Biomod/2011/TeamJapan/Tokyo/Project/Results: Difference between revisions
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=Experimental Results= | =Experimental Results= | ||
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<td align="center" width="200px"><a href="/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results# | <td align="center" width="200px"><a href="/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results#The_construction_of_the_body_of_the_DNA_ciliate"><img src="http://openwetware.org/images/4/4a/BIOMOD_Tokyo20111031Result_figure_ciliate.png" border=0 width=200 height=200></a></td> | ||
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*We constructed the micrometer-sized body of the DNA ciliate by surface modification. [[Biomod/2011/TeamJapan/Tokyo/Project/Results# | *We constructed the micrometer-sized body of the DNA ciliate by surface modification. <br>[[Biomod/2011/TeamJapan/Tokyo/Project/Results#The_construction_of_the_body_of_the_DNA_ciliate|Shown in detail below]] | ||
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*We confirmed that DNA ciliate can move freely and randomly alomost all area based on Brownian motion. [[Biomod/2011/TeamJapan/Tokyo/Project/Results#1. Free moving mode|Shown in detail below | *We confirmed that DNA ciliate can move freely and randomly alomost all area based on Brownian motion. <br>[[Biomod/2011/TeamJapan/Tokyo/Project/Results#1. Free moving mode|Shown in detail below]]</td> | ||
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*We confirmed that substrate DNA are cut by deoxyribozyme legs of DNA ciliate.<br> | *We confirmed that substrate DNA are cut by deoxyribozyme legs of DNA ciliate.<br> | ||
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*We designed the DNA which react. <br> | *We designed the DNA which react. <br> | ||
*When we irradiated UV, we succeeded to gather beads at the spot where we irradiate UV.<br>[[Biomod/2011/TeamJapan/Tokyo/Project/Results#3. Light-irradiated gathering mode|Shown in detail below]] | *When we irradiated UV, we succeeded to gather beads at the spot where we irradiate UV.<br>[[Biomod/2011/TeamJapan/Tokyo/Project/Results#3. Light-irradiated gathering mode|Shown in detail below]]</td> | ||
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:[[Image:Tokyo 200nmEDAC.jpg|thumb|left|The denaturing PAGE image for the investigation of the deoxyribozyme activity on the DNA ciliate <!--PAGE of φ200 nm polystyrene beads using EDAC.-->|500px]] | :[[Image:Tokyo 200nmEDAC.jpg|thumb|left|The denaturing PAGE image for the investigation of the deoxyribozyme activity on the DNA ciliate which is 200nm in diameter<!--PAGE of φ200 nm polystyrene beads using EDAC.-->|500px]] | ||
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:[[Image:Tokyo 1μEDAC.jpg|thumb|left|The | :[[Image:Tokyo 1μEDAC.jpg|thumb|left|The denaturing PAGE image for the investigation of the deoxyribozyme activity on the DNA ciliate which is 1um in diameter<!--PAGE of φ1 um polystyrene beads using EDAC.--> |500px]] | ||
<!--PAGE of φ1 um polystyrene beads using EDAC.--> |500px]] | |||
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===Results=== | ===Results=== | ||
---------------------------------------- | ---------------------------------------- | ||
:Video ( | :Video (A) (the left two videos) shows the observation results of the DNA ciliates with a diameter of 200 nm under the optical microscope. Video (B) (the right two videos) shows the observation results of the DNA ciliates with a diameter of 1 μm. The lower videos are enlarged views of the upper videos. | ||
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:From these videos, we observed that the DNA ciliates were freely and randomly moving in the solution. By comparing the motion of the DNA ciliates with a diameter of 200 nm and 1 μm, the smaller DNA ciliates (200 nm in diameter) moved more strongly than the larger DNA ciliates (1 μm in diameter). We observed a very slow directional flow of the solution as an experimental artifact but the motion of the DNA ciliate was random independently of the flow. In addition, we observed some DNA ciliates that did not move at all; the DNA ciliates were probably crystalized one another or sticking at the surface of the glass slide. | :From these videos, we observed that the DNA ciliates were freely and randomly moving in the solution. By comparing the motion of the DNA ciliates with a diameter of 200 nm and 1 μm, the smaller DNA ciliates (200 nm in diameter) moved more strongly than the larger DNA ciliates (1 μm in diameter). We observed a very slow directional flow of the solution as an experimental artifact but the motion of the DNA ciliate was random independently of the flow. In addition, we observed some DNA ciliates that did not move at all; the DNA ciliates were probably crystalized one another or sticking at the surface of the glass slide. | ||
