molecules have a reversible binding facility for part "A" at one end, a similar facility for part "B" at the other end, and an actuator mechanism in between. As soon as the mechanoenzyme is introduced, parts "A" and "B" attach to their proper places and orientations on each mechanoenzyme molecule. A chemical signal is then introduced into the working fluid, which causes the mechanoenzyme molecule to flex and/or rotate, bringing parts "A" and "B" into contact in a specific position and orientation with sufficient force to overcome potential barriers and induce the mechanical joining of the parts. The binding facilities for "A" and "B" are then disabled, allowing the compound part "AB" to be released (and later recovered, separated and purified by sieving or centrifugation or other similar means), and the mechanoenzyme is reverse-actuated, returning it to its original cocked position and ready for another cycle of activity. Both the binding facility release event and the mechanoenzyme reverse-actuation event may be triggered by additional chemical signal(s), or might possibly be triggered automatically following the prior mechanical sequence. Construction of complex nanomachines is accomplished by employing an ordered sequence of two-part suspensions into which parts-specific mechanoenzymes are introduced, catalyzing each assembly operation, one after the other. Energy must be injected into the mechanoenzyme at some point in its cycle, in order to drive the cycle, and this may also serve as one of the aforementioned chemical "signals".
A benefit of this technique is that assembly operations can be quickly and accurately performed on mole quantities of parts, thus permitting massive parallelicity. One practical concern is that a different mechanoenzyme may be required for each parts pairing that we desire to assemble. However, with proper system design the number of necessary enzymes can probably be significantly reduced because the parts-assembly space will probably reduce to a relatively small number of distinct classes of binding sites, mechanoenzyme backbone lengths, and actuator modes.

Useful product can include addditional mechanoenzymes, which themselves may be relatively simple in structure (unlike replicators). Since in principle only one (or just a few) mechanoenzymes are needed to catalyze the assembly step, you could initially manufacture the mechanoenzymes as one-offs using SPMs or some functionally similar technique. Mechanoenzymes could even be entirely biological.

Pursuit of the mechanoenzyme pathway to molecular assembly must address at least the following issues:

First, a research program to develop mechanoenzymes might first establish a database of useful nanoparts which might be desired to be assembled -- such as variously-shaped blocks, ratchet-shaped and tooth-shaped parts, hinges, toroids and insertable rods of various lengths and diameters, and so forth.

Second, a reliable reversible binding mechanism for each part must be devised. As long as each part has physically distinguishable faces this should be possible. Since only two types of parts will be present at any time, the competitive binding analysis should be much simplified from a situation in which many different parts are simultaneously present. The strength of the binding must be greater than the maximum forces expected to be exerted upon the parts during assembly, unless the assembly force vectors are designed to be additive with the binding forces during the assembly operation, as would be prudent to do, if possible.

Third, a means by which the binding of the part to its receptor facility may be externally controlled in a reversible fashion must be devised. Molecular pumps might provide a possible analog – configurational changes make the binding site active or inactive.

Fourth, a specific mechanism for achieving the externally-controllable mechanoenzyme actuator motion must be devised. Examples of this might include butterfly molecules, Ned Seeman's DNA manipulator device [5], a free-floating dynamin [4] pinch molecule, or even two kinesin motors bearing parts and approaching each other by walking along two adjacent oppositely-oriented microtubule tracks. Can these sorts of molecular motors exert sufficient force to accomplish the desired assembly operation? The kinesin motor stall force is 5-7 pN; using two opposed kinesin motors, one bearing each part and walking towards each other, would allow a total 10-14 pN to be applied to the workpiece. (Note also that the kinesin family includes two types, a plus-walker and a minus-walker [6]. In principle, rigid crossbeams affixed to multiple motor molecules on multiple tracks could provide whatever summed forces might be deemed necessary at the workpiece.)

Fifth, some means of restoring the actuator to its starting position, and of supplying the appropriate energy to drive the actuator motion, must be devised. In the case of chemomechanical kinesin-based or dynamin-based nanomotors, or related biological approaches, this could involve ATP or GTP.


  1. Robert A. Freitas Jr., "A novel pathway to first-generation molecular assemblers," preliminary draft paper, 18 November 1998.
  2. M.S. Mooseker, T.R. Coleman, "The 110-kD protein-calmodulin complex of the intestinal microvillus (brush border myosin I) is a mechanoenzyme," J. Cell Biol. 108(June 1989):2395-2400; A. Garcia et al, "Partial deduced sequence of the 100-kD-calmodulin complex of the avian intestinal microvillus shows that this mechanoenzyme is a member of the myosin I family," J. Cell Biol. 109(December 1989):2895-2903.
  3. G. Steinberg, "A kinesin-like mechanoenzyme from the zygomycete Syncephalastrum racemosum shares biochemical similarities with conventional kinesin from Neurospora crassa," Eur. J. Cell Biol.73(June 1997):124-131.
  4. M.A. McNiven, H. Cao, K.R. Pitts, Y. Yoon, "The dynamin family of mechanoenzymes: pinching in new places," Trends Biochem. Sci. 25(March 2000):115-120; D. Danino, J.E. Hinshaw, "Dynamin family of mechanoenzymes," Curr. Opin. Cell Biol. 13(August 2001):454-460.
  5. C. Mao, W. Sun, Z. Shen, N.C. Seeman, "A nanomechanical device based on the B-Z transition of DNA," Nature 397(14 January 1999):144-146.
  6. Ulrike Henningsen, Manfred Schliwa, "Reversal in the direction of movement of a molecular motor," Nature 389(4 September 1997):93-96, 15-16 (comment).


Last updated on 2 November 2002