Difference between revisions of "Biomod/2013/Sendai/project"

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<h3>Background</h3>
 
<h3>Background</h3>
Recently genomics and proteomics have well studied, and new drugs such as siRNA are created. Delivery technology to the living body is important to cure illness. So DDS is the effective approach. (Referred http://www.dojindo.co.jp/letterj/119/news119.pdf) Liposome and polymers are used for DDS and these are expected to increase the effectiveness of drugs.</br></br>
+
Recently genomics and proteomics have well studied, and new drugs such as siRNA are created. Delivery technology to the living body is important to cure illness. So <a href="http://www.dojindo.co.jp/letterj/119/news119.pdf">DDS is the effective approach</a>.  Liposome and polymers are used for DDS and these are expected to increase the effectiveness of drugs.</br></br>
  
 
<h3>Motivation</h3>
 
<h3>Motivation</h3>

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            <a href="http://openwetware.org/wiki/Biomod/2013/Sendai"><h1 style="color:white;" ><b>Biomod<span>2013<br>&emsp; Team</span>Sendai</b></h1></a> 
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        <h2>Project</h2>

<p>

<h3>Project Goal</h3> Our project goal is construction of the egg-type initiator and the chain-reactive burst by triggers that destroys liposomes released from the egg-type initiator.</br> 1.Construction of the egg-type initiator</br> This is the structure of alginate hydrogel including liposomes that have triggers inside.</br> When liposomes sense external stimulations by rising temperature, EGTA in liposomes are released and diffuse the trigger. At last manytriggers are released to buffer. To achieve this structure, follow experiments are needed.</br>

(1) Construction of liposomes destroyed by sensing external stimulations. </br>
(2) Construction of alginate hydrogel including buffer and many liposomes. </br>
(3) Diffusion of the alginate hydrogel by EGTA included destroyed liposomes. </br></br>

2.Construction of the chain-reactive burst system</br> This is the system of destroying other liposomes continuously by triggers included destroyed liposomes. To destroy liposomes continuously, each liposome includes many kinds of triggers. And these triggers cause the chain reaction what we call “the chain-reactive burst.” </br> To achieve this system, follow experiments are needed.</br>

(1)	Design and construction of trigger that destroy liposomes.</br>
(2)	Destroying liposomes continuously by triggers that are released from other destroyed liposomes.</br></br>

<h3>Background</h3> Recently genomics and proteomics have well studied, and new drugs such as siRNA are created. Delivery technology to the living body is important to cure illness. So <a href="http://www.dojindo.co.jp/letterj/119/news119.pdf">DDS is the effective approach</a>. Liposome and polymers are used for DDS and these are expected to increase the effectiveness of drugs.</br></br>

<h3>Motivation</h3> It is not good to release a large quantity of drugs in DDS, so we have to control it. To solve this problem, we build two systems. First the system that release trigger to destroy liposome on a certain condition. Second the system that release drugs exponentially by liposome being destroyed like a chain reaction by trigger.</br></br>

<h3>Method</h3> To destroy liposomes those are playing a role of transporter of drugs and DNA structure (ex. trigger). When liposomes are destroyed, contents of liposomes are released. If the DNA structure is the same as trigger that destroys liposomes, then the DNA structure released newly destroys other liposomes. In this way, contents of liposome are released one after another.</br></br>


<!--



<h3>Project goal</h3> Our project goal is construction of egg-type-molecular-robot and chain of molecules-releasing systems by DNA trigger released from egg-type-molecular-robot.</br> </br> <ol> <li>Construction of egg-type-molecular-robot: <br> this is accomplished by dual structure that have liposome include structure of trigger DNA for chain breaking in alginic acid gel. It sense a stimulation from outside and release many of trigger DNA. For this aim, we achieve ① construction of liposome that sense a stimulation and breaked it. ② construction of alginic acid gel include buffer and many of liposome. ③ Voluntary dissolution of the alginic acid gel by a chelating agent included breaking-liposome. We achieve them for sub goal.</li><br>

<li>Construction of molecules-releasing systems: <br> we break liposome like a chain reaction. Each liposome include many kinds of trigger DNA structures and causes voluntary and sequential chemical reaction by chain-reaction. For realizing this purpose, we achieve next two sub goal;①design and construction of DNA structure which breaks liposome, ② breaking liposome like chain reaction by the DNA that is released from another destruction of liposome. </li>

</ol> </br> </p>

<p><h3>Merit</h3> By achieving these subproject goals, we implement chain of molecules-releasing systems from one point. This system releases molecules by diffusion of chain reaction from releasing at the point on liposome-alginate hydro gel double membrane. Thereby a difference arises in the time of reaction, and the order of reactions can be controlable by using it. Therefore, we achieve the system which can control the order of reactions by chain reaction. </br> <ol> <li>Merits of releasing by egg-type-molecular-robot<br>

           -It can start diffusion from one point by reaction of one trigger.<br>
            If there are a lot of triggers around eggs, cahain reactions happens somewhere.<br>
           -It can anneal and release triggers without any effect around environment.<br>
            Because of alginic acid protective membrane, triggers are protected. <br>

</li><br> <li>Merits of liposome chain breaking reactions<br>

           -Using time difference of chain reaction, the order of reactions can be controlled.<br>