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===Confirmation of Deoxyribozyme activity=== | ===Confirmation of Deoxyribozyme activity=== | ||
--------------------------------------------------- | --------------------------------------------------- | ||
:We confirmed the cleaving activity of the deoxyribozyme for cilia attached on the DNA ciliate body using the polyacrylamide gel electrophoresis. Actually, the results have already been shown in the section of the confirmation of constructing the DNA ciliate body above [[#The results of | :We confirmed the cleaving activity of the deoxyribozyme for cilia attached on the DNA ciliate body using the polyacrylamide gel electrophoresis. Actually, the results have already been shown in the section of the confirmation of constructing the DNA ciliate body above [[#The results of the investigation of the deoxyribozyme activity on the DNA ciliate|(see the results)]] From the results, we conclude that the deoxyribozyme activity for the substrate DNA worked as we designed. | ||
===Construction of DNA tracks=== | ===Construction of DNA tracks=== | ||
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:To construct the DNA tracks, we used microchannels to immobilize the substrate DNA at a specific region we designed. The construction of the microchannel is as follows. A mold of a microchannel was constructed with polyacetal resin by cutting the polystyrene resin as we designed with an endmill controlled by micro-machining system. The poly(dimethylsiloxane) (PDMS) and its hardener were mixed at the ratio of 10:1, and bubbles in the mixed PDMS solution was cleaned with a vacuum desiccator. The PDMS solution was poured over the mold and cured and hardened the PDMS solution at 75 degree Celsius for 1 hour. Then, the hardened PDMS was peeled off from the mold. The PDMS has a microchannel transferred from the mold. | :To construct the DNA tracks, we used microchannels to immobilize the substrate DNA at a specific region we designed. The construction of the microchannel is as follows. A mold of a microchannel was constructed with polyacetal resin by cutting the polystyrene resin as we designed with an endmill controlled by micro-machining system.<br>The poly(dimethylsiloxane) (PDMS) and its hardener were mixed at the ratio of 10:1, and bubbles in the mixed PDMS solution was cleaned with a vacuum desiccator. The PDMS solution was poured over the mold and cured and hardened the PDMS solution at 75 degree Celsius for 1 hour. Then, the hardened PDMS was peeled off from the mold. The PDMS has a microchannel transferred from the mold. | ||
:Next, we constructed a DNA track using the PDMS microchannel. To make DNA tracks, we used microchannel and arrayed DNAs on a glass plate. To attach DNAs on a glass plate, we used disuccinimidyl suberate (DSS) as a linker between amino-modified DNA and an amino-modified glass plate (MAS-coated glass, Matsunami) [1]. The DSS linker reacts with amino groups that are exposed on the surface of the MAS-coated glass [2]. By the DSS linker, DNAs were attached on the glass plate by a covalent bond. We poured an amino-modified DNA solution into the PDMS microchannel on the MAS-coated glass plate treated with DSS; thus, the DNAs were arrayed as the shape of the microchannel we designed. We can design the shapes of microchannels freely, so we can make DNA tracks with arbitrary shapes. Finally, we observed the arrayed DNA track by hybridizing a fluorescence-labeled DNA complementary to the DNA strands of the DNA track. | :Next, we constructed a DNA track using the PDMS microchannel. To make DNA tracks, we used microchannel and arrayed DNAs on a glass plate. To attach DNAs on a glass plate, we used disuccinimidyl suberate (DSS) as a linker between amino-modified DNA and an amino-modified glass plate (MAS-coated glass, Matsunami) <!