Biomod/2014/Kashiwa/Discussion: Difference between revisions

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<h1 class="title"><a name="Achieve">&nbsp;Achievements</a></h1>
<h1 class="title"><a name="Achieve">&nbsp;Achievements</a></h1>
<br>
<br>
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<img src="http://openwetware.org/images/c/cc/Acheivement_完成版小.png" width="800px" height="430px" align="right">
<img src="http://openwetware.org/images/0/04/AchieveKashiwa.png" width="800px" height="450px">
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<a name="2"></a>
 
<br>
 
<br>
<div>
<br>
<h1 class="title"><a name="Future">&nbsp;Future</a></h1>
<h1 class="title"><a name="Future">&nbsp;Future</a></h1>
<p class="paragraph">In our project during the summer, we focused on one aspect of the moving system, polymerization. We have to approach the other aspect, depolymerization, to move the PoLICe practically. In order to develop the depolymerization step, the following aspects should be satisfied:</p>
</div>


<p class="paragraph">1. The Motor-Polymer is fragile and easily decomposes into the Motor-Monomers.<br>
<p class="paragraph">
2. When a receptor catch outside signals, the Polymerized state is stabilized than the non-Polymerized state.<br>
In order to create completed-PoLICe which can move toward cancer markers and kill cancer cells, the functions we have to equip with PoLICe is as follows:
3. Therefore, Motor-Monomers polymerize in a place near the signal receptor and depolymerize in the other.</p>
</p>
<p class="paragraph">
<a href="#f1">1. A depolymerization system of monomers for self-moving</a>
</p>
<p class="paragraph">
<a href="#f2">2. A cancer recognition system</a>
</p>
<a name="f1"></a>
<p class="paragraph">
<a href="#f3">3. A cancer killing system</a>
</p>
<p class="paragraph">
Below, we will state how we will equip these functions with PoLICe in our next step.
</p><br><br>
 
 
 
 
<h1 class="big">
1. A depolymerization system of monomers
</h1>
 
<img src="http://openwetware.org/images/f/f9/Future_recognition%26breaking_000001.png" width="330px" height="240px">
 
<p class="paragraph">
In order to accomplish the self-moving system beyond the self-transformation, a polymerization of monomers should be occurred only near the front membrane of PoLICe, and the depolymerization should be occurred at the trailing membrane. Therefore, the depolymerization is the key for our next purpose.
</p>
<p class="paragraph">
There are two approaches to accomplish the depolymerization. One is “active depolymerization” method, and the other is “passive depolymerization” through the absence of a polymerization promotion system at the depolymerization site. We chose the latter, “passive” approach. In this approach, the default state of monomers is a depolymerization, and without the polymerization promotion system, all the monomers keep in monomeric state. We, therefore, plan to use weaker interaction than temporal version of the Motor-Monomer.
</p>
<p class="paragraph">
For the localized polymerization promotion, we introduce Supporter, Reserver, and Anchor to our PoLICe.
</p>
<p class="paragraph">
Supporter binds the joint of monomers to stabilize the bond between monomers and prevent the depolymerization.
</p>
<p class="paragraph">
If the Supporters exist in PoLICe universally, all bonds will be stabilized at the same probability, and the polymerization will be occurred everywhere in PoLICe. To prevent this situation, we will use Reserver to localize the Supporter near the front membrane.
</p>
<p class="paragraph">
Reserver exists on the inner surface of the membrane, and can interact Supporter by a weak interaction. Therefore, Reserver keeps Supporters near the membrane, driving the polymerization only near the membrane.
</p>
<p class="paragraph">
Moreover, in order to make PoLICe move toward pathogens, we will use Anchor, which is the transmembrane structure. It recognizes cancer markers (explain later) out of the membrane, and connects the Polymer inside the membrane by the weak interaction, leading to increasing the existence probability of the Polymer near the membrane.
</p>
<p class="paragraph">
Supporter, Reserver, and Anchor can be made of DNA origami, and we can use hybridization as weak interactions between them. Of course we can change the affinity easily by controlling the length of hybridization.
</p>
<a name="f2"></a>
<p class="paragraph">
However, when we build the system only by DNA, the velocity of polymerization and depolymerization may not be fast enough to use in our body as a medical drug. Moreover, the negative charge repulsion of DNA origami may disturb our plan. In contrast, the protein, which is composed from 20 kinds of amino acid, has variety of surface compare to DNA nano structure, which is composed only from 4 kinds of nucleotide, A,T,G, and C. From the vast variety of surface, protein can interact more specific and efficient than DNA only approach. Therefore, we will replace some DNA origami structures with proteins or protein-DNA hybrid to use the high-selectivity and high-affinity of proteins.
</p><br><br>
 
