Agarose Gel Electrophoresis for Purification of DNA Origami Nanotubes + Quantum Dots

Document Type


Publication Date

April 2010

Faculty Sponsor

Dr. William Hughes


The self-assembly of DNA origami structures with different fluorescent semiconductor quantum dots (QD’s) has the potential for creating devices using their novel optical, electrical and magnetic properties. DNA origami nanotubes are structures 412 nm in length consisting of 6 parallel DNA double helices bound together to form a tube 6 nm in diameter. The DNA nanotubes are fabricated by folding M13mp18, a long single-strand (ss) of DNA, with small ss-DNA strands called staple strands. Specific staple strands are modified to create biotin binding sites along the axis of the nanotube. These biotin binding sites are used to attach streptavidin coated QD’s at pre-defined locations on the nanotubes. Current fabrication methods do not create DNA nanotubes with attached QD’s at 100% yield due the interference of other conjugates, staple strands, and free streptavidin molecules. Using agarose gel electrophoresis (AGE), which separates the conjugates and molecules in terms of size and charge, it is expected that the DNA-QD structures can be purified to isolate well formed nanostructures. Once isolated, the well-formed nanostructures can be removed from the agarose gel through electroelution. AGE experiments are being performed on DNA origami nanotubes with 5 and 9 quantum dot attachment sites. The degree of successful purification will be determined with atomic force microscopy images of the DNA-QD nanostructures both before and after gel electrophoresis. Successful implementation of this purification methodology will separate DNA nanotubes with 100% QD attachment from those with incomplete attachment, allowing the purified structures to be incorporated into nanoscale devices.

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