--[1]-->. The DSS linker reacts with amino groups that are exposed on the surface of the MAS-coated glass <!--[2]-->. By the DSS linker, DNAs were attached on the glass plate by a covalent bond. We poured an amino-modified DNA solution into the PDMS microchannel on the MAS-coated glass plate treated with DSS; thus, the DNAs were arrayed as the shape of the microchannel we designed. We can design the shapes of microchannels freely, so we can make DNA tracks with arbitrary shapes. Finally, we observed the arrayed DNA track by hybridizing a fluorescence-labeled DNA complementary to the DNA strands of the DNA track. | ||
|width="400px"|[[Image:Biomod2011 Team Tokyo 111030Biomod Construction of DNA track.png|center|Construction of DNA track|300px]]<br> | |width="400px"|[[Image:Biomod2011 Team Tokyo 111030Biomod Construction of DNA track.png|center|Construction of DNA track|300px]]<br> | ||
[[Image:Tokyo tech:DNAimmobilization 5.png|center|A series of attaching aminated DNA to glass reaction|300px]]<br> | [[Image:Tokyo tech:DNAimmobilization 5.png|center|A series of attaching aminated DNA to glass reaction|300px]]<br> | ||
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:<h4>Results of the construction of DNA tracks</h4> | :<h4>Results of the construction of DNA tracks</h4> | ||
:Figure 1 shows a picture of the polyacetal resin mold (the mold for microchannels are shown by broken lines). This is a part of large microchannels we used to array DNAs. Figure 2 shows a fluorescence microscope image of the DNA tracks. | :Figure 1 shows a picture of the polyacetal resin mold (the mold for microchannels are shown by broken lines). This is a part of large microchannels we used to array DNAs. Figure 2 shows a fluorescence microscope image of the DNA tracks. We observed the fluorescence of the DNA hybridizing with the DNA track arrayed on the glass plate. In addition, Figure 3 shows the whole picture of the large DNA tracks with a human like shape (observed similarly). | ||
{| | {| | ||
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|width="33%" valign="top"|[[Image:Tokyo human formed.jpg|thumb|center|Figure 3. The microchannel of human form The left image is the design drawing. The right figure is the result of hybridization. Because camera view was too narrow to observe total image, we stuck together the part of pictures.|300px]] | |width="33%" valign="top"|[[Image:Tokyo human formed.jpg|thumb|center|Figure 3. The microchannel of human form The left image is the design drawing. The right figure is the result of hybridization. Because camera view was too narrow to observe total image, we stuck together the part of pictures.|300px]] | ||
|} | |} | ||
:In conclusion, we successfully constructed DNA tracks using microchannels, and we confirmed the ability of hybridization between the immobilized DNA as the tracks and its complementary DNA. Thus, we believe that the deoxyribozyme on the DNA ciliate also hybridizes with the track DNA, which has a complementary DNA sequence of the deoxyribozyme. | :In conclusion, we successfully constructed DNA tracks using microchannels, and we confirmed the ability of hybridization between the immobilized DNA as the tracks and its complementary DNA. Thus, we believe that the deoxyribozyme on the DNA ciliate also hybridizes with the track DNA, which has a complementary DNA sequence of the deoxyribozyme. | ||
<center> | |||
{| | |||
|width="50%" valign="top"|[[Image:Tokyo track 2.png|thumb|center|Figure 4. Fluorescent image of DNA ciliate gathering at the specific area by fluorescent microscopy.|400px]] | |||
|width="50%" valign="top"|[[Image:Tokyo track 3.png|thumb|center|Figure 5. Fluorescent image of DNA ciliate gathering at the specific area by fluorescent microscopy.|400px]] | |||
|} | |||
</center> | |||
:In conclusion, we observed the DNA ciliates stayed at the spot of the substrate DNA on a glass plate. | |||
===Investigation of the directional walking by simulations=== | ===Investigation of the directional walking by simulations=== | ||
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===UV-switching system=== | ===UV-switching system=== | ||
