Biomod/2013/Komaba/Discussion: Difference between revisions
No edit summary |
|||
| Line 2: | Line 2: | ||
We designed a ring and a cylinder in one scaffold to avoid the electrostatic interaction between them, which will cause them not to connect to each other. In that case, the cylinder and the ring stay keeping some distance and will have more possibility to connect to each other. However, We had some difficulties; First, we had to make the ring and cylinder within 7250 mer. Second, we had to find enzyme to cut the ring and cylinder. Third, we had to find cylinder and ring with compatible size in diameter. Fourth, we had to find a good design which allows us to put probes in an appropriate interval. | We designed a ring and a cylinder in one scaffold to avoid the electrostatic interaction between them, which will cause them not to connect to each other. In that case, the cylinder and the ring stay keeping some distance and will have more possibility to connect to each other. However, We had some difficulties; First, we had to make the ring and cylinder within 7250 mer. Second, we had to find enzyme to cut the ring and cylinder. Third, we had to find cylinder and ring with compatible size in diameter. Fourth, we had to find a good design which allows us to put probes in an appropriate interval. | ||
We check a lot of designing methods of | We check a lot of designing methods of cylinders and tried them in cadnano. We adopted the method; a rectangular which is made of a scaffold and staples is formed into a cylinder shape. This method has some advantages. This cylinder's design is rigid as well as flexible in designing. In addition, the yield is 88% and quite high. However, we cannot designate which surface becomes the front surface. Probes may come up from the back surface in this method and we can't separate it from the cylinder in which probes grow up from the front surface. The possibility would be 50:50. Also, if the diameter of this gets wide compared to its axial length, this does not form a cylinder shape. We met this difficulty of this in our experiment. | ||
Next, we adopted a designing method of a ring, in which the a scaffold is wound in a helix shape. The main reason why we used this is that with this method we could make a ring with a required diameter. We tried other several designing methods of rings in experiment but they did not form well. Another reason is that a ring designed by the above method does not use many parts of scaffold. We have to make the cylinder and ring in one scaffold so ring and cylinder should be designed with as small mounts of DNAs as possible. Moreover, because there is no crossover, it is easy to grow probes. However, this designing method is not clearly written in the original paper so it was hard to understand. | |||
== How to Detect that the ring actually rotates == | == How to Detect that the ring actually rotates == | ||
Revision as of 20:56, 20 October 2013
Some problems in our design
We designed a ring and a cylinder in one scaffold to avoid the electrostatic interaction between them, which will cause them not to connect to each other. In that case, the cylinder and the ring stay keeping some distance and will have more possibility to connect to each other. However, We had some difficulties; First, we had to make the ring and cylinder within 7250 mer. Second, we had to find enzyme to cut the ring and cylinder. Third, we had to find cylinder and ring with compatible size in diameter. Fourth, we had to find a good design which allows us to put probes in an appropriate interval.
We check a lot of designing methods of cylinders and tried them in cadnano. We adopted the method; a rectangular which is made of a scaffold and staples is formed into a cylinder shape. This method has some advantages. This cylinder's design is rigid as well as flexible in designing. In addition, the yield is 88% and quite high. However, we cannot designate which surface becomes the front surface. Probes may come up from the back surface in this method and we can't separate it from the cylinder in which probes grow up from the front surface. The possibility would be 50:50. Also, if the diameter of this gets wide compared to its axial length, this does not form a cylinder shape. We met this difficulty of this in our experiment.
Next, we adopted a designing method of a ring, in which the a scaffold is wound in a helix shape. The main reason why we used this is that with this method we could make a ring with a required diameter. We tried other several designing methods of rings in experiment but they did not form well. Another reason is that a ring designed by the above method does not use many parts of scaffold. We have to make the cylinder and ring in one scaffold so ring and cylinder should be designed with as small mounts of DNAs as possible. Moreover, because there is no crossover, it is easy to grow probes. However, this designing method is not clearly written in the original paper so it was hard to understand.
How to Detect that the ring actually rotates
Next Step
We developed a design in which the spider's body, streptavidin, is removed and the spider's walking legs are directly connected to the ring. With this design, the DNA screw could be more compact and less complex.
Figure D11
Figure D12
