Literature

The challenge of working at the nanometre level of detail is one that few people can even comprehend. Despite all the media interest in these new technologies, and despite hearing explanations of the first principles many times, it is still mind-blowing! It is not so surprising, therefore, that people have turned to the natural world, where nano-sized machinery is operating within every cell, and where the variety of mechanisms provides a powerful stimulus for innovation.

"[N]ature illustrates that we are nowhere near the limit of exquisite control over organization; it possesses an extraordinary capacity to assemble complex nanostructures with active and specialized functions. Our ability to precisely position components on the nanometer scale the way nature does, and to do so in a parallel rather than a serial manner, is still limited and is a key goal in nanotechnology and materials science."

Results of some early stage research on DNA nanotechnology.

A review paper has just appeared, looking at the potential of DNA nanotechnology. In the natural world, DNA provides materials for self-assembly and the coordination of the process. Can this be utilised by nanotechnologists working with sequences they have put together. The answer is a resounding yes.

"Of the natural self-assembling molecules, DNA is arguably the most remarkable. A cooperative interplay of hydrogen-bonding, [pi]-stacking, electrostatic, and hydrophobic interactions drives one DNA strand to assemble with its complement into a double helix according to extremely precise base-pairing rules. Additional attributes, such as rigidity on the nanoscale, a diameter of ~2 nm, and a near-infinite number of potential sequences, extend DNA's reach beyond a genetic blueprint for life. DNA is emerging as an attractive tool for nanoscience as well; it is a highly promising template for organizing nanomaterials in a programmable way."

The review is well worth reading and there is little merit in summarising. Researchers have moved from 1D molecules to 2D and 3D structures. A great variety of techniques have been developed, providing a rich toolbox for nano-construction projects. "It is of note that in structural DNA nanotechnology, DNA is used to provide all the parameters for self-assembly: connectivity, structural features, and programmability." Synthetic DNA sequences can be made to fold in predetermined ways.

"Hairpins were incorporated into stapling strands to write words, such as "DNA," and to draw complex objects, such as the outline of the Western Hemisphere. DNA origami will be useful for accessing larger DNA shapes with highly addressable surfaces."

Of particular interest is where this research is heading. There are two major challenges: "the correction of errors that arise in DNA assembly, and the replication and scale-up of DNA nanostructures." Regarding error correction:

"As the complexity of DNA assemblies increases, so will the number of the DNA sequences required to form them. This will necessitate using overlapping, degenerate strands that may assemble into undesirable products. Biological systems have developed a number of elegant strategies to proofread and remove errors during and after assembly. Inspired by these systems, Lu used an approach in which deoxyribozymes (DNAzymes) specifically locate and cleave misassembled structures in gold nanoparticle assemblies. In the presence of the "correct" DNA strands, the DNAzyme is not properly folded and is inactive; however, in the presence of the "incorrect" DNA strands, the DNAzyme is properly folded and proceeds to cleave and remove the errors."

Scaling-up again draws inspiration from biological systems. Throughout the review, "Nature" is portrayed as an agent. Nature does this and Nature does that. When such sophistication is on display, it is difficult to insist on the natural world being a Blind Watchmaker - the product of 'chance and necessity'. This research is crying out for a foundation in design-thinking. Even with our best efforts as intelligent agents, we are just scratching the surface of what we find in living things. Nanotechnology in the natural world reveals exquisite design, not the products of tinkering. It deserves to be credited as the product of intelligent agency!

"Nature builds complexity in a hierarchical way. It progressively increases length scales and relies on a number of noncovalent interactions, including DNA base-pairing, to drive assembly. Supramolecular DNA assembly is a means to weave in principles of hierarchical complexity and new interactions into DNA nanostructures, and opens the door to assembling more diverse functional structures with greater ease."

Assembling Materials with DNA as the Guide
Faisal A. Aldaye, Alison L. Palmer, and Hanadi F. Sleiman
Science 321, 26 September 2008: 1795-1799.

Abstract: DNA's remarkable molecular recognition properties and structural features make it one of the most promising templates to pattern materials with nanoscale precision. The emerging field of DNA nanotechnology strips this molecule from any preconceived biological role and exploits its simple code to generate addressable nanostructures in one, two, and three dimensions. These structures have been used to precisely position proteins, nanoparticles, transition metals, and other functional components into deliberately designed patterns. They can also act as templates for the growth of nanowires, aid in the structural determination of proteins, and provide new platforms for genomics applications. The field of DNA nanotechnology is growing in a number of directions, carrying with it the promise to substantially affect materials science and biology.