--------------------------------------------------- | |||
:[[Image:Tokyo-gathering2.png|600px|center]] | :[[Image:Tokyo-gathering2.png|600px|center]] | ||
:The UV-switching DNA has a stem-loop structure and short blocking DNA, which blocks hybridization of deoxyribozyme. After UV irradiation, this loop becomes open, and hybridize with the deoxyribozyme. [[(more detail...)]] | :The UV-switching DNA has a stem-loop structure and short blocking DNA, which blocks hybridization of deoxyribozyme. After UV irradiation, this loop becomes open, and hybridize with the deoxyribozyme. [[Biomod/2011/TeamJapan/Tokyo/Achievements/DNA_Devices#3.UV-switching DNA|(more detail...)]] | ||
=== | ====Confirmation of UV-switching==== | ||
===Method=== | |||
:We did native-PAGE to check UV-switching system. [[Biomod/2011/TeamJapan/Tokyo/Notebook/Protocols#UV_switching_ protocol|(more detail...)]] | |||
===Results=== | ===Results=== | ||
[[Image:Tokyo_UV-gel.jpg|thumb|920px|Image of non-denaturing 20% PAGE for the confirmation of UV-switching]] | [[Image:Tokyo_UV-gel.jpg|thumb|920px|Image of non-denaturing 20% PAGE for the confirmation of UV-switching]] | ||
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*Comparing lane 11 and 12, the density of the band U+D is much the same, so we thought UV-switching finished in 15 minutes in this experimentation. | *Comparing lane 11 and 12, the density of the band U+D is much the same, so we thought UV-switching finished in 15 minutes in this experimentation. | ||
*In conclusion, we confirmed UV-switching DNA changes the structure and branch migration happens when UV is spotted. | *In conclusion, we confirmed UV-switching DNA changes the structure and branch migration happens when UV is spotted. | ||
=== | |||
[[Image:Tokyo gathering.jpg|thumb|right|A fluorescent image of DNA ciliate gathering at the specific area|500px]] | ===Gathering at the specific area=== | ||
=== | --------------------------------------------------- | ||
[[Image:Tokyo gathering.jpg|thumb|right|A fluorescent image of DNA ciliate gathering at the specific area by fluorescent microscopy.|500px]] | |||
===Method=== | |||
*Attaching complementary DNA of deoxyriboazyme on a glass plate | *Attaching complementary DNA of deoxyriboazyme on a glass plate | ||
*Making the situation which deoxyribozymes hybridize with complementary DNA on the glass plate | *Making the situation which deoxyribozymes hybridize with complementary DNA on the glass plate | ||
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*Observing the DNA ciliates under an fluorescent microscope | *Observing the DNA ciliates under an fluorescent microscope | ||
=== | ===Results=== | ||
*A fluorescent image of the DNA ciliates gathering at the spot of complementary DNA is here. | *A fluorescent image of the DNA ciliates gathering at the spot of complementary DNA is here. | ||
*Complementary DNA was attached on upper-right area in this image. | *Complementary DNA was attached on upper-right area in this image. | ||
:There was no DNA in lower-left area in this image. | :There was no DNA in lower-left area in this image. | ||
*DNA ciliates gathered at the spot of complementary DNA, and didn't gather at another area. Following this result, it was confirmed that DNA ciliates can gather at the specific area after UV irradiation. | *DNA ciliates gathered at the spot of complementary DNA, and didn't gather at another area. Following this result, it was confirmed that DNA ciliates can gather at the specific area after UV irradiation. |
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Experimental Results
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<td align="center" width="200px"><a href="/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results#The_construction_of_the_body_of_the_DNA_ciliate"><img src="http://openwetware.org/images/4/4a/BIOMOD_Tokyo20111031Result_figure_ciliate.png" border=0 width=200 height=200></a></td>
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<td align="center" width="200px"><a href="/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results#1._Free_moving_mode"><img src="http://openwetware.org/images/a/ac/BIOMOD_Tokyo20111031Result_figure1.png" border=0 width=200 height=200></a></td>
