DNA origami class
March, 2017, Ochanomizu University, Tokyo
[Theme] DNA origami is about designing and building self-folded nanostructures from DNA (Rothemund, 2006).
[Content] In this educational project, we cover two complementary aspects of folding DNA:
- Computational part (modeling the folding path): We identify necessary constraints such as the change of direction of short staple strands that will give the shape and the locations of crossover that will ensure the stability of the model. We then generate a solution which is a sequence of A-T-C-G in the staple strands . We will use Maya Autodesk + caDNAno plugin to design a DNA folding path. The folded shape can be assessed with CanDo.
- Experimental part (performing the actual fold): The protocol is explained in (Stahl et. al., 2014, Castro et. al., 2011, ). We select M13mp18 to be the single-stranded scaffold that will work as a template. Basically, there are 4 steps in the experiment: (1) Scaffold and staples are annealed in a typical PCR cycle, (2) The sample is then purified to remove excess staples and keep well-folded DNA. We will opt for gel purification, (3) The folding process is assessed using gel electrophoresis. (4) The visualization of the result is not possible with common microscopy due to the nanosize of the folded objects. The alternatives could be TEM or AFM.
3D DNA nano object that will be modeled and folded in this class (picture provided by Tilibit)
- March 6, 15:00 - 16:30: Origami in the real world, DNA origami algorithm, modelling with caDNAno (I)
- March 6, 16:30 - 17:30: DNA origami protocol and annealing program
- March 13, 10:00 - 12:00, 16:00 - 17:30: Gel purification and quality control (1st trial)
- March 16, 15:00 - 16:30: DNA origami algorithm, modelling with caDNAno (II)
- March 21, 15:00 - 16:30: TEM microscopy, evaluation, future plan
- March 22, 10:00 - 11:00, 13:00 - 14:00: Gel purification and quality control (2nd trial)
- April, result of TEM microscopy and discussion, report and TEM microscopy
Contact: ghourabi "dot" fadoua "at" ocha "dot" ac "dot" jp
Office: 人間文化創成科学研究科・全学共用研究棟 603室
For questions, please do not hesitate to contact me.
- This educational project is developped in collaboration with Dr. Sabine Gouraud, Department of Biology, Ochanomizu University.
- The educational project is supported by a grant from the Leading Graduate School Promotion Center, Ochanomizu University.
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.