Research

There are several research areas within the DNA group. A brief description of each is given below.

DNA Lattices

DNA lattices are a great example of how large structures (1mm) can self-assemble from nanoscale components (10nm). If the sequence of bases is designed correctly four strands can be programmed to form a cross structure, known as a Holliday junction. This is the basic builing block, or tile, which will make up the lattice. By including sticky ends on the arms of the Holliday junction that are complementary to one another the tiles can join together to form larger structures. These two dimensional lattices show long range order and can be used to hold other components in a well defined pattern allowing three dimensional reconstruction from transmission electron microscopy images (Malo et al. 2005).

Figure 1: Schematic of the Kagome lattice assembly. A Holliday junction is formed from four DNA oligos (a) which take on a cross stacked conformation (b). The connectivity of these tiles (c) means a Kagome lattice is formed. The unit cell is denoted by a black parallelogram. In the extended lattice (d) the three double helices which interweave to from the lattice can be seen. (e) Atomic force images of Kagome lattices. The scale bar is 100nm for all images.

3D DNA Nanostructures

DNA can also be used to make three dimensional structures. The tetrahedron is an intrinsically braced structure on account of the triangular faces. This means that DNA tetrahedra are rigid, nanoscale, three-dimensional building blocks (Goodman et al. 2005). The cavity inside them can be used to hold cargo such as a protein (Erben et al. 2006). The ability to open and close the tetrahedron (Goodman et al. 2008) opens up the intriguing possibility of using them as drug delivery vehicles capable of protecting the cargo and releasing it in response to a targeted signal.

Figure 2: (a) The DNA tetrahedron. (b) A three dimensional reconstruction of the tetrahedron from TEM data. (c) The DNA bipyramid which has a greater internal volume to face area ratio than the tetrahedron. (d) The DNA octohedron.

DNA Motors

DNA can be used to create tracks, fuel and cargo. Motors can be powered by the energy available from DNA hybridization (Green et al. 2006, Green et al. 2008), or from DNA hydrolysis (Bath et al. 2005, Bath et al. 2009). Challenges in motor building include creating a rigid track to stop the motor jumping along tracks, a motor which is directional and processive, and inclusion of a power stroke.

Figure 3: A schematic diagram showing how the cargo (dark green) is transfered from one stator (light green) to the next in an enzyme-powered "burnt bridges" motor.

DNA Kinesin Nanoshuttles

Kinesin is a homodimeric protein motor which walks in a hand over hand manner along microtubule tracks. It is used to move vesicles and other cargo around the cell and plays many different roles in the cell division cycle. We are using DNA scaffolds to control the stoichiometry and geometry of kinesin motors to create well defined nanoshuttles.

Figure 4: (a) Microtubules glide on top of a surface of teams of single kinesin heads. (b) Several single heads can be linked together by DNA to form teams of heads. (c) Individual teams can be tracked using quantum dots.