<td align="center" width="200px"><a href="/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results#2._The_track_walking_mode"><img src="http://openwetware.org/images/0/05/BIOMOD_Tokyo20111031Result_figure2.png" border=0 width=200 height=200></a></td>
<td align="center" width="200px"><a href="/wiki/Biomod/2011/TeamJapan/Tokyo/Project/Results#3._Light-irradiated_gathering_mode"><img src="http://openwetware.org/images/b/bf/BIOMOD_Tokyo20111031Result_figure3.png" border=0 width=200 height=200></a></td>
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The construction of the body of the DNA ciliate
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Method
- The deoxyribozymes were attached to the polystyrene body of the DNA ciliate using the following chemical reaction by 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDAC). The polystyrene bead for the DNA ciliate body has carboxyl groups on its surface. The EDAC reacts with the carboxyl group and forms a reactive group (see the following figure). An amino-modified DNA reacts with the reactive group on the bead surface, and then the DNA is immobilized on the surface of the polystyrene bead body. We carried out this reaction using a chemical reagent kit, PolyLink Protein Coupling Kit for COOH Microspheres (Polyscience) (see Protocols).
- After the above reaction, we investigated whether the deoxyribozymes were actually attached on the surface of the polystyrene body of the DNA ciliate, using a deoxyribozyme activity assays because the deoxyribozyme cannot be recognized through an optical microscope. The deoxyribozyme activity is an RNA cleaving activity in a solution with a divalent ion, Zn2+.
The results of the investigation of the deoxyribozyme activity on the DNA ciliate
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Three independent modes of the DNA ciliate
1. Free moving mode
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Method
- In the observation of the DNA ciliate, we used 1× saline-sodium citrate (SSC) buffer with 3% bovine serum albumin (BSA) (the materials for experiments are listed in Protocols). The sizes of DNA ciliate bodies were 200 nm and 1 μm. We put the solution including the DNA ciliates on a glass slide and covered by a cover slip. The solutions including the DNA ciliates were observed by a phase-contrast microscope and took videos (the equipment for experiments is also listed in Protocols).
Results
- Video (A) (the left two videos) shows the observation results of the DNA ciliates with a diameter of 200 nm under the optical microscope. Video (B) (the right two videos) shows the observation results of the DNA ciliates with a diameter of 1 μm. The lower videos are enlarged views of the upper videos.
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<tr align="center"> <td>Video (A)
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<td>Video (B)
<iframe width="450" height="259" src="http://www.youtube.com/embed/-zzB6UeWKoM?hl=ja&fs=1" frameborder="0" allowfullscreen></iframe></td>
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<iframe width="450" height="259" src="http://www.youtube.com/embed/E1vW6eaABcQ" frameborder="0" allowfullscreen></iframe></td>
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<iframe width="450" height="259" src="http://www.youtube.com/embed/jKpgMfls3Kw" frameborder="0" allowfullscreen></iframe></td>
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- From these videos, we observed that the DNA ciliates were freely and randomly moving in the solution. By comparing the motion of the DNA ciliates with a diameter of 200 nm and 1 μm, the smaller DNA ciliates (200 nm in diameter) moved more strongly than the larger DNA ciliates (1 μm in diameter). We observed a very slow directional flow of the solution as an experimental artifact but the motion of the DNA ciliate was random independently of the flow. In addition, we observed some DNA ciliates that did not move at all; the DNA ciliates were probably crystalized one another or sticking at the surface of the glass slide.
- In conclusion, we achieved the free moving mode of the DNA ciliate. The motion of the DNA ciliate was based on the Brownian motion of the DNA ciliates. The random motion of the smaller DNA ciliates was stronger than that of the larger DNA ciliate. This result consistent with the theory of the Brownian motion described in Project page.
