Biomod/2013/Komaba/Discussion: Difference between revisions
(New page: == 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...) |
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== 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 rings and cylinders and tried them in cadnano. Finally, we adopted a method; a rectangular 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. | |||
Designing method 3 (From "Unidirectional Scaffold-Strand Arrangement in DNA Origami" by Dongran Han et al.) | |||
<br>Figure D15 | |||
<br>This designing method is useful both to a ring and a cylinder. It would have some flexibility in the length of the diameter. Moreover, because there is no crossover, it is easy to grow probes. However, this designing method of this is not clearly written so hard to copy. | |||
Designing method 6 (From "Self-Assembly of DNA Rings from Scaffold-Free DNA Tiles" by Yang Yang et al.) | |||
<br>Figure D18 | |||
<br>This ring consists of only staples. So this is against our policy in which we construct a ring and a cylinder in one scaffold. You must be careful about the electrical repulsion problem between a ring and a cylinder when you adopt this in DNA screw. However, once it is proved that this ring and a cylinder can connect, it would give a much wider option to the DNA screw design because a cylinder can use all the 7250 mer scaffold and the ring's designing method covers a wide range of a diameter. | |||
== How to Detect that the ring actually rotates == | |||
== Next Step == | == 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. | 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. | ||
Revision as of 09:40, 11 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 rings and cylinders and tried them in cadnano. Finally, we adopted a method; a rectangular 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.
Designing method 3 (From "Unidirectional Scaffold-Strand Arrangement in DNA Origami" by Dongran Han et al.)
Figure D15
This designing method is useful both to a ring and a cylinder. It would have some flexibility in the length of the diameter. Moreover, because there is no crossover, it is easy to grow probes. However, this designing method of this is not clearly written so hard to copy.
Designing method 6 (From "Self-Assembly of DNA Rings from Scaffold-Free DNA Tiles" by Yang Yang et al.)
Figure D18
This ring consists of only staples. So this is against our policy in which we construct a ring and a cylinder in one scaffold. You must be careful about the electrical repulsion problem between a ring and a cylinder when you adopt this in DNA screw. However, once it is proved that this ring and a cylinder can connect, it would give a much wider option to the DNA screw design because a cylinder can use all the 7250 mer scaffold and the ring's designing method covers a wide range of a diameter.
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
