Understanding the rules of life

Category: Standard Studentships

Triplex addressabilty as a basis for functional DNA origami

Project No. 2356


Primary Supervisor

Dr David Rusling- University of Portsmouth


Dr Iris Nandhakumar – University of Southampton


DNA is a wonderful material with which to build and has allowed the fabrication of custom user-defined objects, arrays and devices bearing nanoscale features.

Current research efforts are working towards functionalising these structures with non-nucleic acid components, such as proteins or nanoparticles. Such modified scaffolds will offer applications that include the organisation of nanoelectronics, the manipulation of biological or chemical cascades, and the structure determination of periodically positioned molecules by structural analysis techniques. However, to date the introduction of components has relied on their attachment to the underlying DNA scaffold which can influence folding of the structure and is not compatible with most biological molecules which are denatured during annealing. To address this problem, we have recently developed the triplex approach to DNA recognition as a means to introduce components into DNA nanostructures after structure assembly by exploiting the sequence addressability of the underlying double-helical regions of the complexes (see Nucleic Acids Res, 2018, 46; 1021 for review). Triplex-forming oligonucleotides (TFOs) are short nucleic acid strands that bind specifically within the duplex major groove by hydrogen bonding to exposed groups on the base pairs, generating a triple-helical structure. TFOs can therefore be programmed to target unique duplex sequences within a DNA nanostructure and allow the introduction of components by their covalent attachment to the TFO. So far much of our work has focused on simple tile-based structures and this project will extend this approach to more complex DNA origami. The project will enhance the applicants theoretical and experimental skills in the design, assembly, and characterisation of natural and non-natural DNA structures, as well as their interaction with, and modification by, other biological molecules. The applicant should have a good understanding of basic molecular biology and a strong enthusiasm for investigating nucleic acid structure and function.