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Details of Grant 

EPSRC Reference: EP/J019445/1
Title: Modelling the self-assembly of DNA multi-arm motifs
Principal Investigator: Doye, Professor JPK
Other Investigators:
Louis, Professor AA
Researcher Co-Investigators:
Project Partners:
Department: Oxford Chemistry
Organisation: University of Oxford
Scheme: Standard Research
Starts: 18 February 2013 Ends: 17 February 2016 Value (£): 306,508
EPSRC Research Topic Classifications:
Chemical Structure Physical Organic Chemistry
EPSRC Industrial Sector Classifications:
Related Grants:
Panel History:
Panel DatePanel NameOutcome
18 Apr 2012 EPSRC Physical Sciences Chemistry - April 2012 Announced
Summary on Grant Application Form
DNA is famous for its double helical structure, in which two strands wide around each other held together by the very specific interactions between the DNA bases that was first discovered by Watson and Crick, namely that adenine (A) bonds with thymine (T) and cytosine (C) bonds with guanine (G). The two strands are said to be complementary, because at each nucleotide the bases pair in the Watson-Crick fashion (A-T, and C-G). However, the specificity of the base pairing allows other structures other than one single double helix to be programmed into a set of DNA strands. For example, if you have 3 types of strands, say P, Q and R, where the first half of P is complement to half of Q, and the second half is complementary to half of R, and the remaining halves of Q and R are complementary, the system will want to form a structure with three double helical sections meeting at a junction. This basic approach can be scaled up to make a whole array of precisely-ordered structures on the nanometer length scale that assemble themselves driven by the desire of complementary stretches of DNA molecules to pair up. This field is called DNA nanotechnology, and in this proposal we wish to study nanostructures called DNA multi-arm motifs. The 3-arm example of this class of structures is somewhat similar to the junction mentioned above, except that each arm is made up of two parallel double helices. By designing these motifs so that there are short single-stranded overhangs at the each of arm that are complementary to the overhangs at the ends of other arms, these motifs can be made to form a whole variety of larger structures. For example, the 3-arm motifs can form tetrahedra, dodecahedra and buckyballs (all polyhedra where 3 edges meet at a vertex) depending on the precise design and the conditions under which they assemble, In experiments, the researchers are able to see if their designed sequences successfully assemble into the target structure, but cannot see how they manage to achieve this. This is where computer modelling and this proposal fits in. We want to use techniques that we recently developed to model DNA to visualize the mechanisms by which these remarkable molecules are able to so reliably self-assemble. The insights that we hope to obtain will be of great help to experimentalists, as it will give them a better idea of why some of their designs are successful whereas others fail to do what is expected. This in turn will help them to make the design procedure more rational and hence more likely to succeed. Hopefully, this will enable the experimentalists to significantly increase the types of structures they can produce.
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Organisation Website: http://www.ox.ac.uk