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With the Relentless Rise of DNA Nanotechnology's Popularity, Emma DNA nanOTECHNOLOGY DNA motors on With the relentless rise of DNA nanotechnology’s popularity, Emma Davies explores the role chemistry has played in its success 50 | Chemistry World | January 2012 | www.chemistryworld.org DNA nanOTECHNOLOGY As a supramolecular chemist, Hanadi structures if you bring all of the tools of Sleiman found herself strongly drawn to chemistry into DNA,’ she says. Adding manmade DNA structures. ‘We think of DNA synthetic molecules has the bonus that it as the most programmable structure there is. cuts down on the amount of DNA required. I thought – if it is – let me try to incorporate it DNA is not cheap to buy; an origami can cost into regular supramolecular structures,’ says several hundred pounds to construct. the professor at McGill University, Montreal, ‘We can make any prismatic shape that Canada. She hasn’t looked back. ‘What is we want,’ says Sleiman. ‘You can assemble really beautiful about DNA structures is the these prismatic cages in minutes at room fact that you can control every single aspect temperature at 100% yield.’ The polygons of them,’ she exclaims. are made from single-stranded DNA, with Sleiman is one of an increasing number each DNA building block containing a of chemists who have turned to DNA six carbon long alkyl ‘spacer’ to reduce nanotechnology. Some pin their hopes on electrostatic and steric crowding. using DNA in nanoelectronics or for drug Sleiman has also made DNA cages delivery, while others are excited about its containing transition metals. ‘I have always potential as an analytical tool. been interested in how to organise metals Single strands of DNA bind (hybridise) with DNA because then you can make to each other when the bases cytosine and catalytic factories or sensors or you can GRAHAMHAMBLIN guanine (C-G) and adenine and thymine make artificial photosynthesis systems,’ she (A-T) couple through hydrogen bonds and says. Like metallo–supramolecular cages, a good geometric fit. The fact that a single the metal in metal–DNA cages can be used strand of DNA will only bind to another with for redox, photochemical, magnetic and Guest molecules can the correct base sequence gives researchers catalytic control over the guest molecules be trapped within DNA incredible structure control. Meanwhile, locked inside. nanotubes, and then fully automated DNA synthesisers mean that However, making such cages is tricky. released on demand DNA sequences are easy to construct. Many metals randomly bind to DNA, even In 2006 Paul Rothemund, a computational cleaving it in some cases. The key is to find bioengineer at the California Institute of the right ligand for the structure. In 2009 Technology in the US published a paper Sleiman reported using DNA cages with outlining a strikingly simple way to create ligands at each of the vertices that act as wonderful patterned templates using DNA pockets for transition metals. strands – coining the phrase ‘DNA origami’. Her group has also made DNA nanotubes Long, single DNA strands form a template which contain guest molecules held in place while hundreds of shorter DNA ‘staple’ by DNA strands strands hold the template together and force ‘It is impractical slightly longer than it to fold – like origami – into a series of parallel those in the rest lines within the desired shape outline. The to make of the structure. DNA sections can be bought commercially molecular Bringing in new and construction is done at room motors and DNA strands – temperature. Andrew Turberfield, a physicist ‘eraser’ strands who specialises in DNA nanotechnology at the operate them – that are fully University of Oxford, UK, has described this from the outside’ complementary to technology as triggering ‘a small revolution in these longer strands DNA self-assembly’. peels them away from the nanotubes, ‘DNA origami really works,’ agrees freeing the guest molecules. Friedrich Simmel, a biophysicist at the Inside cells in the body, say in cancer Technical University of Munich in Germany. cells, matching strands of mRNA could ‘What is amazing and exciting for many theoretically trigger the nanotubes to people is that when you mix the DNA release a drug cargo while non-matching sequences in the lab the origami works sequences would leave the cargo entrapped. almost immediately.’ In 2011 Rothemund Or the nanotubes could be used as mRNA reported a method to extend the size of DNA sensors. ‘Yet one of the big hurdles in the structures that can be created by slotting a field of DNA therapeutics is the fact that the series of origami tiles together using base DNA molecule doesn’t go into cells or if it pair stacking between G-C and C-G base does, it is only to a limited extent,’ explains pairs on the edge of tiles. Sleiman. She suggests that playing around with the shapes of DNA structures might Super supramolecules open a route into cells. While McGill’s Sleiman describes Sleiman is unable to reveal too much Rothemund’s original origami as a ‘beautiful about her group’s work to transfer their discovery’, she takes a different approach DNA structures into cells, which is yet to be to DNA structure building. Her team has published. Suffice to say that she is excited added a chemical slant, building 3D DNA about the results. structures with synthetic molecules as Turberfield has also had some success key components. ‘We use a lot of synthetic in this area. In 2011, his group was able to molecules that we embed in the DNA. treat human kidney cells with fluorescently You have more functional, more diverse labelled DNA tetrahedra. The cages made www.chemistryworld.org | January 2012 | Chemistry World | 51 DNA nanOTECHNOLOGY Streptavidin can be attached to DNA staple strands on origami surfaces, and then visualised using AFM researchers can see the intact staple strands, and therefore know which have been cleaved. This technique allows the singlet oxygen’s trail of destruction to be clearly traced. Gothelf also hopes to make macromolecules by chemical reactions between functional groups in fixed positions on the origami. The idea is that chemical selectivity is determined by the position and orientation of the molecule on the DNA scaffold rather than having to use a series of protecting groups. No help needed DNA nanodevices that run by themselves without external control hold an obvious appeal for researchers, especially those hoping one day to create a synthetic version of living cells. ‘It is impractical to make molecular motors and operate them from the outside – you need autonomous motion,’ explains Munich’s Simmel. He has been working on ways to drive DNA nanodevices autonomously by coupling them to a complex oup biochemical process linked to transcription. HINGGR The system is based on two enzymes used S BLI for RNA production and degradation which pu RE influence each other by mutual activation tu NA and inhibition, creating a kind of oscillating ‘molecular clock’. The clock has been used to their way into the cytoplasm of the cells, susceptible to cleavage by singlet oxygen. On control a variety of biomolecular processes remaining ‘substantially intact’ for at least the end of each of these strands is the small including DNA tweezers. two days. ‘This is the first step towards the molecule biotin. A short period of time after The researchers are also putting these use of engineered DNA nanostructures to irradiation, the bacterial protein streptavidin complex systems into micrometre-sized deliver and control the activity of cargoes is added. Streptavidin has an extremely high droplets to see what effect the size restriction within cells,’ he says. affinity for biotin, and therefore attaches has. ‘We expect changes in genetics in these itself to the biotin on the staple strands that little compartments because of the finite Single molecules are untouched by the oxygen. Streptavidin size and possibly because of crowding of Meanwhile, Rothemund’s origami has can be visualised using AFM, meaning the macromolecules,’ says Simmel. a tremendous and growing number of applications, from boards on which to build Making good sense nanoelectronics to analytical tools. Kurt Gothelf is director of the Centre for DNA At the University of Birmingham, UK, Jim Tucker’s differs from many commercial SNP assays, Nanotechnology at Aarhus University in group is developing DNA probes to detect DNA which tend to work through differences in DNA Denmark. His team has been studying single base variations and modifications in the human hybridisation efficiency. ‘One challenge in this area molecule chemical reactions on DNA origami genome. ‘We make DNA by chemical synthesis in is to develop methods which do not rely on the and monitoring them using atomic force the lab and attach to these DNA strands a probe polymerase chain reaction (PCR), for example when microscopy (AFM). ‘DNA origami gives you a molecule – a tag [anthracene] – that enables the monitoring in a cellular environment,’ says Tucker. unique platform for single molecule studies DNA to be luminescent,’ says Tucker. When the His team is also developing methods for detecting and for studies of distance dependent chemical tagged strand interacts with its target to form base modifications in the genome, for example and biochemical phenomena,’ he says. a double strand, the DNA bases near to the tag epigenetic effects such as cytosine methylation. Gothelf’s team has used the origami to quench anthracene luminescence to varying Additionally, his group is working on using redox- 1 study the chemistry of singlet oxygen ( O2) extents, giving a change in emission. active tags to create electrochemical DNA sensors. which is involved in cell death and many The probes can be designed to target single ‘There is quite a lot of interest in electrochemical other biological processes, yet is poorly nucleotide polymorphisms (SNPs) in the human sensing of DNA.
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