introduction to our project

Because every project has to be introduced

Abstract

   UFO catcher is indubitably the symbol of Japanese arcade. Based on these machines, we are aiming to make a device with similar function using DNA origami that has the potential to capture and release tiny particles. The goal of this project is to create a DNA structure that can capture and release materials such as virus and protein, but not limited to these two.

   The structure that this research aims to create is a structure consisting of an outer larger tube with an inner portion connected to a magnetic bead by streptavidin-biotin binding which serves as the part that stretches out to capture incoming particles. This extended portion will take shape of 2 loops which will be pulled inside the larger tube with the help of external magnetic forces, entrapping particles entering the loops through Brownian motion.

Fig 1.1 Animated proposed function of the structure

Problem

   Virus infection is usually treated using medicine. However, after a while the medicine might start becoming ineffective and there might be a need to take more or to change the medications. This phenomenon is called drug resistance, and is common in viruses such as influenza, which is why annual vaccination is required.

Fig 1.2. Resistance of virus makes the immune system less effective.

   Therefore, to address to that problem, by using DNA origami, we designed a structure that can capture viruses. As a comparison, by applying pesticides to weeds, some might acquire resistance and the pesticides will not be effective anymore, however by physically removing the weeds down to the root, there is no chance for the weeds to show resistance. 

Fig 1.3. Mutations will not affect the function of the structure.

   In this project, we took the concept of UFO catcher, or mostly known as claw machines. However, even though the root concept of the project is similar, we modified the “claw” part to strengthen the ability to capture molecules.

goals

   The aim of this project is to prove that this mechanism is a feasible way to catch particles. Even though a method of recognition of molecules might be needed to claim that the structure is applicable, the target of the research at this stage is to simply proof that this method is possible.

Fig 1.4. Flowchart of the project.

The flow of our project is classified into 5 major points.
1. Design of DNA origami by caDNAno.
2. Simulate the behaviour using Cando.
3. Folding of DNA origami.
4a. Confirmation of the completion of structure using AFM.
4b. Confirmation of the movement through FRET
5. Confirmation of magnetically driven movement through FRET.

   In this project, all of the objectives until step 4a and 4b has been completed. The designed UFO catcher was constructed correctly and the FRET signal was observed as expected.

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