2. The track walking mode
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Confirmation of Deoxyribozyme activity
- We confirmed the cleaving activity of the deoxyribozyme for cilia attached on the DNA ciliate body using the polyacrylamide gel electrophoresis. Actually, the results have already been shown in the section of the confirmation of constructing the DNA ciliate body above (see the results) From the results, we conclude that the deoxyribozyme activity for the substrate DNA worked as we designed.
Construction of DNA tracks
Method of the construction of DNA tracks
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Results of the construction of DNA tracks
- Figure 1 shows a picture of the polyacetal resin mold (the mold for microchannels are shown by broken lines). This is a part of large microchannels we used to array DNAs. Figure 2 shows a fluorescence microscope image of the DNA tracks. We observed the fluorescence of the DNA hybridizing with the DNA track arrayed on the glass plate. In addition, Figure 3 shows the whole picture of the large DNA tracks with a human like shape (observed similarly).
- In conclusion, we successfully constructed DNA tracks using microchannels, and we confirmed the ability of hybridization between the immobilized DNA as the tracks and its complementary DNA. Thus, we believe that the deoxyribozyme on the DNA ciliate also hybridizes with the track DNA, which has a complementary DNA sequence of the deoxyribozyme.
- In conclusion, we observed the DNA ciliates stayed at the spot of the substrate DNA on a glass plate.
Investigation of the directional walking by simulations
- We investigated the directional walking of the DNA ciliate by numerical simulations (see Simulations)
3. Light-irradiated gathering mode
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UV-switching system
- The UV-switching DNA has a stem-loop structure and short blocking DNA, which blocks hybridization of deoxyribozyme. After UV irradiation, this loop becomes open, and hybridize with the deoxyribozyme. (more detail...)
Confirmation of UV-switching
Method
- We did native-PAGE to check UV-switching system. (more detail...)
Results
- The control bands were appeared in lane 1 to 6. Lane 4 means the bands when the loop is stable and hybridization U and B . Lane 5 means the bands when the loop is open and not spotted UVhybridization of U and D. Lane 6 means the bands when the loop is open and spotted UV (band U-D).
- In the presence of Mg2+, the switching was caused clearly (lane 10 to 12) because of the stable effect of Mg2+.
- From the picture, in lane 10, there is the band B+U and not the band U+D, so it is confirmed that when UV is not spotted, UV-switching DNA is close the loop. On the other hand, in lane 11 and 12, there is the band U+D and not the band B+U, so it is confirmed that when UV is spotted, UV-swithching DNA is open the loop.
- In lane 4,5, and 6, there is a band which is neither monomer nor hybridized. In lane 1, 2, and 3, there is only a band, so the band is not dimer, so we thought the band is another hybridizing structure. The density of these bands is much weaker than the band of normal hybridizing structure, so we thought this band is little effect to UV-switching system.
- Comparing lane 5 and 6, the density of the bands in lane 6 is weaker than in lane 5. We thought the density of the band U+D becomes weak by spotting UV. We thought that is a reason the band of Lane 11 and 12 are weak.
- Comparing lane 11 and 12, the density of the band U+D is much the same, so we thought UV-switching finished in 15 minutes in this experimentation.
- In conclusion, we confirmed UV-switching DNA changes the structure and branch migration happens when UV is spotted.
Gathering at the specific area
Method
- Attaching complementary DNA of deoxyriboazyme on a glass plate
- Making the situation which deoxyribozymes hybridize with complementary DNA on the glass plate
- How to make the situation for hybridization is here
- Putting DNA ciliates on the glass plate
- Waiting for 2 hours
- Observing the DNA ciliates under an fluorescent microscope
Results
- A fluorescent image of the DNA ciliates gathering at the spot of complementary DNA is here.
- Complementary DNA was attached on upper-right area in this image.
- There was no DNA in lower-left area in this image.
- DNA ciliates gathered at the spot of complementary DNA, and didn't gather at another area. Following this result, it was confirmed that DNA ciliates can gather at the specific area after UV irradiation.