Investigating the fluorous effect to direct DNA origami assembly

DNA origami is a robust method for the creation of nanostructures with arbitrary shapes, whereby a long single strand is folded into extended patterns with the aid of hundreds of short stands. DNA origami has been shown as an ideal technique to control and organise individual molecules with nanoscale accuracy, which is of great importance in the fields like bio-sensing and nano-engineering. Assembly of DNA origami sheets into higher ordered structures is desirable for the fabrication of new materials and devices that are currently beyond the reach of top-down fabrication techniques. However, there are major constraints when attempting to create origami super-structures larger than one micron, including the inefficiency of attachment reactions between individual origami tiles, the complexity of the design, and the number of unique DNA sequences required. The primary focus of this thesis is to explore the fluorous-effect as a new method to promote DNA origami dimerization. Firstly, affecting factors to origami dimerization using stickyends strategy was explored. This work showed that changing the number and length of sticky-ends largely affect the dimer yield. Bridging strands work cooperatively when in proximity, when they were placed in distance, however, the binding of one doesn’t help the binding of another, thus they work independently. The fluorous effect was then introduced as a novel strategy to join distinct origami tiles together. Fluorous-fluorous interactions differ from conventional base-pairing interactions in that they are relatively strong and non-specific. This work showed that fluorous-tagged origami can be used as a mean to direct origami dimerization. Among all of the fluorous species that were explored, branched-RF8 tags were most efficient at directing origami dimerization. A hybrid linker system containing both fluorous strands and sticky-ends was then explored. It was found that the hybrid system significantly improves the dimer yield when compared to the equivalent DNA-only system. The fact that double extension sticky-ends are more efficient than single extensions may suggest that a more stable, higher-yield dimer could form with the use of double-extended RF-oligos. The final experimental chapter demonstrates the construction of an origami based FRET system comprising quantum dots and organic fluorophores. This works explored several dye patterns including linear, checkerboard and a quantum dot - dye complex to obtain an optimized energy transfer network. This is the first time that quantum dots have been used as a FRET donor in an origami platform. It is thought that this work has potential application in multiplex assays as quantum dots can, unlike fluorophores, serve as multiple acceptors