 
 
 
<h1 class="big">
2. A cancer recognition system
</h1>
 
<p class="paragraph">
In conventional DDS, vast kinds of molecular sensors have been developed
and examined. These sensors could be equipped with our PoLICe. In
addition to such sensors, our PoLICe could introduce new function for
cancer recognition.
</p>
<a name="f3"></a>
<p class="paragraph">
PoLICe can move by intrinsic active transport system, allowing precise surveillance at single cell resolution. In other words, PoLICe can detect the spatial difference of some chemical compounds concentration. Moreover, PoLICe can inspect each cell with different investigation time depend on the situation, therefore, could detect the difference of flux easily. These character of PoLICe allow the detection of differential or integral of flux both in temporal and spatial. Combining recent progress of chemical biology (e.g. Urano et al., Sci Transi Med 2011), and / or remote technology using magnetic bead or else (e.g. Hoffmann et al., Nat Nano 2013; Etoc et al., Nat Nano 2013) with information processing such as logic gate of DNA origami (Douglass et al., Science 2012) our PoLICe could recognize cancer cell efficiently. For such purpose, we should develop some processing unit to compute the information flux (Pinheiro et al., Nat Nano 2011).
</p>
<br><br>
 
 
 
 
 
<h1 class="sub">
3. A cancer Killing system
</h1>
 
<p class="paragraph">
To kill the cancer cell, conventional DDS delivers vast kind of low molecular weight compounds (e.g. taxol) and biomolecules (e.g. dsRNA for RNAi). However, most of such medical agent were pre-programmed at the time of loading, and therefore on demand treatment of the target on site is a challenging issue. In contrast, our PoLICe could process the information flux of each cells and therefore could perform optimum treatment on demand: activate cell signaling pathway of the target cells for apoptosis induction, or release some container (e.g. taxol, dsRNA) to the target cancer cell, or direct conversion of the cancer cell to the normal cells using stem cell technology. The latter two approaches might use envelope to encapsulate the container. Recent progress of cell biology revealed the exosome (vesicle) function in cell communication, and this may provide some hint for the precise mechanism of killing system. In such system, artificial particle containing DNA origami structure (Perrault and Shih ACS Nano 2014) may play the key. Also further development of cell free transcription / translation system (Shimizu et al., Nat Biotechnol 2001) to autonomus production of protein, nucleotide and membrane (Kuruma et al., BBA 2009) is crucial.
</p><br><br>
 
 
 
 
 
 
 
<h2 class="reference">Reference</h2>
<p class="reference">1. Rapid cancer detection by topically spraying a
γ-glutamyltranspeptidase-activated fluorescent probe.<br>
Urano, Y.; Sakabe, M.; Kosaka, N.; Ogawa, M.; Mitsunaga, M.; Asanuma,
D.; Kamiya, M.; Young, M. R.; Nagano, T.; Choyke, P. L.; Kobayashi, H.
Sci. Transl. Med. 2011, 129, 1-10.
</p>
 
<p class="reference">2. Spatiotemporal control of microtubule nucleation and assembly using
magnetic nanoparticles.<br>
Hoffmann C, Mazari E, Lallet S, Le Borgne R, Marchi V, Gosse C, Gueroui Z.
Nat Nanotechnol. 2013 Mar;8(3):199-205. doi: 10.1038/nnano.2012.246.
Epub 2013 Jan 20.
</p>
 
<p class="reference">3. Subcellular control of Rac-GTPase signalling by magnetogenetic
manipulation inside living cells.<br>
Etoc F, Lisse D, Bellaiche Y, Piehler J, Coppey M, Dahan M.
Nat Nanotechnol. 2013 Mar;8(3):193-8. doi: 10.1038/nnano.2013.23. Epub
2013 Mar 3.
</p>
 
<p class="reference">4. Challenges and opportunities for structural DNA nanotechnology.<br>
Pinheiro AV, Han D, Shih WM, Yan H.
Nat Nanotechnol. 2011 Nov 6;6(12):763-72. doi: 10.1038/nnano.2011.187.
Review.
</p>
 
<p class="reference">5. Virus-inspired membrane encapsulation of DNA nanostructures to achieve
in vivo stability.<br>
Perrault SD, Shih WM.
ACS Nano. 2014 May 27;8(5):5132-40. doi: 10.1021/nn5011914. Epub 2014
Apr 22.
</p>
 
<p class="reference">6. Cell-free translation reconstituted with purified components.<br>
Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T.
Nat Biotechnol. 2001 Aug;19(8):751-5.
</p>
 
