Category: Bio-nanotechnology

Drug delivery is becoming one of the most often cited application of nanotechnology in the medical arena. For the kind of very toxic molecules that are used in cancer therapy, for example, substantial increases in effectiveness, and reductions in side-effects, can be obtained by wrapping up the molecule in a protective wrapper – a liposome, for example – which isolates the molecule from the body until it reaches its target. Drug delivery systems of this kind are already in clinical use, as I discussed here. But what if, instead of making these drugs in a pharmaceutical factory and wrapping them up in the nanoscale container for injection into the body, you put the factory in the delivery device, and synthesised the drug when it was needed, where it was needed, inside the body? This intriguing possibility is discussed in a commentary (subscription probably required) in the January issue of Nature Nanotechnology. This article is itself based on a discussion held at a National Academies Keck Futures Initiative Conference, which is summarised here.

One of the reasons for wanting to do this is to be able to make drug molecules that aren’t stable enough to be synthesised in the usual way. In a related problem, such a medical nanofactory might be used to help the body dispose of molecules it can’t otherwise process – one example the authors give is the condition phenylketonuria, a relatively common condition in which the amino acid phenylalanine, instead of being converted to tyrosine, is converted to phenylpyruvic acid, the accumulation of which causes incurable brain damage.

What might one need to achieve this goal? The first requirement is a container to separate the chemical machinery from the body. The most likely candidates for such a container are probably polymersomes, robust spherical containers self-assembled from block copolymers. The other requirements for the nanofactory are perhaps less easy to fulfill; one needs ways of getting chemicals in and out of the nanofactory, one needs sensing functions on the outside to tell the nanofactory when it needs to start production, one needs the apparatus to do the chemistry (perhaps a system of enzymes or other catalysts), one needs to be able to target the nanofactory to where one needs it, and finally, one needs to ensure that the nanofactory can be safely disposed of when it has done its work. Cell biology suggests ways to approach some of these requirements, for example one can imagine analogues to the pores and channels which transport molecules through cell membranes. None of this will be easy, but the authors suggest that it would constitute “a platform technology for a variety of therapeutic approaches”.

I’m doing a live interview for the BBC Radio 4 science program The Material World in a couple of hours, at 4.30 pm UK time. The subject of the segment is biocomputing, and the other guest is the computer scientist and author Martyn Amos, whose blog you can read here, who has just published a nice book on the subject, Genesis Machines. You can listen to the broadcast over the internet, either live or up to a week from now, here.

I’m also doing a Café Scientifique in Mumbai and Kolkata tomorrow, by video link, sponsored by the British Council.

I remember, when I was a (probably irritatingly nerdy) child, being absolutely fascinated by making a tic-tac-toe playing automaton out of match-boxes and beads, following a plan in one of Martin Gardner’s books. So my eye was caught by an item on Martyn Amos’s blog, reporting on a recent paper in Nano Letters (abstract and graphic freely available, subscription required for article) from a group in Columbia University, demonstrating a tic-tac-toe playing computer made, not from matchboxes or even more high-tech transistors, but from individual molecules.

The basic logic gate of this molecular computer is a single short DNA strand of a prescribed sequence which can act as a catalyst – a deoxyribozyme. Like the protein molecules used in the molecular computing and signalling operations inside living cells, these molecular logic gates operate by allostery. This is the principle that when one molecule binds to the gate molecule, it changes its shape and makes it either easier or harder for a second, different, molecule to bind. In this way you can get differential catalytic activity – that is, you can get a situation where the logic gate molecule will only catalyse a reaction to produce an output if a given input molecule is present. This simple situation would define a gate that implemented the logical operation YES; if you needed two inputs to stimulate the catalytic activity, you would have an AND gate, and if you have an AND gate whose catalytic activity can be suppressed by the presence of a third molecule, you have the logical operation xANDyANDNOTz. It is these three logical operations that are integrated in their molecular computer, which can play a complete game of tic-tac-toe (or naughts and crosses, as we call it round here) against a human opponent.

The Columbia group have integrated a total of 128 logic gates, plausibly describing it as the first “medium-scale integrated molecular circuit”. In their implementation, the gates were in solution, in macroscopic quantities, in a multi-well plate, and the outputs were determined by detecting the fluorescence of the output molecules. But there’s no reason in principle at all why this kind of molecular computer cannot be scaled down to the level of single or a few molecules, paving the way, as the authors state at the end of their paper, ” for the next generation of fully autonomous molecular devices”.

The work was done by Joanne Macdonald and Milan Stojanovic, of Columbia University, and Benjamin Andrews and Darko Stefanovic of the University of New Mexico – there’s a useful website for the collaboration here. Also on the author list are five NYC high school students, Yang Li, Marko Sutovic, Harvey Lederman, Kiran Pendri, and Wanhong Lu, who must have got a great introduction to the excitement of research by their involvement in this project.

