Biomod/2012/UTokyo/UT-Komaba/Experiment/DNA Tablet

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We combine modified origami and bistable system so that we can realize the DNA tablet.
We combine modified origami and bistable system so that we can realize the DNA tablet.
The purpose of the experiment is to observe the surface of the tablet and make sure that the surface change when we put another kind of DNA.
The purpose of the experiment is to observe the surface of the tablet and make sure that the surface change when we put another kind of DNA.
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==Method==
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===Pseudo-hammerhead Structure===
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To make hammerhead structure, we needed to add some DNA sequences to existing staples witch didn't interact with other parts of DNA origami. We made such sequences from the sequence below.
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[[Image:Biomod_2012_UTokyo_UT-Komaba_Hammerhead.png‎|thumb|right| Hammerhead structure]]
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{|
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|GGAACCTCAGCCCAACTAACAT
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|}
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This sequence is known not to interact with other parts of DNA origami. We made three hammerhead structures from this.
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(5' -> 3' direction)
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{|
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! !! addition to staple !! cover
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|-
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| 1 || CTCCAAGGTTT - TTTAGCCCAAC || GAGGTTCCTCGGGTTG
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|-
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| 2 || CGACTCCATTT - TTTCCAACTAA || TGGGCTGATGATTGTA
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|-
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| 3 || ACCCGACTTTT - TTTACTAACAT || GCTGAGGTGGTTGATT
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|}
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===The design of the DNA tablet===
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Using the three hammerhead structures, we designed the DNA origami.
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[[Image:BIOMOD-2012-UTkyo-UTKomaba-design.png|700px]]
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==Experiment==
==Experiment==

Revision as of 12:09, 25 October 2012

DNA tablet

Contents

Concept

DNA Tablet Concept

The last but the most important experiment is the experiment of the DNA tablet. We combine modified origami and bistable system so that we can realize the DNA tablet. The purpose of the experiment is to observe the surface of the tablet and make sure that the surface change when we put another kind of DNA.


Method

Pseudo-hammerhead Structure

To make hammerhead structure, we needed to add some DNA sequences to existing staples witch didn't interact with other parts of DNA origami. We made such sequences from the sequence below.

Hammerhead structure
Hammerhead structure
GGAACCTCAGCCCAACTAACAT

This sequence is known not to interact with other parts of DNA origami. We made three hammerhead structures from this.

(5' -> 3' direction)

addition to staple cover
1 CTCCAAGGTTT - TTTAGCCCAAC GAGGTTCCTCGGGTTG
2 CGACTCCATTT - TTTCCAACTAA TGGGCTGATGATTGTA
3 ACCCGACTTTT - TTTACTAACAT GCTGAGGTGGTTGATT


The design of the DNA tablet

Using the three hammerhead structures, we designed the DNA origami.


Experiment

October 20th

We got the modified staples, so we made the staple mix for the main body of DNA tablet and tried observing it. In this experiment, we did not put cover DNA for hammerhead structures so that we might not observe pictures on the surface. However, DNA origami wasn't observed clearly.

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October 22nd

We made modified origami in September 20th, but the origami was not structured. Therefore, we carefully made the modified staple mix again.


October 23rd

We made the modified origami again and prepare for the observation in October 24th.

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October 24th

We observed the DNA tablet by AFM at the Komaba Campus. However, we could not get good pictures of the tablets from any tubes. From the pictures, the tablet seemed to not be well structured and partly collapsed.


October 25th

We prepard new staple mix of DNA tablet and made the tablet from staple mix we served in October 20th and the tablet from staple mix we served in October 25th. Because the modified origami succeeded when we put them in room temperature, we decided to keep the both tablets at the room temperature, about 20°C. Of course, there is possibility that we made some mistakes while making staple mix in October 20th so that the tablet did not structured, we kept one tube of the tablet made from staple mix in October 25th at 4°C. The purpose of the experiment is to observe the completely structured DNA tablet. We annealed them from 90°C to 20°C for 2800 seconds.

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