<p class="reference">7. A synthetic biology approach to the construction of membrane proteins in
semi-synthetic minimal cells.<br>
Kuruma Y, Stano P, Ueda T, Luisi PL.
Biochim Biophys Acta. 2009 Feb;1788(2):567-74. doi:
10.1016/j.bbamem.2008.10.017. Epub 2008 Nov 5.
</p>


<img src="http://openwetware.org/images/8/8d/Futurekashiwa.jpg" width="450px" height="263px" align="right" style="margin-left:10px;">
<p class="paragraph">The long term objective is to build a single cell resolution system to kill cancer cells completely by PoLICe. This image shows our idea of PoLICe mechanism combined with existing methods; by recognizing tumor markers, PoLICe attaches to a cancer cell and crawls into the tumor while killing cancer cells attached. In this mechanism, DNA origami structure of the Motor-Monomers enables PoLICe to move in nanoscale, necessary for the single cell resolution. Moreover, it is possible for PoLICe to simulate the movement from the structure sizes or shapes.</p>




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<h1 class="title">Reference</h1>


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<a name="1"></a> <font face="Futura,Arial,Frutiger" font size="24px">DISCUSSION</font> <br> <br>


<h1 class="title"><a name="Achieve">&nbsp;Achievements</a></h1> <br> <img src="http://openwetware.org/images/c/cc/Acheivement_完成版小.png" width="800px" height="430px" align="right">


<div> <h1 class="title"><a name="Future">&nbsp;Future</a></h1> </div>

<p class="paragraph"> In order to create completed-PoLICe which can move toward cancer markers and kill cancer cells, the functions we have to equip with PoLICe is as follows: </p> <p class="paragraph"> <a href="#f1">1. A depolymerization system of monomers for self-moving</a> </p> <p class="paragraph"> <a href="#f2">2. A cancer recognition system</a> </p> <a name="f1"></a> <p class="paragraph"> <a href="#f3">3. A cancer killing system</a> </p> <p class="paragraph"> Below, we will state how we will equip these functions with PoLICe in our next step. </p><br><br>



<h1 class="big"> 1. A depolymerization system of monomers </h1>

<img src="http://openwetware.org/images/f/f9/Future_recognition%26breaking_000001.png" width="330px" height="240px">

<p class="paragraph"> In order to accomplish the self-moving system beyond the self-transformation, a polymerization of monomers should be occurred only near the front membrane of PoLICe, and the depolymerization should be occurred at the trailing membrane. Therefore, the depolymerization is the key for our next purpose. </p> <p class="paragraph"> There are two approaches to accomplish the depolymerization. One is “active depolymerization” method, and the other is “passive depolymerization” through the absence of a polymerization promotion system at the depolymerization site. We chose the latter, “passive” approach. In this approach, the default state of monomers is a depolymerization, and without the polymerization promotion system, all the monomers keep in monomeric state. We, therefore, plan to use weaker interaction than temporal version of the Motor-Monomer. </p> <p class="paragraph"> For the localized polymerization promotion, we introduce Supporter, Reserver, and Anchor to our PoLICe. </p> <p class="paragraph"> Supporter binds the joint of monomers to stabilize the bond between monomers and prevent the depolymerization. </p> <p class="paragraph"> If the Supporters exist in PoLICe universally, all bonds will be stabilized at the same probability, and the polymerization will be occurred everywhere in PoLICe. To prevent this situation, we will use Reserver to localize the Supporter near the front membrane. </p> <p class="paragraph"> Reserver exists on the inner surface of the membrane, and can interact Supporter by a weak interaction. Therefore, Reserver keeps Supporters near the membrane, driving the polymerization only near the membrane. </p> <p class="paragraph"> Moreover, in order to make PoLICe move toward pathogens, we will use Anchor, which is the transmembrane structure. It recognizes cancer markers (explain later) out of the membrane, and connects the Polymer inside the membrane by the weak interaction, leading to increasing the existence probability of the Polymer near the membrane. </p> <p class="paragraph"> Supporter, Reserver, and Anchor can be made of DNA origami, and we can use hybridization as weak interactions between them. Of course we can change the affinity easily by controlling the length of hybridization. </p> <a name="f2"></a> <p class="paragraph"> However, when we build the system only by DNA, the velocity of polymerization and depolymerization may not be fast enough to use in our body as a medical drug. Moreover, the negative charge repulsion of DNA origami may disturb our plan. In contrast, the protein, which is composed from 20 kinds of amino acid, has variety of surface compare to DNA nano structure, which is composed only from 4 kinds of nucleotide, A,T,G, and C. From the vast variety of surface, protein can interact more specific and efficient than DNA only approach. Therefore, we will replace some DNA origami structures with proteins or protein-DNA hybrid to use the high-selectivity and high-affinity of proteins. </p><br><br>