The most sophisticated exercises in using self-assembly to make nanoscale structures and machines have used, as a constructional material, the biomolecule DNA. This field was pioneered by NYU’s Ned Seeman. DNA is not exactly stuff we’re familiar with as a constructional material, though, so I don’t suppose many people have much of a feel for some of its basic mechanical properties, like its stiffness. An elegant experiment, reported in Science at the end of last year, Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication (abstract free, subscription required for full article), sheds a lot of light on this question.

The achievement of this work, reported also in this Science News article, was to devise a method of making rigid DNA tetrahedra, with edges less than 10 nm in size, at high (95%) yield (previous methods of making DNA polyhedra had much lower yields than this). A model of one of these tetrahedra is shown below. But, not satisfied with just making these tetrahedra, Russell Goodman (a graduate student in Andrew Turberfield’s group at Oxford) was able to image them with an atomic force microscope and measure the response of a tetrahedron to being compressed by the AFM tip. In this way he was able to measure the spring constant of each tetrahedron.

The spring constants he found had an average of 0.18 N/m, which is reasonable in the light of what we know about the stiffness of DNA double helices. We can use this number to estimate what the stiffness – the Young’s Modulus – of the solid that would be made if you coupled together many of these tetrahedra. The precise value will depend on how the tetrahedra are linked, but a good estimate is about 20 MPa. Compared with a covalently bonded solid, like diamond (whose modulus, at around 1000 GPa, is 50 thousand times greater than our DNA solid), it’s very much floppier. In fact, this modulus is in the range of a relatively hard rubber, of the kind a shoe sole might be made of. On the other hand, given that the material would be mostly water, it’s pretty stiff – probably about a thousand times stiffer from Jello, which is similarly made up of a network of biopolymers in water.

A rigid tetrahedron formed by self-assembly from DNA, figure from Goodman et al, Science 310 p1661 (2005)

There’s a clear connection between the phenomenon of self-assembly, by which objects at the nanoscale arrange themselves into complex shapes by virtue of programmed patterns of stickiness, and information. The precisely determined three dimensional shape of a protein is entirely specified by the one-dimensional sequence of amino acids along the chain, and the information that specifies this sequence (and thus the shape of the protein) is stored as a sequence of bases on a piece of DNA. If one is talking about information, it’s natural to think of computing, so its natural to ask whether there is any general relationship between computing processes, thought of at their most abstract, and self-assembly.

The person who has, perhaps, done the most to establish this connection is Erik Winfree, at Caltech. Winfree’s colleague, Paul Rothemund, made headlines earlier this year by making a nanoscale smiley face, but I suspect that less well publicised work the pair of them did a couple of years ago will prove just as significant in the long run. In this work, they executed a physical realisation of a cellular automaton whose elements were tiles of DNA with particular patches of programmed stickiness. The work was reported in PLoS Biology here; see also this commentary by Chengde Mao. A simple one-dimensional cellular automaton consists of a row of cells, each of which can take one of two values. The automaton evolves in discrete steps, with a rule that determines the value of a cell on the next step by reference to the values of the adjacent cells on the previous step (for an introduction, to elementary cellular automata, see here). One interesting thing about cellular automata is that very simple rules can generate complex and interesting patterns. Many of these can be seen in Stephen Wolfram’s book, A New Kind of Science, (available on line here. It’s worth noting that some of the grander claims in this book are controversial, as is the respective allocation of credit between Wolfram and the rest of the world, but it remains an excellent overview of the richness of the subject).

I can see at least two aspects of this work that are significant. The first point follows from the fact that a cellular automaton represents a type of computer. It can be shown that some types of cellular automaton are, in fact, equivalent to universal Turing machines, able in principle to carry out any possible computation. Of course, this feature may well be entirely useless in practise. A more recent paper by this group (abstract here, subscription required for full paper), succeeds in using DNA tiles to carry out some elementary calculations, but highlights the difficulties caused by the significant error rate in the elementary operations. Secondly, this offers, in principle, a very effective way of designing and executing very complicated and rich structures that combine design with, in some cases, aperiodicity. In the physical realisation here, the starting conditions are specified by the sequence of a “seed” strand of DNA, while the rule is embodied in the design of the sticky patches on the tiles, itself specified by the sequence of the DNA from which they are made. Simple modifications of the seed strand sequence and the rule implicit in the tile design could result in a wide and rich design space of resulting “algorithmic crystals”.

A physical realisation of a cellular automaton executed using self-assembling DNA tiles. Red crosses indicate propagation errors, which intiatiate or terminate the characteristic Sierpinski triangle patterns. From Rothemund et al, PLOS Biology 2 2041 (2004), copyright the authors, reproduced under a CREATIVE COMMONS ATTRIBUTION LICENSE