Shape-Changing DNA Origami

There is still so much to understand on DNA origami and how it may be most efficiently utilized. DNA origami is the folding of DNA molecules to form nanoparticles with specific structures and may be used as nanocarriers in drug delivery. DNA origami structures contain a single single-stranded DNA scaffold strand and several oligonucleotides (staple strands) that form specific structures. The focus of this research was to design multiple structures of DNA nanoparticles through DNA origami that would contain the same single-stranded scaffold strand and only a few variations within the staple strands. This may lead to real-time shape-changing DNA origami that respond to specific stimuli. The first step towards achieving multiple structures with the same scaffold strand was to design a tetrahedron that would serve as the core backbone of the final shapes. Each shape designed contained three of the original tetrahedron shape. A triangular structure and a crescent structure were both made with the same 1632 base scaffold strand, demonstrating that designing multiple structures from the same strand is possible, and taking a step closer towards real-time shape-changing DNA origami. After completing the design of the shapes in TIAMAT, they will be folded and their ability to transform from one shape to the next will be observed.

Hi, my name is Sally Farag. I am a senior at george mason university majoring in bioengineering with a concentration in biomaterials and nanomedicine and today I am going to be talking about the research that I conducted this summer for my URSP project. The work that I did focused on DNA origami, which just like it sounds is the art of folding DNA molecules into specific nanoparticle structures through the design of its base sequences, and these can be used for drug delivery. DNA origami consists of one single-stranded DNA scaffold strand that runs through the entire nanoparticle structure. It’s like the backbone if you will. This scaffold strand is held together by oligonucleotides, which we call staple strand, to form the desired structure. What I set out to do was to take one singular scaffold strand and fold it into various structures by changing just a few staple strands. Now this is really cool because it can lead to real-time shape-changing DNA origami that responds to specific stimuli for purposes such as biosensing. My first step towards this was I needed to design a structure that I would use to build up the rest of my structures. A tetrahedron. In order for me to be able to design the tetrahedron from DNA, I first had to upload a Computer-Aided Design file, a CAD file into DAEDALUS, which stands for DNA Origami Sequence Design Algorithm for User-defined Structures. DAEDALUS takes CAD files of 3D solid objects and converts them into synthetic DNA sequences, and this information can then be used to build these 3D designs from DNA on a program called TIAMAT. My CAD file for the tetrahedron was provided to me by my mentor Dr. Remi Veneziano from his science paper called Designer nanoscale DNA assemblies programmed from the top down. After uploading the file and obtaining this information from DAEDALUS, I was able to make my tetrahedron design. As you can see, if I highlight my scaffold strand, it has 504 bases and runs through the entire tetrahedron structure. This is in contrast with the staple strands, which, if I select one, you can see it has only 78 bases, much smaller than the scaffold strand.
So after making my tetrahedron, I focused on designing a structure out of it. I took three of the same tetrahedron and designed what I call a triangle. Of course, it’s not actually a triangle, but it has three outer points to it, so. As you can see, if I again select my scaffold strand, it has 1632 bases.
Keep that number in mind. When I finished making that design, I built another one. Again, it was made by taking three of the same tetrahedron. I call this structure a crescent, because it reminds me of a crescent moon. If you squint you’ll see it. Now, I’m going to select the scaffold strand, and would you look at that. 1632 bases. The exact same length as the triangle structure. In fact, it is the exact same sequence.
Now of course I didn’t just design my triangle structure and design my crescent structure and it just worked out like that. I did have to go back a few times and make adjustments in order to reach and maintain the same scaffold strand length so that I could have the exact same scaffold strand in both structures. There are actually only 8 different staple strands between both structures. For reference, there are 32 staple strands in the crescent structure, and 33 in the triangle structure.
This is what I’ve accomplished so far, but I am going to continue my research in this. My next step is to go ahead and actually fold these structures and observe how well they are going to take form. I am very hopeful, but we will see how that goes. Thank you for watching.