</li> </ol> </br> </p>


            <p><h3>Background</h3>

近年、ゲノミクス・プロテオミクス研究によりsiRNAなどの新しい薬が生み出されているが、それらの成否を握るのは、<a href="http://www.dojindo.co.jp/letterj/119/news119.pdf">生体へのデリバリー技術</a>である。DDSはこれに有効なアプローチである。DDSにはリポソームやポリマーが利用され、これらは薬の薬学的・治療の有効性を上げることに寄与しうる。</br> Recently genomics and proteomics have well studied, and new drugs such as siRNA are created. But, Delivery technology to the living body is important so that those drugs show the true value. (Referred http://www.dojindo.co.jp/letterj/119/news119.pdf) DDS is the effective approach for this. Liposome and a polymer are used for DDS, These contribute to giving the effectiveness of drugs.</br> </p> <p><h3>Motivation</h3> DDSでは、過剰に薬剤が投与されてしまうと、組織に損害を与えてしまう。そこで、制御された薬の放出系が必要となる(<a href="http://www.sciencemag.org/content/303/5665/1818.short">Drug delivery systems: entering the mainstream</a>)。</br> 生体分子のうち、人の手で自在にプログラムから生成を行える分子はDNAである。DNAは反応経路を正確にプログラムでき、論理計算も行えるので(何か論文リンク貼る)、 私たちは運び屋としてリポソームを、制御分子としてDNAを用いて、制御された薬剤放出系を実現しようと考えた。 In conventional DDS, the control of the timing to release drugs is difficult in already sent DDS. A large quantity of trigger is necessary to release a large quantity of drugs.</br> To solve these problems, we build two systems. First, the system which release trigger destroying liposome on a certain condition. Second, the system which release drugs exponentially by liposome being destroyed like a chain reaction by trigger. </br>

</p> <p><h3>Method</h3> 薬の運び屋であるリポソームを、DNAをトリガーとして割る。割ったらリポソームの内容物が放出される。リポソームは有効成分と、DNA構造物を含んでいる。内部に含まれるDNA構造体を、トリガーと同じ構造にすれば、出てきた構造物は、新たなトリガーとなり、再び周囲のリポソームを破壊する。こうして、次々とリポソームの内容物が連鎖的に放出される。</br> We destroy the liposome which is bagman of drugs with DNA structure with a role of the trigger. If liposome was destroyed, contents of liposome are released, liposome include active ingredient and DNA structure. This DNA structure is the same as trigger DNA structure. Then DNA structure released newly destroy other liposomes again. As such, contents of liposome are released like a chain reaction one after another.</br> <h4>・The beginning of interaction</h4> 反応を開始するトリガーDNAはリポソーム・アルギン酸二重膜に閉じ込められている。また、リポソーム内部にはキレート剤、ステイプル、M13,尿素が含まれており、高濃度の尿素により、ステイプルとM13は別個に(DNAオリガミ構造体を作らずに)存在している。</br> リポソーム表面には、ニッパム分子が修飾されており、37℃程度に上げることで、ニッパム分子が収縮しリポソームが破壊される。次に、リポソーム内部に含まれていたキレート剤の効果により、アルギン酸膜が破壊される。37℃条件下で両膜が破壊されると、尿素濃度が低下し、ステイプルとM13からDNAオリガミ構造体が生成され、トリガーとして外に出ていく。</br> Trigger DNA structure starting reaction is confined in liposome-alginate hydro gel double membrane In addition, chelating agent, staple, M13mp18, urea are included in the liposome. Because of high density urea, staple and M13mp18 exist separately(without becoming the DNA origami ). </br> On the surface of liposome, NIPAM molecules are modified. NIPAM molecules shrink at around 37℃ and liposome are destroyed by this effect. Then urea (DNA denaturant) is diluted, and DNA origami is completed without annealing. Furthermore, an alginate hydro gel membrane is destroyed by chelating agent included in the liposome, and a trigger DNA structure is released.</br>

<h4>・The chain reaction</h4> リポソームをDNAをトリガーとして割るには、まず、リポソームにコレステロール修飾DNAを添加し、表面に一本鎖DNAが現れるようにする。これを、トリガーDNA構造体の一部と相補的な配列を持つ一本鎖DNAとすれば、トリガーDNAはリポソーム表面に多数ハイブリダイゼーションすることになる。</br> 一本鎖DNA付きリポソームの生成後、相補的な配列をもつトリガーDNA構造物を加える。トリガーDNAがリポソーム表面に付着すると、その物理的な特性により、リポソームが破壊される(影山先輩の数式へリンク貼る。込み入った数式を用いた説明はそこでする)。</br> リポソームは有効成分と、新たなトリガーを含んでおり、放出された構造物は、連鎖反応的に周囲のリポソームを破壊する。</br> To destroy liposome with DNA structure as trigger, we add cholesterol-labeled DNA in liposome. Then single strand DNA emerge on the surface of liposome. If we grow the strand which is complementary for this single strand DNA in Trigger DNA structure, a lot of Trigger DNA structure will hybridization on the surface of liposome. After made liposome with the single strand DNA, we add the trigger DNA structure with a complementary strand. If trigger DNA bind to on the liposomal surface, liposome is destroyed by physical characteristic which come from trigger DNA structure. The liposome includes active ingredient and new trigger DNA structure, and the released structures destroy other liposome for a chain reaction.</br> </br>


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