<h1 class="big"> 2. A cancer recognition system </h1>

<p class="paragraph"> In conventional DDS, vast kinds of molecular sensors have been developed and examined. These sensors could be equipped with our PoLICe. In addition to such sensors, our PoLICe could introduce new function for cancer recognition. </p> <a name="f3"></a> <p class="paragraph"> PoLICe can move by intrinsic active transport system, allowing precise surveillance at single cell resolution. In other words, PoLICe can detect the spatial difference of some chemical compounds concentration. Moreover, PoLICe can inspect each cell with different investigation time depend on the situation, therefore, could detect the difference of flux easily. These character of PoLICe allow the detection of differential or integral of flux both in temporal and spatial. Combining recent progress of chemical biology (e.g. Urano et al., Sci Transi Med 2011), and / or remote technology using magnetic bead or else (e.g. Hoffmann et al., Nat Nano 2013; Etoc et al., Nat Nano 2013) with information processing such as logic gate of DNA origami (Douglass et al., Science 2012) our PoLICe could recognize cancer cell efficiently. For such purpose, we should develop some processing unit to compute the information flux (Pinheiro et al., Nat Nano 2011). </p> <br><br>



<h1 class="sub"> 3. A cancer Killing system </h1>

<p class="paragraph"> To kill the cancer cell, conventional DDS delivers vast kind of low molecular weight compounds (e.g. taxol) and biomolecules (e.g. dsRNA for RNAi). However, most of such medical agent were pre-programmed at the time of loading, and therefore on demand treatment of the target on site is a challenging issue. In contrast, our PoLICe could process the information flux of each cells and therefore could perform optimum treatment on demand: activate cell signaling pathway of the target cells for apoptosis induction, or release some container (e.g. taxol, dsRNA) to the target cancer cell, or direct conversion of the cancer cell to the normal cells using stem cell technology. The latter two approaches might use envelope to encapsulate the container. Recent progress of cell biology revealed the exosome (vesicle) function in cell communication, and this may provide some hint for the precise mechanism of killing system. In such system, artificial particle containing DNA origami structure (Perrault and Shih ACS Nano 2014) may play the key. Also further development of cell free transcription / translation system (Shimizu et al., Nat Biotechnol 2001) to autonomus production of protein, nucleotide and membrane (Kuruma et al., BBA 2009) is crucial. </p><br><br>




<h2 class="reference">Reference</h2> <p class="reference">1. Rapid cancer detection by topically spraying a γ-glutamyltranspeptidase-activated fluorescent probe.<br> 

Urano, Y.; Sakabe, M.; Kosaka, N.; Ogawa, M.; Mitsunaga, M.; Asanuma,

D.; Kamiya, M.; Young, M. R.; Nagano, T.; Choyke, P. L.; Kobayashi, H. Sci. Transl. Med. 2011, 129, 1-10. </p>

<p class="reference">2. Spatiotemporal control of microtubule nucleation and assembly using magnetic nanoparticles.<br> Hoffmann C, Mazari E, Lallet S, Le Borgne R, Marchi V, Gosse C, Gueroui Z. Nat Nanotechnol. 2013 Mar;8(3):199-205. doi: 10.1038/nnano.2012.246. Epub 2013 Jan 20. </p>

<p class="reference">3. Subcellular control of Rac-GTPase signalling by magnetogenetic manipulation inside living cells.<br> Etoc F, Lisse D, Bellaiche Y, Piehler J, Coppey M, Dahan M. Nat Nanotechnol. 2013 Mar;8(3):193-8. doi: 10.1038/nnano.2013.23. Epub 2013 Mar 3. </p>

<p class="reference">4. Challenges and opportunities for structural DNA nanotechnology.<br> Pinheiro AV, Han D, Shih WM, Yan H. Nat Nanotechnol. 2011 Nov 6;6(12):763-72. doi: 10.1038/nnano.2011.187. Review. </p>

<p class="reference">5. Virus-inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability.<br> Perrault SD, Shih WM. ACS Nano. 2014 May 27;8(5):5132-40. doi: 10.1021/nn5011914. Epub 2014 Apr 22. </p>

<p class="reference">6. Cell-free translation reconstituted with purified components.<br> Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T, Nishikawa K, Ueda T. Nat Biotechnol. 2001 Aug;19(8):751-5. </p>

<p class="reference">7. A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells.<br> Kuruma Y, Stano P, Ueda T, Luisi PL. Biochim Biophys Acta. 2009 Feb;1788(2):567-74. doi: 10.1016/j.bbamem.2008.10.017. Epub 2008 Nov 5. </p>



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